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Ganji M, Safarzadeh Kozani P, Rahbarizadeh F. Characterization of novel CD19-specific VHHs isolated from a camelid immune library by phage display. J Transl Med 2023; 21:891. [PMID: 38066569 PMCID: PMC10709854 DOI: 10.1186/s12967-023-04524-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/13/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Monoclonal antibody (mAb)-based immunotherapies have achieved promising outcomes in the treatment of immunological and oncological indications. CD19 is considered one of the most qualified antigens in the treatment of B-cell neoplasms. VHHs (nanobodies) are known for their physicochemical advantages over conventional mAbs rendering them suitable therapeutics and diagnostic tools. Herein, we aimed to isolate CD19-specific VHHs from a novel immune library using phage display. METHODS An immune VHH gene library was constructed. Using phage display and after five biopanning rounds, two monoclonal CD19-specific VHHs were isolated. The selected VHHs were expressed, purified, and characterized in terms of their affinity, specificity, sensitivity, and ability to target CD19-positive cell lines. Moreover, in silico analyses were employed for further characterization. RESULTS A VHH library was developed, and because the outputs of the 4th biopanning round exhibited the most favorable characteristics, a panel of random VHHs was selected from them. Ultimately, two of the most favorable VHHs were selected and DNA sequenced (designated as GR37 and GR41). Precise experiments indicated that GR37 and GR41 exhibited considerable specificity, sensitivity, and affinity (1.15 × 107 M-1 and 2.08 × 107 M-1, respectively) to CD19. Flow cytometric analyses revealed that GR37 and GR41 could bind CD19 on the surface of cell lines expressing the antigen. Moreover, in silico experiments predicted that both VHHs target epitopes that are distinct from that targeted by the CD19-specific single-chain variable fragment (scFv) FMC63. CONCLUSION The selected VHHs can be used as potential targeting tools for the development of CD19-based immunotherapeutics.
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Affiliation(s)
- Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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2
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Sanders C, Dzelamonyuy A, Ntemafack A, Alatoom N, Nchinda G, Georgiadis MM, Bopda Waffo A. Mapping immunological and host receptor binding determinants of SARS-CoV spike protein utilizing the Qubevirus platform. J Biol Chem 2023; 299:105460. [PMID: 37977224 PMCID: PMC10750099 DOI: 10.1016/j.jbc.2023.105460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S425-525 was found to contain the binding determinant of the recombinant human angiotensin-converting enzyme 2, with the shortest active binding motif situated between residues S437-492. Upstream, another fragment, F7, containing an overlapping portion of F6 would not bind to recombinant human angiotensin-converting enzyme 2, confirming that a contiguous stretch of residues could adopt the appropriate structural orientation of F6 as an insertion within the Qubevirus. The F6 (S441-460) and other inserts, including F7/F8 (S601-620) and F10 (S781-800), were demonstrated to contain important immunological determinants through recognition and binding of S protein specific (anti-S) antibodies. An engineered chimeric insert bearing the fusion of all three anti-S reactive epitopes improved substantially the recognition and binding to their cognate antibodies. These results provide insights into humoral immune relevant epitopes and tropism characteristics of the S protein with implications for the development of subunit vaccines or other biologics against SARS-CoV.
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Affiliation(s)
- Carrie Sanders
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Center for Disease Control, Atlanta, Georgia, USA
| | - Aristide Dzelamonyuy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Augustin Ntemafack
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nadia Alatoom
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Godwin Nchinda
- Department of Immunology, Laboratory of Vaccinology and Biobanking, Yaoundé, Cameroon
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Alain Bopda Waffo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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3
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Hou YN, Jin YQ, Zhang XF, Tang F, Hou JW, Liu ZM, Han ZB, Zhang H, Du LF, Shao S, Su JG, Liang Y, Zhang J, Li QM. Chimeric virus-like particles of human norovirus constructed by structure-guided epitope grafting elicit cross-reactive immunity against both GI.1 and GII.4 genotypes. J Virol 2023; 97:e0093823. [PMID: 37792003 PMCID: PMC10617407 DOI: 10.1128/jvi.00938-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Human norovirus (HuNoV) is highly infectious and can result in severe illnesses in the elderly and children. So far, there is no effective antiviral drug to treat HuNoV infection, and thus, the development of HuNoV vaccines is urgent. However, NoV evolves rapidly, and currently, at least 10 genogroups with numerous genotypes have been found. The genetic diversity of NoV and the lack of cross-protection between different genotypes pose challenges to the development of broadly protective vaccines. In this study, guided by structural alignment between GI.1 and GII.4 HuNoV VP1 proteins, several chimeric-type virus-like particles (VLPs) were designed through surface-exposed loop grafting. Mouse immunization studies show that two of the designed chimeric VLPs induced cross-immunity against both GI.1 and GII.4 HuNoVs. To our knowledge, this is the first designed chimeric VLPs that can induce cross-immune activities across different genogroups of HuNoV, which provides valuable strategies for the development of cross-reactive HuNoV vaccines.
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Affiliation(s)
- Ya Nan Hou
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Yu Qin Jin
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Xue Feng Zhang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Fang Tang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Jun Wei Hou
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Zhao Ming Liu
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Zi Bo Han
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Hao Zhang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Li Fang Du
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Shuai Shao
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Ji Guo Su
- National Engineering Center for New Vaccine Research, Beijing, China
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Yu Liang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Jing Zhang
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Qi Ming Li
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
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Guerrini G, Mehn D, Fumagalli F, Gioria S, Pedotti M, Simonelli L, Bianchini F, Robbiani DF, Varani L, Calzolai L. Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer. Int J Mol Sci 2023; 24:14875. [PMID: 37834322 PMCID: PMC10573103 DOI: 10.3390/ijms241914875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.
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Affiliation(s)
- Giuditta Guerrini
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Dora Mehn
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Francesco Fumagalli
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Sabrina Gioria
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
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Casirati G, Cosentino A, Mucci A, Salah Mahmoud M, Ugarte Zabala I, Zeng J, Ficarro SB, Klatt D, Brendel C, Rambaldi A, Ritz J, Marto JA, Pellin D, Bauer DE, Armstrong SA, Genovese P. Epitope editing enables targeted immunotherapy of acute myeloid leukaemia. Nature 2023; 621:404-414. [PMID: 37648862 PMCID: PMC10499609 DOI: 10.1038/s41586-023-06496-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Despite the considerable efficacy observed when targeting a dispensable lineage antigen, such as CD19 in B cell acute lymphoblastic leukaemia1,2, the broader applicability of adoptive immunotherapies is hampered by the absence of tumour-restricted antigens3-5. Acute myeloid leukaemia immunotherapies target genes expressed by haematopoietic stem/progenitor cells (HSPCs) or differentiated myeloid cells, resulting in intolerable on-target/off-tumour toxicity. Here we show that epitope engineering of donor HSPCs used for bone marrow transplantation endows haematopoietic lineages with selective resistance to chimeric antigen receptor (CAR) T cells or monoclonal antibodies, without affecting protein function or regulation. This strategy enables the targeting of genes that are essential for leukaemia survival regardless of shared expression on HSPCs, reducing the risk of tumour immune escape. By performing epitope mapping and library screenings, we identified amino acid changes that abrogate the binding of therapeutic monoclonal antibodies targeting FLT3, CD123 and KIT, and optimized a base-editing approach to introduce them into CD34+ HSPCs, which retain long-term engraftment and multilineage differentiation ability. After CAR T cell treatment, we confirmed resistance of epitope-edited haematopoiesis and concomitant eradication of patient-derived acute myeloid leukaemia xenografts. Furthermore, we show that multiplex epitope engineering of HSPCs is feasible and enables more effective immunotherapies against multiple targets without incurring overlapping off-tumour toxicities. We envision that this approach will provide opportunities to treat relapsed/refractory acute myeloid leukaemia and enable safer non-genotoxic conditioning.
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Affiliation(s)
- Gabriele Casirati
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Milano-Bicocca University, Milan, Italy
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Andrea Cosentino
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Oncology and Hematology, University of Milan and Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Adele Mucci
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Mohammed Salah Mahmoud
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Zoology Department, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Iratxe Ugarte Zabala
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Denise Klatt
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Alessandro Rambaldi
- Department of Oncology and Hematology, University of Milan and Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Jerome Ritz
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Connell and O'Reilly Families Cell Manipulation Core Facility, Dana-Farber Cancer Institute, Boston, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Danilo Pellin
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Scott A Armstrong
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
| | - Pietro Genovese
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA.
- Harvard Medical School, Boston, MA, USA.
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6
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Li T, Li F, Guo X, Hong C, Yu X, Wu B, Lian S, Song L, Tang J, Wen S, Gao K, Hao M, Cheng W, Su Y, Zhang S, Huang S, Fang M, Wang Y, Ng MH, Chen H, Luo W, Ge S, Zhang J, Xia N, Ji M. Anti-Epstein-Barr Virus BNLF2b for Mass Screening for Nasopharyngeal Cancer. N Engl J Med 2023; 389:808-819. [PMID: 37646678 DOI: 10.1056/nejmoa2301496] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
BACKGROUND Population screening of asymptomatic persons with Epstein-Barr virus (EBV) DNA or antibodies has improved the diagnosis of nasopharyngeal carcinoma and survival among affected persons. However, the positive predictive value of current screening strategies is unsatisfactory even in areas where nasopharyngeal carcinoma is endemic. METHODS We designed a peptide library representing highly ranked B-cell epitopes of EBV coding sequences to identify novel serologic biomarkers for nasopharyngeal carcinoma. After a retrospective case-control study, the performance of the novel biomarker anti-BNLF2b total antibody (P85-Ab) was validated through a large-scale prospective screening program and compared with that of the standard two-antibody-based screening method (EBV nuclear antigen 1 [EBNA1]-IgA and EBV-specific viral capsid antigen [VCA]-IgA). RESULTS P85-Ab was the most promising biomarker for nasopharyngeal carcinoma screening, with high sensitivity (94.4%; 95% confidence interval [CI], 86.4 to 97.8) and specificity (99.6%; 95% CI, 97.8 to 99.9) in the retrospective case-control study. Among the 24,852 eligible participants in the prospective cohort, 47 cases of nasopharyngeal carcinoma (38 at an early stage) were identified. P85-Ab showed higher sensitivity than the two-antibody method (97.9% vs. 72.3%; ratio, 1.4 [95% CI, 1.1 to 1.6]), higher specificity (98.3% vs. 97.0%; ratio, 1.01 [95% CI, 1.01 to 1.02]), and a higher positive predictive value (10.0% vs. 4.3%; ratio, 2.3 [95% CI, 1.8 to 2.8]). The combination of P85-Ab and the two-antibody method markedly increased the positive predictive value to 44.6% (95% CI, 33.8 to 55.9), with sensitivity of 70.2% (95% CI, 56.0 to 81.4). CONCLUSIONS Our results suggest that P85-Ab is a promising novel biomarker for nasopharyngeal carcinoma screening, with higher sensitivity, specificity, and positive predictive value than the standard two-antibody method. (Funded by the National Key Research and Development Program of China and others; ClinicalTrials.gov number, NCT04085900.).
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Affiliation(s)
- Tingdong Li
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Fugui Li
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Xiaoyi Guo
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Congming Hong
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Xia Yu
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Biaohua Wu
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shifeng Lian
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Liuwei Song
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Jiabao Tang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shunhua Wen
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Kaimin Gao
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mengling Hao
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Weimin Cheng
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Yingying Su
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shiyin Zhang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shoujie Huang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mujin Fang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Yingbin Wang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mun-Hon Ng
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Honglin Chen
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Wenxin Luo
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shengxiang Ge
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Jun Zhang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Ningshao Xia
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mingfang Ji
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
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7
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Ishimaru H, Nishimura M, Tjan LH, Sutandhio S, Marini MI, Effendi GB, Shigematsu H, Kato K, Hasegawa N, Aoki K, Kurahashi Y, Furukawa K, Shinohara M, Nakamura T, Arii J, Nagano T, Nakamura S, Sano S, Iwata S, Okamura S, Mori Y. Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants. J Virol 2023; 97:e0028623. [PMID: 37191569 PMCID: PMC10308935 DOI: 10.1128/jvi.00286-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
We identified neutralizing monoclonal antibodies against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants (including Omicron variants BA.5 and BA.2.75) from individuals who received two doses of mRNA vaccination after they had been infected with the D614G virus. We named them MO1, MO2, and MO3. Among them, MO1 showed particularly high neutralizing activity against authentic variants: D614G, Delta, BA.1, BA.1.1, BA.2, BA.2.75, and BA.5. Furthermore, MO1 suppressed BA.5 infection in hamsters. A structural analysis revealed that MO1 binds to the conserved epitope of seven variants, including Omicron variants BA.5 and BA.2.75, in the receptor-binding domain of the spike protein. MO1 targets an epitope conserved among Omicron variants BA.1, BA.2, and BA.5 in a unique binding mode. Our findings confirm that D614G-derived vaccination can induce neutralizing antibodies that recognize the epitopes conserved among the SARS-CoV-2 variants. IMPORTANCE Omicron variants of SARS-CoV-2 acquired escape ability from host immunity and authorized antibody therapeutics and thereby have been spreading worldwide. We reported that patients infected with an early SARS-CoV-2 variant, D614G, and who received subsequent two-dose mRNA vaccination have high neutralizing antibody titer against Omicron lineages. It was speculated that the patients have neutralizing antibodies broadly effective against SARS-CoV-2 variants by targeting common epitopes. Here, we explored human monoclonal antibodies from B cells of the patients. One of the monoclonal antibodies, named MO1, showed high potency against broad SARS-CoV-2 variants including BA.2.75 and BA.5 variants. The results prove that monoclonal antibodies that have common neutralizing epitopes among several Omicrons were produced in patients infected with D614G and who received mRNA vaccination.
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Affiliation(s)
- Hanako Ishimaru
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Mitsuhiro Nishimura
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Lidya Handayani Tjan
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Silvia Sutandhio
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Maria Istiqomah Marini
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Gema Barlian Effendi
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute SPring-8, Hyogo, Japan
| | - Koji Kato
- Structural Biology Division, Japan Synchrotron Radiation Research Institute SPring-8, Hyogo, Japan
| | - Natsumi Hasegawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kaito Aoki
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yukiya Kurahashi
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Koichi Furukawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Mai Shinohara
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomoka Nakamura
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Jun Arii
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tatsuya Nagano
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Sachiko Nakamura
- Division of General Internal Medicine, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Hyogo, Japan
| | - Shigeru Sano
- Acute Care Medical Center, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Hyogo, Japan
| | - Sachiyo Iwata
- Division of Cardiovascular Medicine, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Hyogo, Japan
| | - Shinya Okamura
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
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8
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Albaqami FF, Altharawi A, Althurwi HN, Alharthy KM, Tahir ul Qamar M, Muhseen ZT, Iqbal M. Development of a Novel Vaccine Candidates against Cardiobacterium valvarum through Reverse Vaccinology and Computational Approaches. Biomed Res Int 2023; 2023:6325568. [PMID: 37415928 PMCID: PMC10322295 DOI: 10.1155/2023/6325568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/10/2023] [Accepted: 05/05/2023] [Indexed: 07/08/2023]
Abstract
Antibiotic resistance is a major public health concern that has resulted in high healthcare costs, increased mortality, and the emergence of novel bacterial diseases. Cardiobacterium valvarum, an antibiotic-resistant bacterium, is one of the leading causes of heart disease. Currently, there is no licensed vaccination against C. valvarum. In this research, an in silico-based vaccine was designed against C. valvarum using reverse vaccinology, bioinformatics, and immunoinformatics techniques. 4206 core proteins, 2027 nonredundant proteins, and 2179 redundant proteins were predicted. Among nonredundant proteins, 23 proteins were predicted in an extracellular membrane, 30 in the outer membrane, and 62 in the periplasmic membrane region. After applying several subtractive proteomics filters, two proteins, TonB-dependent siderophore receptor and hypothetical protein, were chosen for epitope prediction. In the epitope selection phase, B and T-cellepitopes were analyzed and shortlisted for vaccine design. The vaccine model was designed by linking selected epitopes with GPGPG linkers to avoid flexibility. Furthermore, the vaccine model was linked to cholera toxin B adjuvant to induce a proper immune response. The docking approach was utilized to analyze binding affinity to immune cell receptors. Molecular docking results predicted 12.75 kcal/mol for a Vaccine with MHC-I, 6.89 for a vaccine with MHC-II, and 19.51 vaccine with TLR-4. The MMGBSA estimated -94, -78, and -76 kcal/mol for TLR-4 and vaccine, MHC-I and vaccine, and MHC-II and vaccine, while the MMPBSA analysis estimated -97, -61, and -72 kcal/mol for TLR-4 with the vaccine, MHC-I with vaccine, and MHC-II with a vaccine. Molecular dynamic simulation analysis revealed that the designed vaccine construct has proper stability with immune cell receptors as it is essential for inducing an immune response. In conclusion, we observed that the model vaccine candidate has the potency to induce an immune response in the host. However, the study is designed purely on a computational basis; hence, experimental validation is strongly recommended.
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Affiliation(s)
- Faisal F. Albaqami
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ali Altharawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hassan N. Althurwi
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Khalid M. Alharthy
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon 51001, Iraq
| | - Madiha Iqbal
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
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9
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Stamos JD, Rahman MA, Gorini G, Silva de Castro I, Becerra-Flores M, Van Wazer DJ, N’Guessan KF, Clark NM, Bissa M, Gutowska A, Mason RD, Kim J, Rao M, Roederer M, Paquin-Proulx D, Evans DT, Cicala C, Arthos J, Kwong PD, Zhou T, Cardozo T, Franchini G. Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or β-Sheet Conformations on Time of SIV mac251 Acquisition. J Virol 2023; 97:e0186422. [PMID: 36976017 PMCID: PMC10134845 DOI: 10.1128/jvi.01864-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
The monoclonal antibodies (MAbs) NCI05 and NCI09, isolated from a vaccinated macaque that was protected from multiple simian immunodeficiency virus (SIV) challenges, both target an overlapping, conformationally dynamic epitope in SIV envelope variable region 2 (V2). Here, we show that NCI05 recognizes a CH59-like coil/helical epitope, whereas NCI09 recognizes a β-hairpin linear epitope. In vitro, NCI05 and, to a lesser extent, NCI09 mediate the killing of SIV-infected cells in a CD4-dependent manner. Compared to NCI05, NCI09 mediates higher titers of antibody-dependent cellular cytotoxicity (ADCC) to gp120-coated cells, as well as higher levels of trogocytosis, a monocyte function that contributes to immune evasion. We also found that passive administration of NCI05 or NCI09 to macaques did not affect the risk of SIVmac251 acquisition compared to controls, demonstrating that these anti-V2 antibodies alone are not protective. However, NCI05 but not NCI09 mucosal levels strongly correlated with delayed SIVmac251 acquisition, and functional and structural data suggest that NCI05 targets a transient state of the viral spike apex that is partially opened, compared to its prefusion-closed conformation. IMPORTANCE Studies suggest that the protection against SIV/simian-human immunodeficiency virus (SHIV) acquisition afforded by the SIV/HIV V1 deletion-containing envelope immunogens, delivered by the DNA/ALVAC vaccine platform, requires multiple innate and adaptive host responses. Anti-inflammatory macrophages and tolerogenic dendritic cells (DC-10), together with CD14+ efferocytes, are consistently found to correlate with a vaccine-induced decrease in the risk of SIV/SHIV acquisition. Similarly, V2-specific antibody responses mediating ADCC, Th1 and Th2 cells expressing no or low levels of CCR5, and envelope-specific NKp44+ cells producing interleukin 17 (IL-17) also are reproducible correlates of decreased risk of virus acquisition. We focused on the function and the antiviral potential of two monoclonal antibodies (NCI05 and NCI09) isolated from vaccinated animals that differ in antiviral function in vitro and recognize V2 in a linear (NCI09) or coil/helical (NCI05) conformation. We demonstrate that NCI05, but not NCI09, delays SIVmac251 acquisition, highlighting the complexity of antibody responses to V2.
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Affiliation(s)
- James D. Stamos
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Mohammad Arif Rahman
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Giacomo Gorini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Isabela Silva de Castro
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Manuel Becerra-Flores
- New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - David J. Van Wazer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kombo F. N’Guessan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Innate Immunology Laboratory, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Natasha M. Clark
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Anna Gutowska
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Rosemarie D. Mason
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiae Kim
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dominic Paquin-Proulx
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Innate Immunology Laboratory, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - David T. Evans
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Timothy Cardozo
- New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
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10
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Gong YM, Wei XF, Zheng YY, Li Y, Yu Q, Li PF, Zhu B. Combining Phage Display Technology with In Silico-Designed Epitope Vaccine to Elicit Robust Antibody Responses against Emerging Pathogen Tilapia Lake Virus. J Virol 2023; 97:e0005023. [PMID: 36975794 PMCID: PMC10134809 DOI: 10.1128/jvi.00050-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Antigen epitope identification is a critical step in the vaccine development process and is a momentous cornerstone for the development of safe and efficient epitope vaccines. In particular, vaccine design is difficult when the function of the protein encoded by the pathogen is unknown. The genome of Tilapia lake virus (TiLV), an emerging virus from fish, encodes protein functions that have not been elucidated, resulting in a lag and uncertainty in vaccine development. Here, we propose a feasible strategy for emerging viral disease epitope vaccine development using TiLV. We determined the targets of specific antibodies in serum from a TiLV survivor by panning a Ph.D.-12 phage library, and we identified a mimotope, TYTTRMHITLPI, referred to as Pep3, which provided protection against TiLV after prime-boost vaccination; its immune protection rate was 57.6%. Based on amino acid sequence alignment and structure analysis of the target protein from TiLV, we further identified a protective antigenic site (399TYTTRNEDFLPT410) which is located on TiLV segment 1 (S1). The epitope vaccine with keyhole limpet hemocyanin (KLH-S1399-410) corresponding to the mimotope induced the tilapia to produce a durable and effective antibody response after immunization, and the antibody depletion test confirmed that the specific antibody against S1399-410 was necessary to neutralize TiLV. Surprisingly, the challenge studies in tilapia demonstrated that the epitope vaccine elicited a robust protective response against TiLV challenge, and the survival rate reached 81.8%. In conclusion, this study revealed a concept for screening antigen epitopes of emerging viral diseases, providing promising approaches for development and evaluation of protective epitope vaccines against viral diseases. IMPORTANCE Antigen epitope determination is an important cornerstone for developing efficient vaccines. In this study, we attempted to explore a novel approach for epitope discovery of TiLV, which is a new virus in fish. We investigated the immunogenicity and protective efficacy of all antigenic sites (mimotopes) identified in serum of primary TiLV survivors by using a Ph.D.-12 phage library. We also recognized and identified the natural epitope of TiLV by bioinformatics, evaluated the immunogenicity and protective effect of this antigenic site by immunization, and revealed 2 amino acid residues that play important roles in this epitope. Both Pep3 and S1399-410 (a natural epitope identified by Pep3) elicited antibody titers in tilapia, but S1399-410 was more prominent. Antibody depletion studies showed that anti-S1399-410-specific antibodies were essential for neutralizing TiLV. Our study demonstrated a model for combining experimental and computational screens to identify antigen epitopes, which is attractive for epitope-based vaccine development.
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Affiliation(s)
- Yu-Ming Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xue-Feng Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu-Ying Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qing Yu
- Guangxi Key Laboratory of Aquatic Biotechnology and Modern Ecological Aquaculture, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Peng-Fei Li
- Guangxi Key Laboratory of Aquatic Biotechnology and Modern Ecological Aquaculture, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Bin Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China
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11
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Jalal K, Khan K, Uddin R. Immunoinformatic-guided designing of multi-epitope vaccine construct against Brucella Suis 1300. Immunol Res 2022; 71:247-266. [PMID: 36459272 PMCID: PMC9716126 DOI: 10.1007/s12026-022-09346-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/20/2022] [Indexed: 12/05/2022]
Abstract
Brucella suis mediates the transmission of brucellosis in humans and animals and a significant facultative zoonotic pathogen found in livestock. It has the capacity to survive and multiply in a phagocytic environment and to acquire resistance under hostile conditions thus becoming a threat globally. Antibiotic resistance is posing a substantial public health threat, hence there is an unmet and urgent clinical need for immune-based non-antibiotic methods to treat brucellosis. Hence, we aimed to explore the whole proteome of Brucella suis to predict antigenic proteins as a vaccine target and designed a novel chimeric vaccine (multi-epitope vaccine) through subtractive genomics-based reverse vaccinology approaches. The applied subsequent hierarchical shortlisting resulted in the identification of Multidrug efflux Resistance-nodulation-division (RND) transporter outer membrane subunit (gene BepC) that may act as a potential vaccine target. T-cell and B-cell epitopes have been predicted from target proteins using a number of immunoinformatic methods. Six MHC I, ten MHC II, and four B-cell epitopes were used to create a 324-amino-acid MEV construct, which was coupled with appropriate linkers and adjuvant. To boost the immunological response to the vaccine, the vaccine was combined with the TLR4 agonist HBHA protein. The MEV structure predicted was found to be highly antigenic, non-toxic, non-allergenic, flexible, stable, and soluble. To confirm the interactions with the receptors, a molecular docking simulation of the MEV was done using the human TLR4 (toll-like receptor 4) and HLAs. The stability and binding of the MEV-docked complexes with TLR4 were assessed using molecular dynamics (MD) simulation. Finally, MEV was reverse translated, its cDNA structure was evaluated, and then, in silico cloning into an E. coli expression host was conducted to promote maximum vaccine protein production with appropriate post-translational modifications. These comprehensive computer calculations backed up the efficacy of the suggested MEV in protecting against B. suis infections. However, more experimental validations are needed to adequately assess the vaccine candidate's potential. HIGHLIGHTS: • Subtractive genomic analysis and reverse vaccinology for the prioritization of novel vaccine target • Examination of chimeric vaccine in terms of allergenicity, antigenicity, MHC I, II binding efficacy, and structural-based studies • Molecular docking simulation method to rank based vaccine candidate and understand their binding modes.
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Affiliation(s)
- Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Lab 103 PCMD Ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Reaz Uddin
- Lab 103 PCMD Ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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12
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Wang P, Casner RG, Nair MS, Yu J, Guo Y, Wang M, Chan JFW, Cerutti G, Iketani S, Liu L, Sheng Z, Chen Z, Yuen KY, Kwong PD, Huang Y, Shapiro L, Ho DD. A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerg Microbes Infect 2022; 11:147-157. [PMID: 34836485 PMCID: PMC8725896 DOI: 10.1080/22221751.2021.2011623] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023]
Abstract
The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses in vitro and confirmed that K378 T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.
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Affiliation(s)
- Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ryan G Casner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jasper F-W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zhiwei Chen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Vaccine Research Center, National Institutes of Health, Bethesda, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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13
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Wang X, Zhao X, Song J, Wu J, Zhu Y, Li M, Cui Y, Chen Y, Yang L, Liu J, Zhu H, Jiang S, Wang P. Homologous or heterologous booster of inactivated vaccine reduces SARS-CoV-2 Omicron variant escape from neutralizing antibodies. Emerg Microbes Infect 2022; 11:477-481. [PMID: 35034583 PMCID: PMC8820826 DOI: 10.1080/22221751.2022.2030200] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/12/2022] [Indexed: 11/24/2022]
Abstract
The massive and rapid transmission of SARS-CoV-2 has led to the emergence of several viral variants of concern (VOCs), with the most recent one, B.1.1.529 (Omicron), which accumulated a large number of spike mutations, raising the specter that this newly identified variant may escape from the currently available vaccines and therapeutic antibodies. Using VSV-based pseudovirus, we found that Omicron variant is markedly resistant to neutralization of sera from convalescents or individuals vaccinated by two doses of inactivated whole-virion vaccines (BBIBP-CorV). However, a homologous inactivated vaccine booster or a heterologous booster with protein subunit vaccine (ZF2001) significantly increased neutralization titers to both WT and Omicron variant. Moreover, at day 14 post the third dose, neutralizing antibody titer reduction for Omicron was less than that for convalescents or individuals who had only two doses of the vaccine, indicating that a homologous or heterologous booster can reduce the Omicron escape from neutralizing. In addition, we tested a panel of 17 SARS-CoV-2 monoclonal antibodies (mAbs). Omicron resists seven of eight authorized/approved mAbs, as well as most of the other mAbs targeting distinct epitopes on RBD and NTD. Taken together, our results suggest the urgency to push forward the booster vaccination to combat the emerging SARS-CoV-2 variants.
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Affiliation(s)
- Xun Wang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Xiaoyu Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jieyu Song
- Department of Infectious Diseases, Huashan Hospital affiliated with Fudan University, Shanghai, People’s Republic of China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital affiliated with Fudan University, Shanghai, People’s Republic of China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Minghui Li
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yuchen Cui
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yanjia Chen
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Lulu Yang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Jun Liu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Fubio (Suzhou) Biomedical Technology Co., Ltd., Suzhou, People’s Republic of China
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Pengfei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
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14
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Abstract
Antibodies against epitopes in S1 give the most accurate CoP against infection by the SARS-CoV-2 coronavirus. Measurement of those antibodies by neutralization or binding assays both have predictive value, with binding antibody titers giving the highest statistical correlation. However, the protective functions of antibodies are multiple. Antibodies with multiple functions other than neutralization influence efficacy. The role of cellular responses can be discerned with respect to CD4+ T cells and their augmentation of antibodies, and with respect to CD8+ cells with regard to control of viral replication, particularly in the presence of insufficient antibody. More information is needed on mucosal responses.
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Affiliation(s)
- David Goldblatt
- Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Galit Alter
- Massachusetts General HospitalRagon Institute of MGH, MIT and HarvardCambridgeMassachusettsUSA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine ResearchLa Jolla Institute for Immunology (LJI)La JollaCaliforniaUSA
- Department of Medicine, Division of Infectious Diseases and Global Public HealthUniversity of California San Diego (UCSD)La JollaCaliforniaUSA
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15
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Dacon C, Tucker C, Peng L, Lee CCD, Lin TH, Yuan M, Cong Y, Wang L, Purser L, Williams JK, Pyo CW, Kosik I, Hu Z, Zhao M, Mohan D, Cooper AJR, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Drawbaugh D, Eaton B, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Holbrook MR, Nemazee D, Mascola JR, Wilson IA, Tan J. Broadly neutralizing antibodies target the coronavirus fusion peptide. Science 2022; 377:728-735. [PMID: 35857439 PMCID: PMC9348754 DOI: 10.1126/science.abq3773] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/06/2022] [Indexed: 02/05/2023]
Abstract
The potential for future coronavirus outbreaks highlights the need to broadly target this group of pathogens. We used an epitope-agnostic approach to identify six monoclonal antibodies that bind to spike proteins from all seven human-infecting coronaviruses. All six antibodies target the conserved fusion peptide region adjacent to the S2' cleavage site. COV44-62 and COV44-79 broadly neutralize alpha- and betacoronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants BA.2 and BA.4/5, albeit with lower potency than receptor binding domain-specific antibodies. In crystal structures of COV44-62 and COV44-79 antigen-binding fragments with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine residue at the S2' cleavage site. COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings highlight the fusion peptide as a candidate epitope for next-generation coronavirus vaccine development.
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Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J. R. Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Drawbaugh
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S. Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W. Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Michael R. Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
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16
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Moyo-Gwete T, Madzivhandila M, Mkhize NN, Kgagudi P, Ayres F, Lambson BE, Manamela NP, Richardson SI, Makhado Z, van der Mescht MA, de Beer Z, de Villiers TR, Burgers WA, Ntusi NAB, Rossouw T, Ueckermann V, Boswell MT, Moore PL. Shared N417-Dependent Epitope on the SARS-CoV-2 Omicron, Beta, and Delta Plus Variants. J Virol 2022; 96:e0055822. [PMID: 35867572 PMCID: PMC9364786 DOI: 10.1128/jvi.00558-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, several variants of concern (VOCs) have arisen which are defined by multiple mutations in their spike proteins. These VOCs have shown variable escape from antibody responses and have been shown to trigger qualitatively different antibody responses during infection. By studying plasma from individuals infected with either the original D614G, Beta, or Delta variants, we showed that the Beta and Delta variants elicit antibody responses that are overall more cross-reactive than those triggered by D614G. Patterns of cross-reactivity varied, and the Beta and Delta variants did not elicit cross-reactive responses to each other. However, Beta-elicited plasma was highly cross-reactive against Delta Plus (Delta+), which differs from Delta by a single K417N mutation in the receptor binding domain, suggesting that the plasma response targets the N417 residue. To probe this further, we isolated monoclonal antibodies from a Beta-infected individual with plasma responses against Beta, Delta+, and Omicron, which all possess the N417 residue. We isolated an N417-dependent antibody, 084-7D, which showed similar neutralization breadth to the plasma. The 084-7D MAb utilized the IGHV3-23*01 germ line gene and had somatic hypermutations similar to those of previously described public antibodies which target the 417 residue. Thus, we have identified a novel antibody which targets a shared epitope found on three distinct VOCs, enabling their cross-neutralization. Understanding antibodies targeting escape mutations, such as K417N, which repeatedly emerge through convergent evolution in SARS-CoV-2 variants, may aid in the development of next-generation antibody therapeutics and vaccines. IMPORTANCE The evolution of SARS-CoV-2 has resulted in variants of concern (VOCs) with distinct spike mutations conferring various immune escape profiles. These variable mutations also influence the cross-reactivity of the antibody response mounted by individuals infected with each of these variants. This study sought to understand the antibody responses elicited by different SARS-CoV-2 variants and to define shared epitopes. We show that Beta and Delta infections resulted in antibody responses that were more cross-reactive than the original D614G variant, but they had differing patterns of cross-reactivity. We further isolated an antibody from Beta infection which targeted the N417 site, enabling cross-neutralization of Beta, Delta+, and Omicron, all of which possess this residue. The discovery of antibodies which target escape mutations common to multiple variants highlights conserved epitopes to target in future vaccines and therapeutics.
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Affiliation(s)
- Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mashudu Madzivhandila
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonhlanhla N. Mkhize
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Frances Ayres
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwen E. Lambson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nelia P. Manamela
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simone I. Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Makhado
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mieke A. van der Mescht
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | | | | | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Ntobeko A. B. Ntusi
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Theresa Rossouw
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Veronica Ueckermann
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Michael T. Boswell
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Penny L. Moore
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
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17
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Cohen AA, van Doremalen N, Greaney AJ, Andersen H, Sharma A, Starr TN, Keeffe JR, Fan C, Schulz JE, Gnanapragasam PNP, Kakutani LM, West AP, Saturday G, Lee YE, Gao H, Jette CA, Lewis MG, Tan TK, Townsend AR, Bloom JD, Munster VJ, Bjorkman PJ. Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models. Science 2022; 377:eabq0839. [PMID: 35857620 PMCID: PMC9273039 DOI: 10.1126/science.abq0839] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/29/2022] [Indexed: 12/12/2022]
Abstract
To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | | | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jonathan E. Schulz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Greg Saturday
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tiong K. Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford OX3 9DS, UK
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Vincent J. Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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18
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Jalal K, Khan K, Basharat Z, Abbas MN, Uddin R, Ali F, Khan SA, Hassan SSU. Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2. Environ Sci Pollut Res Int 2022; 29:60035-60053. [PMID: 35414157 PMCID: PMC9005162 DOI: 10.1007/s11356-022-19979-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/25/2022] [Indexed: 06/01/2023]
Abstract
The ongoing COVID-19 outbreak, initially identified in Wuhan, China, has impacted people all over the globe and new variants of concern continue to threaten hundreds of thousands of people. The delta variant (first reported in India) is currently classified as one of the most contagious variants of SARS-CoV-2. It is estimated that the transmission rate of delta variant is 225% times faster than the alpha variant, and it is causing havoc worldwide (especially in the USA, UK, and South Asia). The mutations found in the spike protein of delta variant make it more infective than other variants in addition to ruining the global efficacy of available vaccines. In the current study, an in silico reverse vaccinology approach was applied for multi-epitope vaccine construction against the spike protein of delta variant, which could induce an immune response against COVID-19 infection. Non-toxic, highly conserved, non-allergenic and highly antigenic B-cell, HTL, and CTL epitopes were identified to minimize adverse effects and maximize the efficacy of chimeric vaccines that could be developed from these epitopes. Finally, V1 vaccine construct model was shortlisted and 3D modeling was performed by refinement, docking against HLAs and TLR4 protein, simulation and in silico expression. In silico evaluation showed that the designed chimeric vaccine could elicit an immune response (i.e., cell-mediated and humoral) identified through immune simulation. This study could add to the efforts of overcoming global burden of COVID-19 particularly the variants of concern.
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Affiliation(s)
- Khurshid Jalal
- International Center for Chemical and Biological Sciences, HEJ Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS University of Karachi, Karachi, Pakistan
| | | | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
| | - Fawad Ali
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Saeed Ahmad Khan
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Syed Shams Ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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19
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Olczak P, Matsui K, Wong M, Alvarez J, Lambert P, Christensen ND, Hu J, Huber B, Kirnbauer R, Wang JW, Roden RBS. RG2-VLP: a Vaccine Designed to Broadly Protect against Anogenital and Skin Human Papillomaviruses Causing Human Cancer. J Virol 2022; 96:e0056622. [PMID: 35703545 PMCID: PMC9278150 DOI: 10.1128/jvi.00566-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/20/2022] [Indexed: 12/20/2022] Open
Abstract
The family of human papillomaviruses (HPV) includes over 400 genotypes. Genus α genotypes generally infect the anogenital mucosa, and a subset of these HPV are a necessary, but not sufficient, cause of cervical cancer. Of the 13 high-risk (HR) and 11 intermediate-risk (IR) HPV associated with cervical cancer, genotypes 16 and 18 cause 50% and 20% of cases, respectively, whereas HPV16 dominates in other anogenital and oropharyngeal cancers. A plethora of βHPVs are associated with cutaneous squamous cell carcinoma (CSCC), especially in sun-exposed skin sites of epidermodysplasia verruciformis (EV), AIDS, and immunosuppressed patients. Licensed L1 virus-like particle (VLP) vaccines, such as Gardasil 9, target a subset of αHPV but no βHPV. To comprehensively target both α- and βHPVs, we developed a two-component VLP vaccine, RG2-VLP, in which L2 protective epitopes derived from a conserved αHPV epitope (amino acids 17 to 36 of HPV16 L2) and a consensus βHPV sequence in the same region are displayed within the DE loop of HPV16 and HPV18 L1 VLP, respectively. Unlike vaccination with Gardasil 9, vaccination of wild-type and EV model mice (Tmc6Δ/Δ or Tmc8Δ/Δ) with RG2-VLP induced robust L2-specific antibody titers and protected against β-type HPV5. RG2-VLP protected rabbits against 17 αHPV, including those not covered by Gardasil 9. HPV16- and HPV18-specific neutralizing antibody responses were similar between RG2-VLP- and Gardasil 9-vaccinated animals. However, only transfer of RG2-VLP antiserum effectively protected naive mice from challenge with all βHPVs tested. Taken together, these observations suggest RG2-VLP's potential as a broad-spectrum vaccine to prevent αHPV-driven anogenital, oropharyngeal, and βHPV-associated cutaneous cancers. IMPORTANCE Licensed preventive HPV vaccines are composed of VLPs derived by expression of major capsid protein L1. They confer protection generally restricted to infection by the αHPVs targeted by the up-to-9-valent vaccine, and their associated anogenital cancers and genital warts, but do not target βHPV that are associated with CSCC in EV and immunocompromised patients. We describe the development of a two-antigen vaccine protective in animal models against known oncogenic αHPVs as well as diverse βHPVs by incorporation into HPV16 and HPV18 L1 VLP of 20-amino-acid conserved protective epitopes derived from minor capsid protein L2.
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Affiliation(s)
- Pola Olczak
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Margaret Wong
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jade Alvarez
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Paul Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Neil D. Christensen
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
- Department of Pathology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
| | - Jiafen Hu
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
- Department of Pathology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
| | - Bettina Huber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Reinhard Kirnbauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
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20
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Banerjee A, Huang J, Rush SA, Murray J, Gingerich AD, Royer F, Hsieh CL, Tripp RA, McLellan JS, Mousa JJ. Structural basis for ultrapotent antibody-mediated neutralization of human metapneumovirus. Proc Natl Acad Sci U S A 2022; 119:e2203326119. [PMID: 35696580 PMCID: PMC9231621 DOI: 10.1073/pnas.2203326119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/23/2022] [Indexed: 12/15/2022] Open
Abstract
Human metapneumovirus (hMPV) is a leading cause of morbidity and hospitalization among children worldwide, however, no vaccines or therapeutics are currently available for hMPV disease prevention and treatment. The hMPV fusion (F) protein is the sole target of neutralizing antibodies. To map the immunodominant epitopes on the hMPV F protein, we isolated a panel of human monoclonal antibodies (mAbs), and the mAbs were assessed for binding avidity, neutralization potency, and epitope specificity. We found the majority of the mAbs target diverse epitopes on the hMPV F protein, and we discovered multiple mAb binding approaches for antigenic site III. The most potent mAb, MPV467, which had picomolar potency, was examined in prophylactic and therapeutic mouse challenge studies, and MPV467 limited virus replication in mouse lungs when administered 24 h before or 72 h after viral infection. We determined the structure of MPV467 in complex with the hMPV F protein using cryo-electron microscopy to a resolution of 3.3 Å, which revealed a complex novel prefusion-specific epitope overlapping antigenic sites II and V on a single protomer. Overall, our data reveal insights into the immunodominant antigenic epitopes on the hMPV F protein, identify a mAb therapy for hMPV F disease prevention and treatment, and provide the discovery of a prefusion-specific epitope on the hMPV F protein.
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MESH Headings
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/isolation & purification
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/isolation & purification
- Antibodies, Viral/therapeutic use
- Antigens, Viral/chemistry
- Antigens, Viral/immunology
- Cryoelectron Microscopy
- Epitopes/immunology
- Humans
- Metapneumovirus/immunology
- Mice
- Paramyxoviridae Infections/prevention & control
- Primary Prevention
- Viral Fusion Proteins/chemistry
- Viral Fusion Proteins/immunology
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Affiliation(s)
- Avik Banerjee
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Jiachen Huang
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Scott A. Rush
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jackelyn Murray
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Aaron D. Gingerich
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Fredejah Royer
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Ralph A. Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jarrod J. Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602
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21
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Kirkpatrick Roubidoux E, Sano K, McMahon M, Carreño JM, Capuano C, Jiang K, Simon V, van Bakel H, Wilson P, Krammer F. Novel Epitopes of the Influenza Virus N1 Neuraminidase Targeted by Human Monoclonal Antibodies. J Virol 2022; 96:e0033222. [PMID: 35446141 PMCID: PMC9093090 DOI: 10.1128/jvi.00332-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/16/2022] [Indexed: 12/30/2022] Open
Abstract
Influenza virus neuraminidase (NA)-targeting antibodies are an independent correlate of protection against influenza. Antibodies against the NA act by blocking enzymatic activity, preventing virus release and transmission. As we advance the development of improved influenza virus vaccines that incorporate standard amounts of NA antigen, it is important to identify the antigenic targets of human monoclonal antibodies (mAbs). Here, we describe escape mutants generated by serial passage of A/Netherlands/602/2009 (H1N1)pdm09 in the presence of human anti-N1 mAbs. We observed escape mutations on the head domain of the N1 protein around the enzymatic site (S364N, N369T, and R430Q) and also detected escape mutations located on the sides and bottom of the NA (N88D, N270D, and Q313K/R). This work increases our understanding of how human antibody responses target the N1 protein. IMPORTANCE As improved influenza virus vaccines are being developed, the influenza virus neuraminidase (NA) is becoming an important new target for immune responses. By identifying novel epitopes of anti-NA antibodies, we can improve vaccine design. Additionally, characterizing escape mutations in these epitopes aids in identifying NA antigenic drift in circulating viruses.
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Affiliation(s)
- Ericka Kirkpatrick Roubidoux
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kaori Sano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christina Capuano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kaijun Jiang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patrick Wilson
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, Illinois, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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22
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Höllerhage M, Wolff A, Chakroun T, Evsyukov V, Duan L, Chua OWH, Tang Q, Koeglsperger T, Höglinger GU. Binding Stability of Antibody-α-Synuclein Complexes Predicts the Protective Efficacy of Anti-α-synuclein Antibodies. Mol Neurobiol 2022; 59:3980-3995. [PMID: 35460053 PMCID: PMC9167191 DOI: 10.1007/s12035-022-02824-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/01/2022] [Indexed: 01/01/2023]
Abstract
Spreading of alpha-synuclein (αSyn) may play an important role in Parkinson’s disease and related synucleinopathies. Passive immunization with anti-αSyn antibodies is a promising method to slow down the spreading process and thereby the progression of synucleinopathies. Currently, it remains elusive which specific characteristics are essential to render therapeutic antibodies efficacious. Here, we established a neuronal co-culture model, in which αSyn species are being released from αSyn-overexpressing cells and induce toxicity in a priori healthy GFP-expressing cells. In this model, we investigated the protective efficacy of three anti-αSyn antibodies. Only two of these antibodies, one C-terminal and one N-terminal, protected from αSyn-induced toxicity by inhibiting the uptake of spreading-competent αSyn from the cell culture medium. Neither the binding epitope nor the affinity of the antibodies towards recombinant αSyn could explain differences in biological efficacy. However, both protective antibodies formed more stable antibody-αSyn complexes than the non-protective antibody. These findings indicate that the stability of antibody-αSyn complexes may be more important to confer protection than the binding epitope or affinity to recombinant αSyn.
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Affiliation(s)
- Matthias Höllerhage
- Department of Neurology, Hannover Medical School, Hannover, D-30625, Germany.
| | - Andreas Wolff
- Department of Neurology, Technical University of Munich (TUM), D-81675, Munich, Germany
| | - Tasnim Chakroun
- Department of Neurology, Technical University of Munich (TUM), D-81675, Munich, Germany
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), D-81377, Munich, Germany
| | - Valentin Evsyukov
- Department of Neurology, Hannover Medical School, Hannover, D-30625, Germany
| | - Linghan Duan
- Department of Neurology, Hannover Medical School, Hannover, D-30625, Germany
| | - Oscar Wing-Ho Chua
- Department of Neurology, Hannover Medical School, Hannover, D-30625, Germany
| | - Qilin Tang
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), D-81377, Munich, Germany
| | - Thomas Koeglsperger
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), D-81377, Munich, Germany
- Department of Neurology, Ludwig Maximilian University Munich, D-81377, Munich, Germany
| | - Günter U Höglinger
- Department of Neurology, Hannover Medical School, Hannover, D-30625, Germany
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), D-81377, Munich, Germany
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23
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Le Gall C, Cammarata A, de Haas L, Ramos-Tomillero I, Cuenca-Escalona J, Schouren K, Wijfjes Z, Becker AMD, Bödder J, Dölen Y, de Vries IJM, Figdor CG, Flórez-Grau G, Verdoes M. Efficient targeting of NY-ESO-1 tumor antigen to human cDC1s by lymphotactin results in cross-presentation and antigen-specific T cell expansion. J Immunother Cancer 2022; 10:jitc-2021-004309. [PMID: 35428705 PMCID: PMC9014073 DOI: 10.1136/jitc-2021-004309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2022] [Indexed: 12/20/2022] Open
Abstract
Background Type 1 conventional dendritic cells (cDC1s) are characterized by their ability to induce potent CD8+ T cell responses. In efforts to generate novel vaccination strategies, notably against cancer, human cDC1s emerge as an ideal target to deliver antigens. cDC1s uniquely express XCR1, a seven transmembrane G protein-coupled receptor. Due to its restricted expression and endocytic nature, XCR1 represents an attractive receptor to mediate antigen-delivery to human cDC1s. Methods To explore tumor antigen delivery to human cDC1s, we used an engineered version of XCR1-binding lymphotactin (XCL1), XCL1(CC3). Site-specific sortase-mediated transpeptidation was performed to conjugate XCL1(CC3) to an analog of the HLA-A*02:01 epitope of the cancer testis antigen New York Esophageal Squamous Cell Carcinoma-1 (NY-ESO-1). While poor epitope solubility prevented isolation of stable XCL1-antigen conjugates, incorporation of a single polyethylene glycol (PEG) chain upstream of the epitope-containing peptide enabled generation of soluble XCL1(CC3)-antigen fusion constructs. Binding and chemotactic characteristics of the XCL1-antigen conjugate, as well as its ability to induce antigen-specific CD8+ T cell activation by cDC1s, was assessed. Results PEGylated XCL1(CC3)-antigen conjugates retained binding to XCR1, and induced cDC1 chemoattraction in vitro. The model epitope was efficiently cross-presented by human cDC1s to activate NY-ESO-1-specific CD8+ T cells. Importantly, vaccine activity was increased by targeting XCR1 at the surface of cDC1s. Conclusion Our results present a novel strategy for the generation of targeted vaccines fused to insoluble antigens. Moreover, our data emphasize the potential of targeting XCR1 at the surface of primary human cDC1s to induce potent CD8+ T cell responses.
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Affiliation(s)
- Camille Le Gall
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Tumor Immunology, Oncode Institute, Nijmegen, The Netherlands
| | - Anna Cammarata
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lukas de Haas
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Iván Ramos-Tomillero
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - Jorge Cuenca-Escalona
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Kayleigh Schouren
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Zacharias Wijfjes
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - Anouk M D Becker
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Johanna Bödder
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Yusuf Dölen
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Tumor Immunology, Oncode Institute, Nijmegen, The Netherlands
| | - I Jolanda M de Vries
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Tumor Immunology, Oncode Institute, Nijmegen, The Netherlands
| | - Georgina Flórez-Grau
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
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24
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Tarke A, Coelho CH, Zhang Z, Dan JM, Yu ED, Methot N, Bloom NI, Goodwin B, Phillips E, Mallal S, Sidney J, Filaci G, Weiskopf D, da Silva Antunes R, Crotty S, Grifoni A, Sette A. SARS-CoV-2 vaccination induces immunological T cell memory able to cross-recognize variants from Alpha to Omicron. Cell 2022; 185:847-859.e11. [PMID: 35139340 PMCID: PMC8784649 DOI: 10.1016/j.cell.2022.01.015] [Citation(s) in RCA: 469] [Impact Index Per Article: 234.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 12/19/2022]
Abstract
We address whether T cell responses induced by different vaccine platforms (mRNA-1273, BNT162b2, Ad26.COV2.S, and NVX-CoV2373) cross-recognize early SARS-CoV-2 variants. T cell responses to early variants were preserved across vaccine platforms. By contrast, significant overall decreases were observed for memory B cells and neutralizing antibodies. In subjects ∼6 months post-vaccination, 90% (CD4+) and 87% (CD8+) of memory T cell responses were preserved against variants on average by AIM assay, and 84% (CD4+) and 85% (CD8+) preserved against Omicron. Omicron RBD memory B cell recognition was substantially reduced to 42% compared with other variants. T cell epitope repertoire analysis revealed a median of 11 and 10 spike epitopes recognized by CD4+ and CD8+ T cells, with average preservation > 80% for Omicron. Functional preservation of the majority of T cell responses may play an important role as a second-level defense against diverse variants.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa 16132, Italy
| | - Camila H Coelho
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Zeli Zhang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Nathaniel I Bloom
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Benjamin Goodwin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa 16132, Italy; Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, Genoa 16132, Italy
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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25
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Borriello F, Poli V, Shrock E, Spreafico R, Liu X, Pishesha N, Carpenet C, Chou J, Di Gioia M, McGrath ME, Dillen CA, Barrett NA, Lacanfora L, Franco ME, Marongiu L, Iwakura Y, Pucci F, Kruppa MD, Ma Z, Lowman DW, Ensley HE, Nanishi E, Saito Y, O'Meara TR, Seo HS, Dhe-Paganon S, Dowling DJ, Frieman M, Elledge SJ, Levy O, Irvine DJ, Ploegh HL, Williams DL, Zanoni I. An adjuvant strategy enabled by modulation of the physical properties of microbial ligands expands antigen immunogenicity. Cell 2022; 185:614-629.e21. [PMID: 35148840 PMCID: PMC8857056 DOI: 10.1016/j.cell.2022.01.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/19/2021] [Accepted: 01/14/2022] [Indexed: 12/15/2022]
Abstract
Activation of the innate immune system via pattern recognition receptors (PRRs) is key to generate lasting adaptive immunity. PRRs detect unique chemical patterns associated with invading microorganisms, but whether and how the physical properties of PRR ligands influence the development of the immune response remains unknown. Through the study of fungal mannans, we show that the physical form of PRR ligands dictates the immune response. Soluble mannans are immunosilent in the periphery but elicit a potent pro-inflammatory response in the draining lymph node (dLN). By modulating the physical form of mannans, we developed a formulation that targets both the periphery and the dLN. When combined with viral glycoprotein antigens, this mannan formulation broadens epitope recognition, elicits potent antigen-specific neutralizing antibodies, and confers protection against viral infections of the lung. Thus, the physical properties of microbial ligands determine the outcome of the immune response and can be harnessed for vaccine development.
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Affiliation(s)
- Francesco Borriello
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Division of Immunology, Boston, MA, USA; Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Valentina Poli
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Division of Immunology, Boston, MA, USA
| | - Ellen Shrock
- Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Program in Virology, Boston, MA, USA
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xin Liu
- Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Novalia Pishesha
- Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Claire Carpenet
- Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Janet Chou
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Division of Immunology, Boston, MA, USA
| | - Marco Di Gioia
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Division of Immunology, Boston, MA, USA
| | - Marisa E McGrath
- University of Maryland School of Medicine, Department of Microbiology and Immunology, Baltimore, MD, USA
| | - Carly A Dillen
- University of Maryland School of Medicine, Department of Microbiology and Immunology, Baltimore, MD, USA
| | - Nora A Barrett
- Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Division of Allergy and Clinical Immunology, Boston, MA, USA
| | - Lucrezia Lacanfora
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Division of Immunology, Boston, MA, USA; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Marcella E Franco
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Division of Immunology, Boston, MA, USA; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Laura Marongiu
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Yoichiro Iwakura
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Tokyo, Japan
| | - Ferdinando Pucci
- Department of Otolaryngology-Head and Neck Surgery, Department of Cell, Developmental & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Michael D Kruppa
- Department of Biomedical Sciences, Quillen College of Medicine, Center of Excellence in Inflammation, Infectious Disease and Immunity, East Tennessee State University, Johnson City, TN, USA
| | - Zuchao Ma
- Department of Surgery, Quillen College of Medicine, Center of Excellence in Inflammation, Infectious Disease and Immunity, East Tennessee State University, Johnson City, TN, USA
| | - Douglas W Lowman
- Department of Surgery, Quillen College of Medicine, Center of Excellence in Inflammation, Infectious Disease and Immunity, East Tennessee State University, Johnson City, TN, USA
| | - Harry E Ensley
- Department of Surgery, Quillen College of Medicine, Center of Excellence in Inflammation, Infectious Disease and Immunity, East Tennessee State University, Johnson City, TN, USA
| | - Etsuro Nanishi
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Precision Vaccines Program, Boston, MA, USA
| | - Yoshine Saito
- Boston Children's Hospital, Precision Vaccines Program, Boston, MA, USA
| | - Timothy R O'Meara
- Boston Children's Hospital, Precision Vaccines Program, Boston, MA, USA
| | - Hyuk-Soo Seo
- Harvard Medical School, Boston, MA, USA; Dana-Farber Cancer Institute, Department of Cancer Biology, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Harvard Medical School, Boston, MA, USA; Dana-Farber Cancer Institute, Department of Cancer Biology, Boston, MA, USA
| | - David J Dowling
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Precision Vaccines Program, Boston, MA, USA
| | - Matthew Frieman
- University of Maryland School of Medicine, Department of Microbiology and Immunology, Baltimore, MD, USA
| | - Stephen J Elledge
- Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Program in Virology, Boston, MA, USA
| | - Ofer Levy
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Precision Vaccines Program, Boston, MA, USA; Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Darrell J Irvine
- Massachusetts Institute of Technology, Department of Biological Engineering and Department of Materials Science and Engineering, Koch Institute for Integrative Cancer Research, Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Hidde L Ploegh
- Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - David L Williams
- Department of Biomedical Sciences, Quillen College of Medicine, Center of Excellence in Inflammation, Infectious Disease and Immunity, East Tennessee State University, Johnson City, TN, USA
| | - Ivan Zanoni
- Harvard Medical School, Boston, MA, USA; Boston Children's Hospital, Division of Immunology, Boston, MA, USA; Boston Children's Hospital, Division of Gastroenterology, Boston, MA, USA.
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26
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Abstract
A major goal of SARS-CoV-2 vaccination is the induction of neutralizing antibodies (nAbs) capable of blocking infection by preventing interaction of the SARS-CoV-2 Spike protein with ACE2 on target cells. Cocktails of monoclonal nAbs can reduce the risk of severe disease if administered early in infection. However, multiple variants of concern (VOCs) have arisen during the pandemic that may escape from nAbs. In this issue of the JCI, Jia Zou, Li Li, and colleagues used yeast display libraries to identify mAbs that bind to Spike proteins with a vast array of single amino acid substitutions. The authors identified mutation-resistant monoclonal nAbs for potential use as therapeutics. Multimerization further improved the potency of selected nAbs. These findings suggest a way forward in development of better nAb cocktails. However, the emergence of the highly mutated omicron (B.1.1.529) variant heightens the importance of finding effective anti-SARS-CoV-2 nAb therapeutics despite rapid viral evolution.
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27
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Miller NL, Clark T, Raman R, Sasisekharan R. Insights on the mutational landscape of the SARS-CoV-2 Omicron variant receptor-binding domain. Cell Rep Med 2022; 3:100527. [PMID: 35233548 PMCID: PMC8784435 DOI: 10.1016/j.xcrm.2022.100527] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 11/27/2022]
Abstract
The Omicron variant features enhanced transmissibility and antibody escape. Here, we describe the Omicron receptor-binding domain (RBD) mutational landscape using amino acid interaction (AAI) networks, which are well suited for interrogating constellations of mutations that function in an epistatic manner. Using AAI, we map Omicron mutations directly and indirectly driving increased escape breadth and depth in class 1-4 antibody epitopes. Further, we present epitope networks for authorized therapeutic antibodies and assess perturbations to each antibody's epitope. Since our initial modeling following the identification of Omicron, these predictions have been realized by experimental findings of Omicron neutralization escape from therapeutic antibodies ADG20, AZD8895, and AZD1061. Importantly, the AAI predicted escape resulting from indirect epitope perturbations was not captured by previous sequence or point mutation analyses. Finally, for several Omicron RBD mutations, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBDdown-RBDdown interface.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance in Research and Technology (SMART), Singapore 138602, Singapore
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28
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Lim SA, Zhou J, Martinko AJ, Wang YH, Filippova EV, Steri V, Wang D, Remesh SG, Liu J, Hann B, Kossiakoff AA, Evans MJ, Leung KK, Wells JA. Targeting a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) for RAS-driven cancers. J Clin Invest 2022; 132:e154604. [PMID: 35166238 PMCID: PMC8843743 DOI: 10.1172/jci154604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Extracellular proteolysis is frequently dysregulated in disease and can generate proteoforms with unique neoepitopes not found in healthy tissue. Here, we demonstrate that Abs that selectively recognize a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) could enable more effective and safer treatments for solid tumors. CDCP1 is highly overexpressed in RAS-driven cancers, and its ectodomain is cleaved by extracellular proteases. Biochemical, biophysical, and structural characterization revealed that the 2 cleaved fragments of CDCP1 remain tightly associated with minimal proteolysis-induced conformational change. Using differential phage display, we generated recombinant Abs that are exquisitely selective to cleaved CDCP1 with no detectable binding to the uncleaved form. These Abs potently targeted cleaved CDCP1-expressing cancer cells as an Ab-drug conjugate, an Ab-radionuclide conjugate, and a bispecific T cell engager. In a syngeneic pancreatic tumor model, these cleaved-specific Abs showed tumor-specific localization and antitumor activity with superior safety profiles compared with a pan-CDCP1 approach. Targeting proteolytic neoepitopes could provide an orthogonal "AND" gate for improving the therapeutic index.
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Affiliation(s)
| | - Jie Zhou
- Department of Pharmaceutical Chemistry
| | | | - Yung-Hua Wang
- Department of Radiology and Biomedical Imaging, and
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Ekaterina V. Filippova
- Department of Biochemistry and Molecular Biology, and
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Preclinical Therapeutics Core, UCSF, San Francisco, California, USA
| | - Donghui Wang
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Preclinical Therapeutics Core, UCSF, San Francisco, California, USA
| | | | - Jia Liu
- Department of Pharmaceutical Chemistry
| | - Byron Hann
- Preclinical Therapeutics Core, UCSF, San Francisco, California, USA
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, and
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
| | - Michael J. Evans
- Department of Radiology and Biomedical Imaging, and
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | | | - James A. Wells
- Department of Pharmaceutical Chemistry
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
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29
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Cia G, Pucci F, Rooman M. Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations. Int J Mol Sci 2022; 23:ijms23042078. [PMID: 35216194 PMCID: PMC8876721 DOI: 10.3390/ijms23042078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 infection elicits a polyclonal neutralizing antibody (nAb) response that primarily targets the spike protein, but it is still unclear which nAbs are immunodominant and what distinguishes them from subdominant nAbs. This information would however be crucial to predict the evolutionary trajectory of the virus and design future vaccines. To shed light on this issue, we gathered 83 structures of nAbs in complex with spike protein domains. We analyzed in silico the ability of these nAbs to bind the full spike protein trimer in open and closed conformations, and predicted the change in binding affinity of the most frequently observed spike protein variants in the circulating strains. This led us to define four nAb classes with distinct variant escape fractions. By comparing these fractions with those measured from plasma of infected patients, we showed that the class of nAbs that most contributes to the immune response is able to bind the spike protein in its closed conformation. Although this class of nAbs only partially inhibits the spike protein binding to the host’s angiotensin converting enzyme 2 (ACE2), it has been suggested to lock the closed pre-fusion spike protein conformation and therefore prevent its transition to an open state. Furthermore, comparison of our predictions with mRNA-1273 vaccinated patient plasma measurements suggests that spike proteins contained in vaccines elicit a different nAb class than the one elicited by natural SARS-CoV-2 infection and suggests the design of highly stable closed-form spike proteins as next-generation vaccine immunogens.
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Affiliation(s)
- Gabriel Cia
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (G.C.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (G.C.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (G.C.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
- Correspondence:
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30
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Xu Z, Walker S, Wise MC, Chokkalingam N, Purwar M, Moore A, Tello-Ruiz E, Wu Y, Majumdar S, Konrath KM, Kulkarni A, Tursi NJ, Zaidi FI, Reuschel EL, Patel I, Obeirne A, Du J, Schultheis K, Gites L, Smith T, Mendoza J, Broderick KE, Humeau L, Pallesen J, Weiner DB, Kulp DW. Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer. Nat Commun 2022; 13:695. [PMID: 35121758 PMCID: PMC8816947 DOI: 10.1038/s41467-022-28363-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 01/11/2022] [Indexed: 12/30/2022] Open
Abstract
HIV Envelope (Env) is the main vaccine target for induction of neutralizing antibodies. Stabilizing Env into native-like trimer (NLT) conformations is required for recombinant protein immunogens to induce autologous neutralizing antibodies(nAbs) against difficult to neutralize HIV strains (tier-2) in rabbits and non-human primates. Immunizations of mice with NLTs have generally failed to induce tier-2 nAbs. Here, we show that DNA-encoded NLTs fold properly in vivo and induce autologous tier-2 nAbs in mice. DNA-encoded NLTs also uniquely induce both CD4 + and CD8 + T-cell responses as compared to corresponding protein immunizations. Murine neutralizing antibodies are identified with an advanced sequencing technology. The structure of an Env-Ab (C05) complex, as determined by cryo-EM, identifies a previously undescribed neutralizing Env C3/V5 epitope. Beyond potential functional immunity gains, DNA vaccines permit in vivo folding of structured antigens and provide significant cost and speed advantages for enabling rapid evaluation of new HIV vaccines.
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Affiliation(s)
- Ziyang Xu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Susanne Walker
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Megan C Wise
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Neethu Chokkalingam
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Mansi Purwar
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Alan Moore
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Edgar Tello-Ruiz
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Yuanhan Wu
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Sonali Majumdar
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Kylie M Konrath
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Abhijeet Kulkarni
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Nicholas J Tursi
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Faraz I Zaidi
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Emma L Reuschel
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Ishaan Patel
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - April Obeirne
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Jianqiu Du
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | | | - Lauren Gites
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Trevor Smith
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Janess Mendoza
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | | | - Laurent Humeau
- Inovio Pharmaceuticals, Plymouth Meeting, PA, 19462, USA
| | - Jesper Pallesen
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - David B Weiner
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Daniel W Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA, 19104, USA.
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31
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de Bourayne M, Meunier S, Bitoun S, Correia E, Mariette X, Nozach H, Maillère B. Pegylation Reduces the Uptake of Certolizumab Pegol by Dendritic Cells and Epitope Presentation to T-Cells. Front Immunol 2022; 13:808606. [PMID: 35185895 PMCID: PMC8854214 DOI: 10.3389/fimmu.2022.808606] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Pegylation of biopharmaceuticals is the most common strategy to increase their half-life in the blood and is associated with a reduced immunogenicity. As antigen presentation is a primary event in the activation of CD4 T-cells and initiation of Anti-Drug Antibody (ADA) response, we investigated the role of the PEG molecule on the T-cell reactivity of certolizumab pegol (CZP), a pegylated anti-TNFα Fab. We generated T-cell lines raised against CZP and its non-pegylated form (CZNP) and demonstrated CZP primed few T-cells in comparison to CZNP. CZP-primed lines from 3 donors responded to a total of 5 epitopes, while CZNP-primed lines from 3 donors responded to a total of 7 epitopes, 4 epitopes were recognized by both CZP- and CZNP-primed lines. In line with this difference of T-cell reactivity, CZP is less internalized by the dendritic cells than CZNP. In vitro digestion assay of CZP by Cathepsin B showed a rapid removal of the PEG moiety, suggesting a limited influence of PEG on CZP proteolysis. We therefore demonstrate that pegylation diminishes antigen capture by dendritic cells, peptide presentation to T-cells and T-cell priming. This mechanism might reduce immunogenicity and contribute to the long half-life of CZP and possibly of other pegylated molecules.
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Affiliation(s)
- Marie de Bourayne
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Sylvain Meunier
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Samuel Bitoun
- Université Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Department of Rheumatology, INSERM UMR1184, Le Kremlin Bicêtre, France
| | - Evelyne Correia
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Xavier Mariette
- Université Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Department of Rheumatology, INSERM UMR1184, Le Kremlin Bicêtre, France
| | - Hervé Nozach
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Bernard Maillère
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
- *Correspondence: Bernard Maillère,
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Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. PLoS Pathog 2022; 18:e1010248. [PMID: 35134084 PMCID: PMC8856557 DOI: 10.1371/journal.ppat.1010248] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/18/2022] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the "class 3" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
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Affiliation(s)
- Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rachel T. Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrea N. Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - David Veesler
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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33
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Jones RM, Seo H, Zhang W, Sack DA. A multi-epitope fusion antigen candidate vaccine for Enterotoxigenic Escherichia coli is protective against strain B7A colonization in a rabbit model. PLoS Negl Trop Dis 2022; 16:e0010177. [PMID: 35139116 PMCID: PMC8863229 DOI: 10.1371/journal.pntd.0010177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/22/2022] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) strains are a leading cause of children's and travelers' diarrhea. Developing effective vaccines against this heterologous group has proven difficult due to the varied nature of toxins and adhesins that determine their pathology. A multivalent candidate vaccine was developed using a multi-epitope fusion antigen (MEFA) vaccinology platform and shown to effectively elicit broad protective antibody responses in mice and pigs. However, direct protection against ETEC colonization of the small intestine was not measured in these systems. Colonization of ETEC strains is known to be a determining factor in disease outcomes and is adhesin-dependent. In this study, we developed a non-surgical rabbit colonization model to study immune protection against ETEC colonization in rabbits. We tested the ability for the MEFA-based vaccine adhesin antigen, in combination with dmLT adjuvant, to induce broad immune responses and to protect from ETEC colonization of the rabbit small intestine. Our results indicate that the candidate vaccine MEFA antigen elicits antibodies in rabbits that react to seven adhesins included in its construction and protects against colonization of a challenge strain that consistently colonized naïve rabbits.
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Affiliation(s)
- Richard M. Jones
- Johns Hopkins Bloomberg School of Public Health, Department of International Health, Baltimore, Maryland, United States of America
- University of Washington, Department of Microbiology, Seattle, Washington, United States of America
- * E-mail:
| | - Hyesuk Seo
- University of Illinois at Urbana-Champaign, Department of Pathobiology, Urbana, Illinois, United States of America
| | - Weiping Zhang
- University of Illinois at Urbana-Champaign, Department of Pathobiology, Urbana, Illinois, United States of America
| | - David A. Sack
- Johns Hopkins Bloomberg School of Public Health, Department of International Health, Baltimore, Maryland, United States of America
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34
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Guthmiller JJ, Han J, Utset HA, Li L, Lan LYL, Henry C, Stamper CT, McMahon M, O'Dell G, Fernández-Quintero ML, Freyn AW, Amanat F, Stovicek O, Gentles L, Richey ST, de la Peña AT, Rosado V, Dugan HL, Zheng NY, Tepora ME, Bitar DJ, Changrob S, Strohmeier S, Huang M, García-Sastre A, Liedl KR, Bloom JD, Nachbagauer R, Palese P, Krammer F, Coughlan L, Ward AB, Wilson PC. Broadly neutralizing antibodies target a haemagglutinin anchor epitope. Nature 2022; 602:314-320. [PMID: 34942633 PMCID: PMC8828479 DOI: 10.1038/s41586-021-04356-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection1. However, viral mutants that escape broadly neutralizing antibodies have been reported2,3. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine4,5, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | | | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Moderna Inc., Cambridge, MA, USA
| | | | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George O'Dell
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Alec W Freyn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lauren Gentles
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Victoria Rosado
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Micah E Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Siriruk Changrob
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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35
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Sahin M, Remy MM, Fallet B, Sommerstein R, Florova M, Langner A, Klausz K, Straub T, Kreutzfeldt M, Wagner I, Schmidt CT, Malinge P, Magistrelli G, Izui S, Pircher H, Verbeek JS, Merkler D, Peipp M, Pinschewer DD. Antibody bivalency improves antiviral efficacy by inhibiting virion release independently of Fc gamma receptors. Cell Rep 2022; 38:110303. [PMID: 35108544 PMCID: PMC8822495 DOI: 10.1016/j.celrep.2022.110303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022] Open
Abstract
Across the animal kingdom, multivalency discriminates antibodies from all other immunoglobulin superfamily members. The evolutionary forces conserving multivalency above other structural hallmarks of antibodies remain, however, incompletely defined. Here, we engineer monovalent either Fc-competent or -deficient antibody formats to investigate mechanisms of protection of neutralizing antibodies (nAbs) and non-neutralizing antibodies (nnAbs) in virus-infected mice. Antibody bivalency enables the tethering of virions to the infected cell surface, inhibits the release of virions in cell culture, and suppresses viral loads in vivo independently of Fc gamma receptor (FcγR) interactions. In return, monovalent antibody formats either do not inhibit virion release and fail to protect in vivo or their protective efficacy is largely FcγR dependent. Protection in mice correlates with virus-release-inhibiting activity of nAb and nnAb rather than with their neutralizing capacity. These observations provide mechanistic insights into the evolutionary conservation of antibody bivalency and help refining correlates of nnAb protection for vaccine development.
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Affiliation(s)
- Mehmet Sahin
- Department of Biomedicine - Haus Petersplatz, Division of Experimental Virology, University of Basel, 4009 Basel, Switzerland
| | - Melissa M Remy
- Department of Biomedicine - Haus Petersplatz, Division of Experimental Virology, University of Basel, 4009 Basel, Switzerland; Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland
| | - Benedict Fallet
- Department of Biomedicine - Haus Petersplatz, Division of Experimental Virology, University of Basel, 4009 Basel, Switzerland; Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland
| | - Rami Sommerstein
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland
| | - Marianna Florova
- Department of Biomedicine - Haus Petersplatz, Division of Experimental Virology, University of Basel, 4009 Basel, Switzerland
| | - Anna Langner
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Katja Klausz
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Tobias Straub
- Institute for Immunology, Department for Medical Microbiology and Hygiene, University Medical Center Freiburg, 79104 Freiburg, Germany
| | - Mario Kreutzfeldt
- Department of Pathology and Immunology, Division of Clinical Pathology, University and University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Ingrid Wagner
- Department of Pathology and Immunology, Division of Clinical Pathology, University and University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Cinzia T Schmidt
- BioEM Lab, Center for Cellular Imaging & Nano Analytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Pauline Malinge
- Light Chain Bioscience, Novimmune SA, Plan-les-Ouates, Switzerland
| | | | - Shozo Izui
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland
| | - Hanspeter Pircher
- Institute for Immunology, Department for Medical Microbiology and Hygiene, University Medical Center Freiburg, 79104 Freiburg, Germany
| | - J Sjef Verbeek
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Biomedical Engineering, Toin University of Yokohama, Yokohama, Japan
| | - Doron Merkler
- Department of Pathology and Immunology, Division of Clinical Pathology, University and University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Matthias Peipp
- Division of Stem Cell Transplantation and Immunotherapy, Department of Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Daniel D Pinschewer
- Department of Biomedicine - Haus Petersplatz, Division of Experimental Virology, University of Basel, 4009 Basel, Switzerland; Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland.
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36
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Wu D, Gowathaman R, Pierce BG, Mariuzza RA. T cell receptors (TCRs) employ diverse strategies to target a p53 cancer neoantigen. J Biol Chem 2022; 298:101684. [PMID: 35124005 PMCID: PMC8897694 DOI: 10.1016/j.jbc.2022.101684] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/16/2022] [Accepted: 02/02/2022] [Indexed: 11/20/2022] Open
Abstract
Adoptive cell therapy with tumor-specific T cells can mediate durable cancer regression. The prime target of tumor-specific T cells are neoantigens arising from mutations in self-proteins during malignant transformation. To understand T cell recognition of cancer neoantigens at the atomic level, we studied oligoclonal T cell receptors (TCRs) that recognize a neoepitope arising from a driver mutation in the p53 oncogene (p53R175H) presented by the major histocompatibility complex class I molecule HLA-A2. We previously reported the structures of three p53R175H-specific TCRs (38-10, 12-6, and 1a2) bound to p53R175H and HLA-A2. The structures showed that these TCRs discriminate between WT and mutant p53 by forming extensive interactions with the R175H mutation. Here, we report the structure of a fourth p53R175H-specific TCR (6-11) in complex with p53R175H and HLA-A2. In contrast to 38-10, 12-6, and 1a2, TCR 6-11 makes no direct contacts with the R175H mutation, yet is still able to distinguish mutant from WT p53. Structure-based in silico mutagenesis revealed that the 60-fold loss in 6-11 binding affinity for WT p53 compared to p53R175H is mainly due to the higher energetic cost of desolvating R175 in the WT p53 peptide during complex formation than H175 in the mutant. This indirect strategy for preferential neoantigen recognition by 6-11 is fundamentally different from the direct strategies employed by other TCRs and highlights the multiplicity of solutions to recognizing p53R175H with sufficient selectivity to mediate T cell killing of tumor but not normal cells.
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Affiliation(s)
- Daichao Wu
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, China; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Ragul Gowathaman
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA.
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Foix A, López D, Díez-Fuertes F, McConnell MJ, Martín-Galiano AJ. Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2. PLoS Comput Biol 2022; 18:e1009726. [PMID: 35143484 PMCID: PMC8830725 DOI: 10.1371/journal.pcbi.1009726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022] Open
Abstract
The massive assessment of immune evasion due to viral mutations that increase COVID-19 susceptibility can be computationally facilitated. The adaptive cytotoxic T response is critical during primary infection and the generation of long-term protection. Here, potential HLA class I epitopes in the SARS-CoV-2 proteome were predicted for 2,915 human alleles of 71 families using the netMHCIpan EL algorithm. Allele families showed extreme epitopic differences, underscoring genetic variability of protective capacity between humans. Up to 1,222 epitopes were associated with any of the twelve supertypes, that is, allele clusters covering 90% population. Next, from all mutations identified in ~118,000 viral NCBI isolates, those causing significant epitope score reduction were considered epitope escape mutations. These mutations mainly involved non-conservative substitutions at the second and C-terminal position of the ligand core, or total ligand removal by large recurrent deletions. Escape mutations affected 47% of supertype epitopes, which in 21% of cases concerned isolates from two or more sub-continental areas. Some of these changes were coupled, but never surpassed 15% of evaded epitopes for the same supertype in the same isolate, except for B27. In contrast to most supertypes, eight allele families mostly contained alleles with few SARS-CoV-2 ligands. Isolates harboring cytotoxic escape mutations for these families co-existed geographically within sub-Saharan and Asian populations enriched in these alleles according to the Allele Frequency Net Database. Collectively, our findings indicate that escape mutation events have already occurred for half of HLA class I supertype epitopes. However, it is presently unlikely that, overall, it poses a threat to the global population. In contrast, single and double mutations for susceptible alleles may be associated with viral selective pressure and alarming local outbreaks. The integration of genomic, geographical and immunoinformatic information eases the surveillance of variants potentially affecting the global population, as well as minority subpopulations.
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Affiliation(s)
- Anna Foix
- European Bioinformatic Institute, European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Daniel López
- Presentation and Immune Regulation Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Michael J. McConnell
- Intrahospital Infections Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Antonio J. Martín-Galiano
- Intrahospital Infections Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
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38
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Lee JH, Jung Y, Lee SK, Kim J, Lee CS, Kim S, Lee JS, Kim NH, Kim HG. Rapid Biosensor of SARS-CoV-2 Using Specific Monoclonal Antibodies Recognizing Conserved Nucleocapsid Protein Epitopes. Viruses 2022; 14:v14020255. [PMID: 35215848 PMCID: PMC8879994 DOI: 10.3390/v14020255] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is characterized by symptoms such as fever, fatigue, a sore throat, diarrhea, and coughing. Although various new vaccines against COVID-19 have been developed, early diagnostics, isolation, and prevention remain important due to virus mutations resulting in rapid and high disease transmission. Amino acid substitutions in the major diagnostic target antigens of SARS-CoV-2 may lower the sensitivity for the detection of SARS-CoV-2. For this reason, we developed specific monoclonal antibodies that bind to epitope peptides as antigens for the rapid detection of SARS-CoV-2 NP. The binding affinity between antigenic peptides and monoclonal antibodies was investigated, and a sandwich pair for capture and detection was employed to develop a rapid biosensor for SARS-CoV-2 NP. The rapid biosensor, based on a monoclonal antibody pair binding to conserved epitopes of SARS-CoV-2 NP, detected cultured virus samples of SARS-CoV-2 (1.4 × 103 TCID50/reaction) and recombinant NP (1 ng/mL). Laboratory confirmation of the rapid biosensor was performed with clinical specimens (n = 16) from COVID-19 patients and other pathogens. The rapid biosensor consisting of a monoclonal antibody pair (75E12 for capture and the 54G6/54G10 combination for detection) binding to conserved epitopes of SARS-CoV-2 NP could assist in the detection of SARS-CoV-2 NP under the circumstance of spreading SARS-CoV-2 variants.
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Affiliation(s)
- Jong-Hwan Lee
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Yujin Jung
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Sung-Kyun Lee
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Jung Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Chang-Seop Lee
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju 54896, Jeollabuk-do, Korea;
- Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Jeollabuk-do, Korea
| | - Soohyun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Ji-Seon Lee
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
| | - Nam-Hoon Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
- Correspondence: (N.-H.K.); (H.-G.K.)
| | - Hong-Gi Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea; (J.-H.L.); (Y.J.); (S.-K.L.); (J.K.); (S.K.); (J.-S.L.)
- Correspondence: (N.-H.K.); (H.-G.K.)
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Wu J, Nie J, Zhang L, Song H, An Y, Liang Z, Yang J, Ding R, Liu S, Li Q, Li T, Cui Z, Zhang M, He P, Wang Y, Qu X, Hu Z, Wang Q, Huang W. The antigenicity of SARS-CoV-2 Delta variants aggregated 10 high-frequency mutations in RBD has not changed sufficiently to replace the current vaccine strain. Signal Transduct Target Ther 2022; 7:18. [PMID: 35046385 PMCID: PMC8767530 DOI: 10.1038/s41392-022-00874-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/08/2021] [Accepted: 12/24/2021] [Indexed: 11/08/2022] Open
Abstract
Emerging SARS-CoV-2 variants are the most serious problem for COVID-19 prophylaxis and treatment. To determine whether the SARS-CoV-2 vaccine strain should be updated following variant emergence like seasonal flu vaccine, the changed degree on antigenicity of SARS-CoV-2 variants and H3N2 flu vaccine strains was compared. The neutralization activities of Alpha, Beta and Gamma variants' spike protein-immunized sera were analysed against the eight current epidemic variants and 20 possible variants combining the top 10 prevalent RBD mutations based on the Delta variant, which were constructed using pseudotyped viruses. Meanwhile, the neutralization activities of convalescent sera and current inactivated and recombinant protein vaccine-elicited sera were also examined against all possible Delta variants. Eight HA protein-expressing DNAs elicited-animal sera were also tested against eight pseudotyped viruses of H3N2 flu vaccine strains from 2011-2019. Our results indicate that the antigenicity changes of possible Delta variants were mostly within four folds, whereas the antigenicity changes among different H3N2 vaccine strains were approximately 10-100-fold. Structural analysis of the antigenic characterization of the SARS-CoV-2 and H3N2 mutations supports the neutralization results. This study indicates that the antigenicity changes of the current SARS-CoV-2 may not be sufficient to require replacement of the current vaccine strain.
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MESH Headings
- Amino Acid Substitution
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/metabolism
- Binding Sites
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/chemistry
- COVID-19 Vaccines/metabolism
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Gene Expression
- Humans
- Immune Sera/chemistry
- Immunogenicity, Vaccine
- Influenza A Virus, H3N2 Subtype/chemistry
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/chemistry
- Influenza Vaccines/metabolism
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Binding
- Protein Conformation
- Protein Interaction Domains and Motifs
- SARS-CoV-2/chemistry
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Viral Pseudotyping
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Affiliation(s)
- Jiajing Wu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Li Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yimeng An
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Ziteng Liang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Jing Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, 100101, Beijing, China
| | - Ruxia Ding
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Shuo Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Qianqian Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Tao Li
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Zhimin Cui
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Mengyi Zhang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Peng He
- Division of Hepatitis and Enteric Viral Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, 102629, Beijing, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China
| | - Xiaowang Qu
- Translational Medicine Institute, First People's Hospital of Chenzhou, University of South China, Chenzhou, China
| | - Zhongyu Hu
- Division of Hepatitis and Enteric Viral Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, 102629, Beijing, China.
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), 102629, Beijing, China.
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Murin CD, Gilchuk P, Crowe JE, Ward AB. Structural Biology Illuminates Molecular Determinants of Broad Ebolavirus Neutralization by Human Antibodies for Pan-Ebolavirus Therapeutic Development. Front Immunol 2022; 12:808047. [PMID: 35082794 PMCID: PMC8784787 DOI: 10.3389/fimmu.2021.808047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 01/13/2023] Open
Abstract
Monoclonal antibodies (mAbs) have proven effective for the treatment of ebolavirus infection in humans, with two mAb-based drugs Inmazeb™ and Ebanga™ receiving FDA approval in 2020. While these drugs represent a major advance in the field of filoviral therapeutics, they are composed of antibodies with single-species specificity for Zaire ebolavirus. The Ebolavirus genus includes five additional species, two of which, Bundibugyo ebolavirus and Sudan ebolavirus, have caused severe disease and significant outbreaks in the past. There are several recently identified broadly neutralizing ebolavirus antibodies, including some in the clinical development pipeline, that have demonstrated broad protection in preclinical studies. In this review, we describe how structural biology has illuminated the molecular basis of broad ebolavirus neutralization, including details of common antigenic sites of vulnerability on the glycoprotein surface. We begin with a discussion outlining the history of monoclonal antibody therapeutics for ebolaviruses, with an emphasis on how structural biology has contributed to these efforts. Next, we highlight key structural studies that have advanced our understanding of ebolavirus glycoprotein structures and mechanisms of antibody-mediated neutralization. Finally, we offer examples of how structural biology has contributed to advances in anti-viral medicines and discuss what opportunities the future holds, including rationally designed next-generation therapeutics with increased potency, breadth, and specificity against ebolaviruses.
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MESH Headings
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antiviral Agents/immunology
- Antiviral Agents/therapeutic use
- Drug Combinations
- Ebolavirus/drug effects
- Ebolavirus/immunology
- Ebolavirus/physiology
- Epitopes/chemistry
- Epitopes/immunology
- Glycoproteins/chemistry
- Glycoproteins/immunology
- Hemorrhagic Fever, Ebola/drug therapy
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/virology
- Humans
- Models, Molecular
- Protein Domains/immunology
- Viral Proteins/chemistry
- Viral Proteins/immunology
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Affiliation(s)
- Charles D. Murin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
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Morozov V, Lagaye S, Morozov A. The TZM-bl Reporter Cell Line Expresses Kynureninase That Can Neutralize 2F5-like Antibodies in the HIV-1 Neutralization Assay. Int J Mol Sci 2022; 23:ijms23020641. [PMID: 35054825 PMCID: PMC8775840 DOI: 10.3390/ijms23020641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Induction of broadly neutralizing antibodies targeting ectodomain of the transmembrane (TM) glycoprotein gp41 HIV-1 provides a basis for the development of a universal anti-viral vaccine. The HeLa cell-derived TZM-bl reporter cell line is widely used for the estimation of lentiviruses neutralization by immune sera. The cell line is highly permissive to infection by most strains of HIV, SIV, and SHIV. Here we demonstrated that TZM-bl cells express a 48 kDa non-glycosylated protein (p48) recognized by broadly neutralizing monoclonal antibody (mAb) 2F5 targeting the ELDKWA (aa 669–674) epitope of gp41TM of HIV-1. A significant amount of p48 was found in the cell supernatant. The protein was identified as human kynureninase (KYNU), which has the ELDKWA epitope. The protein is further called “p48 KYNU”. The HIV-1 neutralization by mAb 2F5 and 4E10 in the presence of p48KYNU was tested on Jurkat and TZM-bl cells. It was demonstrated that p48KYNU reduces neutralization by 2F5-like antibodies, but it has almost no effect on mAb 4E10. Therefore, p48KYNU can attenuate HIV-1 neutralization by 2F5-like antibodies and hence create false-negative results. Thus, previously tested immune sera that recognized the ELDKWA-epitope and demonstrated a “weak neutralization” of HIV-1 in TZM-bl assay should be reevaluated.
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Affiliation(s)
- Vladimir Morozov
- Institute of Human Virology, University of Maryland, Baltimore, MD 21201, USA
- Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
- Correspondence: (V.M.); (A.M.)
| | - Sylvie Lagaye
- Centre de Recherche Saint-Antoine (CRSA), INSERM—UMR-S 938/Sorbonne Université, CEDEX 12, 75571 Paris, France;
| | - Alexey Morozov
- Laboratory of Regulation of Intracellular Proteolysis, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence: (V.M.); (A.M.)
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Vanderheijden N, Stevaert A, Xie J, Ren X, Barbezange C, Noppen S, Desombere I, Verhasselt B, Geldhof P, Vereecke N, Stroobants V, Oh D, Vanhee M, Naesens LMJ, Nauwynck HJ. Functional Analysis of Human and Feline Coronavirus Cross-Reactive Antibodies Directed Against the SARS-CoV-2 Fusion Peptide. Front Immunol 2022; 12:790415. [PMID: 35069571 PMCID: PMC8766817 DOI: 10.3389/fimmu.2021.790415] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022] Open
Abstract
To face the continuous emergence of SARS-CoV-2 variants, broadly protective therapeutic antibodies are highly needed. We here focused on the fusion peptide (FP) region of the viral spike antigen since it is highly conserved among alpha- and betacoronaviruses. First, we found that coronavirus cross-reactive antibodies are commonly formed during infection, being omnipresent in sera from COVID-19 patients, in ~50% of pre-pandemic human sera (rich in antibodies against endemic human coronaviruses), and even in feline coronavirus-infected cats. Pepscan analyses demonstrated that a confined N-terminal region of the FP is strongly immunogenic across diverse coronaviruses. Peptide-purified human antibodies targeting this conserved FP epitope exhibited broad binding of alpha- and betacoronaviruses, besides weak and transient SARS-CoV-2 neutralizing activity. Being frequently elicited by coronavirus infection, these FP-binding antibodies might potentially exhibit Fc-mediated effector functions and influence the kinetics or severity of coronavirus infection and disease.
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Affiliation(s)
- Nathalie Vanderheijden
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Annelies Stevaert
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven – University of Leuven, Leuven, Belgium
| | - Jiexiong Xie
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Xiaolei Ren
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Cyril Barbezange
- National Influenza Centre and Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
| | - Sam Noppen
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven – University of Leuven, Leuven, Belgium
| | | | - Bruno Verhasselt
- Laboratory for Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Peter Geldhof
- Laboratory of Parasitology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Nick Vereecke
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- PathoSense BV, Lier, Belgium
| | - Veerle Stroobants
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Dayoung Oh
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Merijn Vanhee
- Department of Laboratory Medicine, AZ Sint-Jan Brugge-Oostende, Bruges, Belgium
| | - Lieve M. J. Naesens
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven – University of Leuven, Leuven, Belgium
| | - Hans J. Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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43
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Fertig TE, Chitoiu L, Terinte‐Balcan G, Peteu V, Marta D, Gherghiceanu M. The atomic portrait of SARS-CoV-2 as captured by cryo-electron microscopy. J Cell Mol Med 2022; 26:25-34. [PMID: 34904376 PMCID: PMC8742239 DOI: 10.1111/jcmm.17103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 01/18/2023] Open
Abstract
Transmission electron microscopy has historically been indispensable for virology research, as it offers unique insight into virus function. In the past decade, as cryo-electron microscopy (cryo-EM) has matured and become more accessible, we have been able to peer into the structure of viruses at the atomic level and understand how they interact with the host cell, with drugs or with antibodies. Perhaps, there was no time in recent history where cryo-EM was more needed, as SARS-CoV-2 has spread around the globe, causing millions of deaths and almost unquantifiable economic devastation. In this concise review, we aim to mark the most important contributions of cryo-EM to understanding the structure and function of SARS-CoV-2 proteins, from surface spikes to the virus core and from virus-receptor interactions to antibody binding.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/immunology
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Viral/biosynthesis
- Antibodies, Viral/chemistry
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/biosynthesis
- COVID-19 Vaccines/chemistry
- Cryoelectron Microscopy
- Epitopes/chemistry
- Epitopes/immunology
- Epitopes/metabolism
- Humans
- Models, Molecular
- Protein Binding
- Protein Interaction Domains and Motifs
- Protein Structure, Secondary
- Receptors, Virus/chemistry
- Receptors, Virus/immunology
- Receptors, Virus/metabolism
- SARS-CoV-2/drug effects
- SARS-CoV-2/pathogenicity
- SARS-CoV-2/ultrastructure
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/immunology
- Serine Endopeptidases/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Virion/drug effects
- Virion/pathogenicity
- Virion/ultrastructure
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Affiliation(s)
- Tudor Emanuel Fertig
- Ultrastructural Pathology and Bioimaging LabVictor Babeș National Institute of PathologyBucharestRomania
- Carol Davila University of Medicine and PharmacyBucharestRomania
| | - Leona Chitoiu
- Ultrastructural Pathology and Bioimaging LabVictor Babeș National Institute of PathologyBucharestRomania
| | - George Terinte‐Balcan
- Ultrastructural Pathology and Bioimaging LabVictor Babeș National Institute of PathologyBucharestRomania
| | - Victor‐Eduard Peteu
- Ultrastructural Pathology and Bioimaging LabVictor Babeș National Institute of PathologyBucharestRomania
| | - Daciana Marta
- Ultrastructural Pathology and Bioimaging LabVictor Babeș National Institute of PathologyBucharestRomania
| | - Mihaela Gherghiceanu
- Ultrastructural Pathology and Bioimaging LabVictor Babeș National Institute of PathologyBucharestRomania
- Carol Davila University of Medicine and PharmacyBucharestRomania
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Berendam SJ, Morgan-Asiedu PK, Mangan RJ, Li SH, Heimsath H, Luo K, Curtis AD, Eudailey JA, Fox CB, Tomai MA, Phillips B, Itell HL, Kunz E, Hudgens M, Cronin K, Wiehe K, Alam SM, Van Rompay KKA, De Paris K, Permar SR, Moody MA, Fouda GG. Different adjuvanted pediatric HIV envelope vaccines induced distinct plasma antibody responses despite similar B cell receptor repertoires in infant rhesus macaques. PLoS One 2022; 16:e0256885. [PMID: 34972105 PMCID: PMC8719683 DOI: 10.1371/journal.pone.0256885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022] Open
Abstract
Different HIV vaccine regimens elicit distinct plasma antibody responses in both human and nonhuman primate models. Previous studies in human and non-human primate infants showed that adjuvants influenced the quality of plasma antibody responses induced by pediatric HIV envelope vaccine regimens. We recently reported that use of the 3M052-SE adjuvant and longer intervals between vaccinations are associated with higher magnitude of antibody responses in infant rhesus macaques. However, the impact of different adjuvants in HIV vaccine regimens on the developing infant B cell receptor (BCR) repertoire has not been studied. This study evaluated whether pediatric HIV envelope vaccine regimens with different adjuvants induced distinct antigen-specific memory B cell repertoires and whether specific immunoglobulin (Ig) immunogenetic characteristics are associated with higher magnitude of plasma antibody responses in vaccinated infant rhesus macaques. We utilized archived preclinical pediatric HIV vaccine studies PBMCs and tissue samples from 19 infant rhesus macaques immunized either with (i) HIV Env protein with a squalene adjuvant, (ii) MVA-HIV and Env protein co-administered using a 3-week interval, (iii) MVA-HIV prime/ protein boost with an extended 6-week interval between immunizations, or (iv) with HIV Env administered with 3M-052-SE adjuvant. Frequencies of vaccine-elicited HIV Env-specific memory B cells from PBMCs and tissues were similar across vaccination groups (frequency range of 0.06–1.72%). There was no association between vaccine-elicited antigen-specific memory B cell frequencies and plasma antibody titer or avidity. Moreover, the epitope specificity and Ig immunogenetic features of vaccine-elicited monoclonal antibodies did not differ between the different vaccine regimens. These data suggest that pediatric HIV envelope vaccine candidates with different adjuvants that previously induced higher magnitude and quality of plasma antibody responses in infant rhesus macaques were not driven by distinct antigen-specific memory BCR repertoires.
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Affiliation(s)
- Stella J. Berendam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Papa K. Morgan-Asiedu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Riley J. Mangan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Shuk Hang Li
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Holly Heimsath
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Alan D. Curtis
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joshua A. Eudailey
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Weill Cornell College of Medicine, New York City, New York, United States of America
| | - Christopher B. Fox
- Infectious Disease Research Institute (IDRI), Seattle, Washington State, United States of America
- Department of Global Health, University of Washington, Seattle, Washington State, United States of America
| | - Mark A. Tomai
- 3M Center, 3 M Drug Delivery Systems, St. Paul, Minnesota, United States of America
| | - Bonnie Phillips
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hannah L. Itell
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Erika Kunz
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California at Davis, Davis, California, United States of America
| | - Kristina De Paris
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Weill Cornell College of Medicine, New York City, New York, United States of America
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Genevieve G. Fouda
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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45
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Issafras H, Fan S, Tseng CL, Cheng Y, Lin P, Xiao L, Huang YJ, Tu CH, Hsiao YC, Li M, Chen YH, Ho CH, Li O, Wang Y, Chen S, Ji Z, Zhang E, Mao YT, Liu E, Yang S, Jiang W. Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody clinical candidate for cancer immunotherapy. PLoS One 2021; 16:e0257972. [PMID: 34972111 PMCID: PMC8719770 DOI: 10.1371/journal.pone.0257972] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 09/14/2021] [Indexed: 12/30/2022] Open
Abstract
Cancer immunotherapies, such as checkpoint blockade of programmed cell death protein-1 (PD-1), represents a breakthrough in cancer treatment, resulting in unprecedented results in terms of overall and progression-free survival. Discovery and development of novel anti PD-1 inhibitors remains a field of intense investigation, where novel monoclonal antibodies (mAbs) and novel antibody formats (e.g., novel isotype, bispecific mAb and low-molecular-weight compounds) are major source of future therapeutic candidates. HLX10, a fully humanized IgG4 monoclonal antibody against PD-1 receptor, increased functional activities of human T-cells and showed in vitro, and anti-tumor activity in several tumor models. The combined inhibition of PD-1/PDL-1 and angiogenesis pathways using anti-VEGF antibody may enhance a sustained suppression of cancer-related angiogenesis and tumor elimination. To elucidate HLX10's mode of action, we solved the structure of HLX10 in complex with PD-1 receptor. Detailed epitope analysis showed that HLX10 has a unique mode of recognition compared to the clinically approved PD1 antibodies Pembrolizumab and Nivolumab. Notably, HLX10's epitope was closer to Pembrolizumab's epitope than Nivolumab's epitope. However, HLX10 and Pembrolizumab showed an opposite heavy chain (HC) and light chain (LC) usage, which recognizes several overlapping amino acid residues on PD-1. We compared HLX10 to Nivolumab and Pembrolizumab and it showed similar or better bioactivity in vitro and in vivo, providing a rationale for clinical evaluation in cancer immunotherapy.
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MESH Headings
- Angiogenesis Inhibitors/therapeutic use
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/pharmacokinetics
- Antibodies, Monoclonal, Humanized/chemistry
- Antibodies, Monoclonal, Humanized/therapeutic use
- Bevacizumab/therapeutic use
- CD4-Positive T-Lymphocytes/immunology
- Cell Line, Tumor
- Cell Proliferation
- Epithelial-Mesenchymal Transition/drug effects
- Epitopes/immunology
- Humans
- Immunoglobulin Fab Fragments/metabolism
- Immunotherapy
- Interferon-gamma/metabolism
- Interleukin-2/metabolism
- Ligands
- Macaca fascicularis
- Mice, Inbred NOD
- Mice, SCID
- Models, Molecular
- Neoplasms/drug therapy
- Neoplasms/immunology
- Neoplasms/therapy
- Nivolumab/chemistry
- Nivolumab/therapeutic use
- Programmed Cell Death 1 Receptor/chemistry
- Programmed Cell Death 1 Receptor/immunology
- Protein Binding
- Rats
- Vascular Endothelial Growth Factor A/antagonists & inhibitors
- Vascular Endothelial Growth Factor A/metabolism
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
| | - Shilong Fan
- National Protein Science Facility, Tsinghua University, Beijing, China
| | | | | | - Peihua Lin
- Hengenix Inc., Fremont, CA, United States of America
| | - Lisa Xiao
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | | | | | | | - Min Li
- National Protein Science Facility, Tsinghua University, Beijing, China
| | | | | | - Ou Li
- Hengenix Inc., Fremont, CA, United States of America
| | - Yanling Wang
- Hengenix Inc., Fremont, CA, United States of America
| | - Sandra Chen
- Anwita Biosciences, San Carlos, CA, United States of America
| | - Zhenyu Ji
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | - Eric Zhang
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | - Yi-Ting Mao
- Hengenix Inc., Fremont, CA, United States of America
| | - Eugene Liu
- Taipei Medical University, Taipei, Taiwan
| | - Shumin Yang
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
| | - Weidong Jiang
- Hengenix Inc., Fremont, CA, United States of America
- Shanghai Henlius Biotech, Inc., Shanghai, P. R. China
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46
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Nyanhete TE, Edwards RJ, LaBranche CC, Mansouri K, Eaton A, Dennison SM, Saunders KO, Goodman D, Janowska K, Spreng RL, Zhang L, Mudrak SV, Hope TJ, Hora B, Bradley T, Georgiev IS, Montefiori DC, Acharya P, Tomaras GD. Polyclonal Broadly Neutralizing Antibody Activity Characterized by CD4 Binding Site and V3-Glycan Antibodies in a Subset of HIV-1 Virus Controllers. Front Immunol 2021; 12:670561. [PMID: 35003053 PMCID: PMC8733328 DOI: 10.3389/fimmu.2021.670561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs), known to mediate immune control of HIV-1 infection, only develop in a small subset of HIV-1 infected individuals. Despite being traditionally associated with patients with high viral loads, bNAbs have also been observed in therapy naïve HIV-1+ patients naturally controlling virus replication [Virus Controllers (VCs)]. Thus, dissecting the bNAb response in VCs will provide key information about what constitutes an effective humoral response to natural HIV-1 infection. In this study, we identified a polyclonal bNAb response to natural HIV-1 infection targeting CD4 binding site (CD4bs), V3-glycan, gp120-gp41 interface and membrane-proximal external region (MPER) epitopes on the HIV-1 envelope (Env). The polyclonal antiviral antibody (Ab) response also included antibody-dependent cellular phagocytosis of clade AE, B and C viruses, consistent with both the Fv and Fc domain contributing to function. Sequence analysis of envs from one of the VCs revealed features consistent with potential immune pressure and virus escape from V3-glycan targeting bNAbs. Epitope mapping of the polyclonal bNAb response in VCs with bNAb activity highlighted the presence of gp120-gp41 interface and CD4bs antibody classes with similar binding profiles to known potent bNAbs. Thus, these findings reveal the induction of a broad and polyfunctional humoral response in VCs in response to natural HIV-1 infection.
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Affiliation(s)
- Tinashe E. Nyanhete
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Celia C. LaBranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Amanda Eaton
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - S. Moses Dennison
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Derrick Goodman
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Katarzyna Janowska
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Rachel L. Spreng
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Lu Zhang
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Sarah V. Mudrak
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Thomas J. Hope
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, United States
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
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47
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Takagi A, Matsui M. Identification of HLA-A*24:02-Restricted CTL Candidate Epitopes Derived from the Nonstructural Polyprotein 1a of SARS-CoV-2 and Analysis of Their Conservation Using the Mutation Database of SARS-CoV-2 Variants. Microbiol Spectr 2021; 9:e0165921. [PMID: 34937174 PMCID: PMC8694169 DOI: 10.1128/spectrum.01659-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/24/2021] [Indexed: 01/11/2023] Open
Abstract
COVID-19 vaccines are currently being administered worldwide and playing a critical role in controlling the pandemic. They have been designed to elicit neutralizing antibodies against Spike protein of the original SARS-CoV-2, and hence they are less effective against SARS-CoV-2 variants with mutated Spike than the original virus. It is possible that novel variants with abilities of enhanced transmissibility and/or immunoevasion will appear in the near future and perfectly escape from vaccine-elicited immunity. Therefore, the current vaccines may need to be improved to compensate for the viral evolution. For this purpose, it may be beneficial to take advantage of CD8+ cytotoxic T lymphocytes (CTLs). Several lines of evidence suggest the contribution of CTLs on the viral control in COVID-19, and CTLs target a wide range of proteins involving comparatively conserved nonstructural proteins. Here, we identified 22 HLA-A*24:02-restricted CTL candidate epitopes derived from the nonstructural polyprotein 1a (pp1a) of SARS-CoV-2 using computational algorithms, HLA-A*24:02 transgenic mice and the peptide-encapsulated liposomes. We focused on pp1a and HLA-A*24:02 because pp1a is relatively conserved and HLA-A*24:02 is predominant in East Asians such as Japanese. The conservation analysis revealed that the amino acid sequences of 7 out of the 22 epitopes were hardly affected by a number of mutations in the Sequence Read Archive database of SARS-CoV-2 variants. The information of such conserved epitopes might be useful for designing the next-generation COVID-19 vaccine that is universally effective against any SARS-CoV-2 variants by the induction of both anti-Spike neutralizing antibodies and CTLs specific for conserved epitopes. IMPORTANCE COVID-19 vaccines have been designed to elicit neutralizing antibodies against the Spike protein of the original SARS-CoV-2, and hence they are less effective against variants. It is possible that novel variants will appear and escape from vaccine-elicited immunity. Therefore, the current vaccines may need to be improved to compensate for the viral evolution. For this purpose, it may be beneficial to take advantage of CD8+ cytotoxic T lymphocytes (CTLs). Here, we identified 22 HLA-A*24:02-restricted CTL candidate epitopes derived from the nonstructural polyprotein 1a (pp1a) of SARS-CoV-2. We focused on pp1a and HLA-A*24:02 because pp1a is conserved and HLA-A*24:02 is predominant in East Asians. The conservation analysis revealed that the amino acid sequences of 7 out of the 22 epitopes were hardly affected by mutations in the database of SARS-CoV-2 variants. The information might be useful for designing the next-generation COVID-19 vaccine that is universally effective against any variants.
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Affiliation(s)
- Akira Takagi
- School of Medical Technology, Faculty of Health and Medical Care, Saitama Medical University, Yamane, Hidaka-city, Saitama, Japan
| | - Masanori Matsui
- Department of Microbiology, Faculty of Medicine, Saitama Medical University, Morohongo, Moroyama-cho, Iruma-gun, Saitama, Japan
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48
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Niemann M, Matern BM, Spierings E, Schaub S, Hönger G. Peptides Derived From Mismatched Paternal Human Leukocyte Antigen Predicted to Be Presented by HLA-DRB1, -DRB3/4/5, -DQ, and -DP Induce Child-Specific Antibodies in Pregnant Women. Front Immunol 2021; 12:797360. [PMID: 34992608 PMCID: PMC8725048 DOI: 10.3389/fimmu.2021.797360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Predicted Indirectly ReCognizable Human Leukocyte Antigen (HLA) Epitopes (PIRCHE) are known to be a significant risk factor for the development of donor HLA-specific antibodies after organ transplantation. Most previous studies on PIRCHE limited their analyses on the presentation of the HLA-DRB1 locus, although HLA-DRB3/4/5, -DQ, and -DP are also known for presenting allopeptides to CD4+ T cells. In this study, we analyzed the impact of predicted allopeptides presented by these additional loci on the incidence of HLA-specific antibodies after an immunization event. We considered pregnancy as a model system of an HLA immunization and observed child-specific HLA antibody (CSA) development of 231 mothers during pregnancy by samples being taken at delivery. Our data confirm that PIRCHE presented by HLA-DRB1 along with HLA-DRB3/4/5, -DQ, and -DP are significant predictors for the development of CSA. Although there was limited peptidome overlap observed within the mothers’ presenting HLA proteins, combining multiple presenting loci in a single predictor improved the model only marginally. Prediction performance of PIRCHE further improved when normalizing scores by the respective presenters’ binding promiscuity. Immunogenicity analysis of specific allopeptides could not identify significant drivers of an immune response in this small cohort, suggesting confirmatory studies.
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Affiliation(s)
- Matthias Niemann
- Research and Development, PIRCHE AG, Berlin, Germany
- *Correspondence: Matthias Niemann,
| | - Benedict M. Matern
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
- Transplantation Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
- HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Gideon Hönger
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
- Transplantation Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
- HLA-Diagnostics and Immunogenetics, Department of Laboratory Medicine, University Hospital Basel, Basel, Switzerland
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49
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Riaz S, Steinsland H, Thorsing M, Andersen AZ, Boysen A, Hanevik K. Characterization of Glycosylation-Specific Systemic and Mucosal IgA Antibody Responses to Escherichia coli Mucinase YghJ (SslE). Front Immunol 2021; 12:760135. [PMID: 34975849 PMCID: PMC8718676 DOI: 10.3389/fimmu.2021.760135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/01/2021] [Indexed: 12/04/2022] Open
Abstract
Efforts to develop broadly protective vaccines against pathogenic Escherichia coli are ongoing. A potential antigen candidate for vaccine development is the metalloprotease YghJ, or SslE. YghJ is a conserved mucinase that is immunogenic, heavily glycosylated, and produced by most pathogenic E. coli. To develop efficacious YghJ-based vaccines, there is a need to investigate to what extent potentially protective antibody responses target glycosylated epitopes in YghJ and to describe variations in the quality of YghJ glycosylation in the E. coli population. In this study we estimated the proportion of anti-YghJ IgA antibodies that targeted glycosylated epitopes in serum and intestinal lavage samples from 21 volunteers experimentally infected with wild-type enterotoxigenic E. coli (ETEC) strain TW10722. Glycosylated and non-glycosylated YghJ was expressed, purified, and then gycosylation pattern was verified by BEMAP analysis. Then we used a multiplex bead flow cytometric assay to analyse samples from before and 10 days after TW10722 was ingested. We found that 20 (95%) of the 21 volunteers had IgA antibody responses to homologous, glycosylated YghJ, with a median fold increase in IgA levels of 7.9 (interquartile range [IQR]: 7.1, 11.1) in serum and 3.7 (IQR: 2.1, 10.7) in lavage. The median proportion of anti-YghJ IgA response that specifically targeted glycosylated epitopes was 0.45 (IQR: 0.30, 0.59) in serum and 0.07 (IQR: 0.01, 0.22) in lavage. Our findings suggest that a substantial, but variable, proportion of the IgA antibody response to YghJ in serum during ETEC infection is targeted against glycosylated epitopes, but that gut IgA responses largely target non-glycosylated epitopes. Further research into IgA targeting glycosylated YghJ epitopes is of interest to the vaccine development efforts.
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Affiliation(s)
- Saman Riaz
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Hans Steinsland
- Centre for Intervention Science in Maternal and Child Health (CISMAC), Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | | | | | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Javanmardi K, Chou CW, Terrace CI, Annapareddy A, Kaoud TS, Guo Q, Lutgens J, Zorkic H, Horton AP, Gardner EC, Nguyen G, Boutz DR, Goike J, Voss WN, Kuo HC, Dalby KN, Gollihar JD, Finkelstein IJ. Rapid characterization of spike variants via mammalian cell surface display. Mol Cell 2021; 81:5099-5111.e8. [PMID: 34919820 PMCID: PMC8675084 DOI: 10.1016/j.molcel.2021.11.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.
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Affiliation(s)
- Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Ankur Annapareddy
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Josh Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hayley Zorkic
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew P Horton
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Elizabeth C Gardner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Giaochau Nguyen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - William N Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; CCDC Army Research Laboratory-South, Austin, TX, USA; Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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