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Wu TTH, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner W, Kim PS, Blish CA, Krasnow MA. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. J Exp Med 2024; 221:e20232192. [PMID: 38597954 PMCID: PMC11009983 DOI: 10.1084/jem.20232192] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.
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Affiliation(s)
- Timothy Ting-Hsuan Wu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Yue Zhang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - SoRi Jang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanny J. Martínez-Colón
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aimee Beck
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron J. Wilk
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Winston L. Trope
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rob Bierman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B. Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christin S. Kuo
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - W.E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Catherine A. Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark A. Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
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Keller AL, Reiman LT, Perez de Acha O, Parzych SE, Forsberg PA, Kim PS, Bisht K, Wang H, van de Velde H, Sherbenou DW. Ex Vivo Efficacy of SAR442257 Anti-CD38 Trispecific T-cell Engager in Multiple Myeloma Relapsed After Daratumumab and BCMA-targeted Therapies. Cancer Res Commun 2024; 4:757-764. [PMID: 38421887 DOI: 10.1158/2767-9764.crc-23-0434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/11/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
T cell-engaging antibodies (TCEs) are showing promising efficacy in relapsed/refractory multiple myeloma, even in patients that relapsed after B-cell maturation antigen (BCMA)-targeted therapy. Patients with multiple myeloma may have compromised T-cell health unaccounted for by preclinical models. Here, we use Myeloma Drug Sensitivity Testing (My-DST) for ex vivo measurement of anti-multiple myeloma cytotoxicity for the trispecific CD38/CD28xCD3 TCE SAR442257 through activation of the patients' own endogenous T cells to inform clinical development of the compound in multiple myeloma. My-DST incubates primary mononuclear cells in humanized media for 48 hours followed by flow cytometry for multiple myeloma cell viability with or without drug treatment. SAR442257 was tested on 34 samples from patients with multiple myeloma across disease settings. Potential biomarkers, T-cell dependence, and degranulation were assessed. SAR442257 was effective at low dose in My-DST cultures. High ex vivo response rates were observed in primary aspirates taken from patients with multiple myeloma at diagnosis, with modestly reduced response in multiple myeloma recently treated with anti-CD38 mAbs. SAR442257 was highly effective in patients relapsing after BCMA therapy. The CD38/CD28xCD3 trispecific format was substantially more effective than a conventional bispecific CD38/CD3 antibody format and CD38 mAbs. Anti-multiple myeloma cell cytotoxicity was dependent on the presence of endogenous T cells. Surface CD38 expression was the strongest biomarker of TCE response. My-DST is capable of measuring T cell-dependent killing using the multiple myeloma patient's own bone marrow-derived T cells. SAR442257 shows promise for multiple myeloma and may be best suited for patients declared resistant to both CD38 mAbs and BCMA-targeted therapy. SIGNIFICANCE This study introduces the use of My-DST to measure and characterize sensitivity to anti-CD38 T-cell engager SAR442257 in primary samples using matched endogenous T cells. Preclinical testing in samples from patients with diverse treatment history supports further testing in post-chimeric antigen receptor T-cell multiple myeloma.
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Affiliation(s)
- Alana L Keller
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Lauren T Reiman
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Olivia Perez de Acha
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sarah E Parzych
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Peter A Forsberg
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Peter S Kim
- Sanofi R&D, North America, Cambridge, Massachusetts
| | | | | | | | - Daniel W Sherbenou
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten JJ, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. Proc Natl Acad Sci U S A 2024; 121:e2316960121. [PMID: 38319964 PMCID: PMC10873634 DOI: 10.1073/pnas.2316960121] [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: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024] Open
Abstract
The Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV)-one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here, we describe a universal Ebola virus vaccine approach using a structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA94305
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA94305
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - J. J. Patten
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
- Department of Biology, Boston University, Boston, MA02118
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
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Hie BL, Shanker VR, Xu D, Bruun TUJ, Weidenbacher PA, Tang S, Wu W, Pak JE, Kim PS. Efficient evolution of human antibodies from general protein language models. Nat Biotechnol 2024; 42:275-283. [PMID: 37095349 PMCID: PMC10869273 DOI: 10.1038/s41587-023-01763-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [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: 11/23/2022] [Accepted: 03/28/2023] [Indexed: 04/26/2023]
Abstract
Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could guide artificial evolution. Here we report that general protein language models can efficiently evolve human antibodies by suggesting mutations that are evolutionarily plausible, despite providing the model with no information about the target antigen, binding specificity or protein structure. We performed language-model-guided affinity maturation of seven antibodies, screening 20 or fewer variants of each antibody across only two rounds of laboratory evolution, and improved the binding affinities of four clinically relevant, highly mature antibodies up to sevenfold and three unmatured antibodies up to 160-fold, with many designs also demonstrating favorable thermostability and viral neutralization activity against Ebola and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudoviruses. The same models that improve antibody binding also guide efficient evolution across diverse protein families and selection pressures, including antibiotic resistance and enzyme activity, suggesting that these results generalize to many settings.
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Affiliation(s)
- Brian L Hie
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Varun R Shanker
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Theodora U J Bruun
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter S Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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5
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Xu D, Carter JJ, Li C, Utz A, Weidenbacher PAB, Tang S, Sanyal M, Pulendran B, Barnes CO, Kim PS. Vaccine design via antigen reorientation. Nat Chem Biol 2024:10.1038/s41589-023-01529-6. [PMID: 38225471 DOI: 10.1038/s41589-023-01529-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily conserved stem region (HA-stem). Here we introduce an approach to control antigen orientation via site-specific insertion of aspartate residues that facilitates antigen binding to alum. We demonstrate the generalizability of this approach with antigens from Ebola, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses and observe enhanced neutralizing antibody responses in all cases. We then reorient an H2 HA in an 'upside-down' configuration to increase the exposure and immunogenicity of HA-stem. The reoriented H2 HA (reoH2HA) on alum induced stem-directed antibodies that cross-react with both group 1 and group 2 influenza A subtypes. Electron microscopy polyclonal epitope mapping (EMPEM) revealed that reoH2HA (group 1) elicits cross-reactive antibodies targeting group 2 HA-stems. Our results highlight antigen reorientation as a generalizable approach for designing epitope-focused vaccines.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joshua J Carter
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A B Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher O Barnes
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter S Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Musunuri S, Weidenbacher PAB, Kim PS. Bringing immunofocusing into focus. NPJ Vaccines 2024; 9:11. [PMID: 38195562 PMCID: PMC10776678 DOI: 10.1038/s41541-023-00792-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Immunofocusing is a strategy to create immunogens that redirect humoral immune responses towards a targeted epitope and away from non-desirable epitopes. Immunofocusing methods often aim to develop "universal" vaccines that provide broad protection against highly variant viruses such as influenza virus, human immunodeficiency virus (HIV-1), and most recently, severe acute respiratory syndrome coronavirus (SARS-CoV-2). We use existing examples to illustrate five main immunofocusing strategies-cross-strain boosting, mosaic display, protein dissection, epitope scaffolding, and epitope masking. We also discuss obstacles for immunofocusing like immune imprinting. A thorough understanding, advancement, and application of the methods we outline here will enable the design of high-resolution vaccines that protect against future viral outbreaks.
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Affiliation(s)
- Sriharshita Musunuri
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Payton A B Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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Shanker VR, Bruun TU, Hie BL, Kim PS. Inverse folding of protein complexes with a structure-informed language model enables unsupervised antibody evolution. bioRxiv 2023:2023.12.19.572475. [PMID: 38187780 PMCID: PMC10769282 DOI: 10.1101/2023.12.19.572475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Large language models trained on sequence information alone are capable of learning high level principles of protein design. However, beyond sequence, the three-dimensional structures of proteins determine their specific function, activity, and evolvability. Here we show that a general protein language model augmented with protein structure backbone coordinates and trained on the inverse folding problem can guide evolution for diverse proteins without needing to explicitly model individual functional tasks. We demonstrate inverse folding to be an effective unsupervised, structure-based sequence optimization strategy that also generalizes to multimeric complexes by implicitly learning features of binding and amino acid epistasis. Using this approach, we screened ~30 variants of two therapeutic clinical antibodies used to treat SARS-CoV-2 infection and achieved up to 26-fold improvement in neutralization and 37-fold improvement in affinity against antibody-escaped viral variants-of-concern BQ.1.1 and XBB.1.5, respectively. In addition to substantial overall improvements in protein function, we find inverse folding performs with leading experimental success rates among other reported machine learning-guided directed evolution methods, without requiring any task-specific training data.
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Affiliation(s)
- Varun R. Shanker
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Theodora U.J. Bruun
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian L. Hie
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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8
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Flynn AL, Gans J, Escobedo J, Zhu C, Florescu AM, Shankara S, Madden SL, Kim PS, Pao LI. RGS1 Modulates Autophagic and Metabolic Programs and Is a Critical Mediator of Human Regulatory T Cell Function. J Immunol 2023; 211:1656-1668. [PMID: 37850953 DOI: 10.4049/jimmunol.2200402] [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] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/27/2023] [Indexed: 10/19/2023]
Abstract
Regulatory T cells (Tregs) are critical mediators of immune tolerance and play a diametric role in cancer and autoimmunity. Tumor-infiltrating Tregs are often associated with poor prognosis in solid tumors because their enrichment in the tumor microenvironment contributes to immunosuppression. Conversely, dysregulation in the Treg compartment can disrupt self-tolerance, leading to autoimmunity. In the present study, we describe what is, to our knowledge, a novel regulator of Tregs, the GTPase activator regulator of G protein 1 (RGS1), demonstrating that RGS1-deficient human Tregs show downregulation of Treg-associated genes and are less immunosuppressive. These RGS1-deficient Tregs exhibit perturbations to the FOXP3-c-MYC transcriptional axis and downstream metabolic and autophagy programs by shifting their energy demands toward glycolysis and rendering them less autophagic. Taken together, RGS1 may serve as an apical node of Treg function by regulating the FOXP3-c-MYC transcriptional axis, thereby providing a therapeutic rationale for targeting RGS1 for treatment of cancer and autoimmune diseases.
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Affiliation(s)
| | - Joseph Gans
- Department of Translational Sciences, Sanofi, Cambridge, MA
| | | | - Cheng Zhu
- Department of Translational Sciences, Sanofi, Cambridge, MA
| | | | | | | | - Peter S Kim
- Department of Oncology, Sanofi, Cambridge, MA
| | - Lily I Pao
- Department of Oncology, Sanofi, Cambridge, MA
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Kumru OS, Sanyal M, Friedland N, Hickey JM, Joshi R, Weidenbacher P, Do J, Cheng YC, Kim PS, Joshi SB, Volkin DB. Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 spike ferritin nanoparticle vaccine antigen produced from two different cell lines. Vaccine 2023; 41:6502-6513. [PMID: 37620203 DOI: 10.1016/j.vaccine.2023.08.037] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/25/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
The development of safe and effective second-generation COVID-19 vaccines to improve affordability and storage stability requirements remains a high priority to expand global coverage. In this report, we describe formulation development and comparability studies with a self-assembled SARS-CoV-2 spike ferritin nanoparticle vaccine antigen (called DCFHP), when produced in two different cell lines and formulated with an aluminum-salt adjuvant (Alhydrogel, AH). Varying levels of phosphate buffer altered the extent and strength of antigen-adjuvant interactions, and these formulations were evaluated for their (1) in vivo performance in mice and (2) in vitro stability profiles. Unadjuvanted DCFHP produced minimal immune responses while AH-adjuvanted formulations elicited greatly enhanced pseudovirus neutralization titers independent of ∼100%, ∼40% or ∼10% of the DCFHP antigen adsorbed to AH. These formulations differed, however, in their in vitro stability properties as determined by biophysical studies and a competitive ELISA for measuring ACE2 receptor binding of AH-bound antigen. Interestingly, after one month of 4°C storage, small increases in antigenicity with concomitant decreases in the ability to desorb the antigen from the AH were observed. Finally, we performed a comparability assessment of DCFHP antigen produced in Expi293 and CHO cells, which displayed expected differences in their N-linked oligosaccharide profiles. Despite consisting of different DCFHP glycoforms, these two preparations were highly similar in their key quality attributes including molecular size, structural integrity, conformational stability, binding to ACE2 receptor and mouse immunogenicity profiles. Taken together, these studies support future preclinical and clinical development of an AH-adjuvanted DCFHP vaccine candidate produced in CHO cells.
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Affiliation(s)
- Ozan S Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Natalia Friedland
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - John M Hickey
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Richa Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Payton Weidenbacher
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Ya-Chen Cheng
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Peter S Kim
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA.
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10
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten J, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. bioRxiv 2023:2023.10.14.562364. [PMID: 37904982 PMCID: PMC10614775 DOI: 10.1101/2023.10.14.562364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV) - one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here we describe a universal Ebola virus vaccine approach using structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - J.J. Patten
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Biology, Boston University, Boston, MA 02118, USA
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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11
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Weidenbacher PAB, Sanyal M, Friedland N, Tang S, Arunachalam PS, Hu M, Kumru OS, Morris MK, Fontenot J, Shirreff L, Do J, Cheng YC, Vasudevan G, Feinberg MB, Villinger FJ, Hanson C, Joshi SB, Volkin DB, Pulendran B, Kim PS. Author Correction: A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates. Nat Commun 2023; 14:6211. [PMID: 37798288 PMCID: PMC10556009 DOI: 10.1038/s41467-023-42061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Affiliation(s)
- Payton A-B Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Ozan S Kumru
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | | | - Jane Fontenot
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Lisa Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Jonathan Do
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Ya-Chen Cheng
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Francois J Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - Sangeeta B Joshi
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - David B Volkin
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter S Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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12
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Kim PS, Stirratt MJ, Morton TM, Rausch DM. Ensuring impact of long-acting HIV therapeutics through multi-level treatment research: a view from NIH. J Int AIDS Soc 2023; 26 Suppl 2:e26091. [PMID: 37439059 DOI: 10.1002/jia2.26091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/27/2023] [Indexed: 07/14/2023] Open
Affiliation(s)
- Peter S Kim
- Therapeutics Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, Maryland, USA
| | - Michael J Stirratt
- Division of AIDS Research, National Institute of Mental Health (NIMH), National Institutes of Health, Bethesda, Maryland, USA
| | - Tia M Morton
- Therapeutics Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, Maryland, USA
| | - Dianne M Rausch
- Division of AIDS Research, National Institute of Mental Health (NIMH), National Institutes of Health, Bethesda, Maryland, USA
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13
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Kim PS, Beran RG. Legal medicine implications of a multidisciplinary approach to managing Traumatic Encephalopathy Syndrome in Australia. Front Neurol 2023; 14:1179319. [PMID: 37456643 PMCID: PMC10348871 DOI: 10.3389/fneur.2023.1179319] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
The medical profession has a fundamental obligation to accurately diagnose and effectively treat a range of diseases and conditions. In the case of Traumatic Encephalopathy Syndrome (TES), where there are no universally accepted clinical diagnostic criteria, a clear clinical diagnosis can pose significant challenges for healthcare providers and for subsequent appropriate management. "Nihilism" or an uncertain working diagnosis is not acceptable in the medical field and deserves further consideration. This paper explores the legal obligations that are placed upon healthcare professionals, both individually and as a part of a multidisciplinary team. This article analyses the responsibilities and expectations of medical professionals in diagnosing and treating complex medical conditions, such as TES. The authors address legal issues that must be considered for an effective operation of integrated medicine to enhance the overall quality of care and improving patient outcomes for those affected with underlying Chronic Traumatic Encephalopathy (CTE).
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Affiliation(s)
- Peter S. Kim
- Australasian College of Legal Medicine, Sydney, NSW, Australia
| | - Roy G. Beran
- South Western Clinical School, University of New South Wales, Sydney, NSW, Australia
- South Western Sydney Area Health Service, Ingham Institute for Medical Research, Liverpool, NSW, Australia
- School of Medicine, Griffith University, Southport, QLD, Australia
- Department of Medical Law, Sechenov Moscow First State University, Moscow, Russia
- Medical School, Western Sydney University, Sydney, NSW, Australia
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14
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Weidenbacher PAB, Friedland N, Sanyal M, Morris MK, Do J, Hanson C, Kim PS. Decreased efficacy of a COVID-19 vaccine due to mutations present in early SARS-CoV-2 variants of concern. bioRxiv 2023:2023.06.27.546764. [PMID: 37425802 PMCID: PMC10326996 DOI: 10.1101/2023.06.27.546764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
With the SARS-CoV-2 virus still circulating and evolving, there remains an outstanding question if variant-specific vaccines represent the optimal path forward, or if other strategies might be more efficacious towards providing broad protection against emerging variants. Here, we examine the efficacy of strain-specific variants of our previously reported, pan-sarbecovirus vaccine candidate, DCFHP-alum, a ferritin nanoparticle functionalized with an engineered form of the SARS-CoV-2 spike protein. In non-human primates, DCFHP-alum elicits neutralizing antibodies against all known VOCs that have emerged to date and SARS-CoV-1. During development of the DCFHP antigen, we investigated the incorporation of strain-specific mutations from the major VOCs that had emerged to date: D614G, Epsilon, Alpha, Beta, and Gamma. Here, we report the biochemical and immunological characterizations that led us to choose the ancestral Wuhan-1 sequence as the basis for the final DCFHP antigen design. Specifically, we show by size exclusion chromatography and differential scanning fluorimetry that mutations in the VOCs adversely alter the antigen's structure and stability. More importantly, we determined that DCFHP without strain-specific mutations elicits the most robust, cross-reactive response in both pseudovirus and live virus neutralization assays. Our data suggest potential limitations to the variant-chasing approach in the development of protein nanoparticle vaccines, but also have implications for other approaches including mRNA-based vaccines.
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Affiliation(s)
- Payton A.-B. Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jonathan Do
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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15
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Weidenbacher PAB, Sanyal M, Friedland N, Tang S, Arunachalam PS, Hu M, Kumru OS, Morris MK, Fontenot J, Shirreff L, Do J, Cheng YC, Vasudevan G, Feinberg MB, Villinger FJ, Hanson C, Joshi SB, Volkin DB, Pulendran B, Kim PS. A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates. Nat Commun 2023; 14:2149. [PMID: 37069151 PMCID: PMC10110616 DOI: 10.1038/s41467-023-37417-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [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: 12/19/2022] [Accepted: 03/16/2023] [Indexed: 04/19/2023] Open
Abstract
While the rapid development of COVID-19 vaccines has been a scientific triumph, the need remains for a globally available vaccine that provides longer-lasting immunity against present and future SARS-CoV-2 variants of concern (VOCs). Here, we describe DCFHP, a ferritin-based, protein-nanoparticle vaccine candidate that, when formulated with aluminum hydroxide as the sole adjuvant (DCFHP-alum), elicits potent and durable neutralizing antisera in non-human primates against known VOCs, including Omicron BQ.1, as well as against SARS-CoV-1. Following a booster ~one year after the initial immunization, DCFHP-alum elicits a robust anamnestic response. To enable global accessibility, we generated a cell line that can enable production of thousands of vaccine doses per liter of cell culture and show that DCFHP-alum maintains potency for at least 14 days at temperatures exceeding standard room temperature. DCFHP-alum has potential as a once-yearly (or less frequent) booster vaccine, and as a primary vaccine for pediatric use including in infants.
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Affiliation(s)
- Payton A-B Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Ozan S Kumru
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | | | - Jane Fontenot
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Lisa Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Jonathan Do
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Ya-Chen Cheng
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Francois J Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - Sangeeta B Joshi
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - David B Volkin
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter S Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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16
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Kumru OS, Sanyal M, Friedland N, Hickey J, Joshi R, Weidenbacher P, Do J, Cheng YC, Kim PS, Joshi SB, Volkin DB. Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 Spike ferritin nanoparticle vaccine antigen produced from two different cell lines. bioRxiv 2023:2023.04.03.535447. [PMID: 37066156 PMCID: PMC10103975 DOI: 10.1101/2023.04.03.535447] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The development of safe and effective second-generation COVID-19 vaccines to improve affordability and storage stability requirements remains a high priority to expand global coverage. In this report, we describe formulation development and comparability studies with a self-assembled SARS-CoV-2 spike ferritin nanoparticle vaccine antigen (called DCFHP), when produced in two different cell lines and formulated with an aluminum-salt adjuvant (Alhydrogel, AH). Varying levels of phosphate buffer altered the extent and strength of antigen-adjuvant interactions, and these formulations were evaluated for their (1) in vivo performance in mice and (2) in vitro stability profiles. Unadjuvanted DCFHP produced minimal immune responses while AH-adjuvanted formulations elicited greatly enhanced pseudovirus neutralization titers independent of ∼100%, ∼40% or ∼10% of the DCFHP antigen adsorbed to AH. These formulations differed, however, in their in vitro stability properties as determined by biophysical studies and a competitive ELISA for measuring ACE2 receptor binding of AH-bound antigen. Interestingly, after one month of 4°C storage, small increases in antigenicity with concomitant decreases in the ability to desorb the antigen from the AH were observed. Finally, we performed a comparability assessment of DCFHP antigen produced in Expi293 and CHO cells, which displayed expected differences in their N-linked oligosaccharide profiles. Despite consisting of different DCFHP glycoforms, these two preparations were highly similar in their key quality attributes including molecular size, structural integrity, conformational stability, binding to ACE2 receptor and mouse immunogenicity profiles. Taken together, these studies support future preclinical and clinical development of an AH-adjuvanted DCFHP vaccine candidate produced in CHO cells.
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Affiliation(s)
- Ozan S Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA, 94305 USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Natalia Friedland
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA, 94305 USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - John Hickey
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Richa Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Payton Weidenbacher
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA, 94305 USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA, 94305 USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Ya-Chen Cheng
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA, 94305 USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Peter S Kim
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA, 94305 USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
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17
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Bruun TUJ, Tang S, Erwin G, Deis L, Fernandez D, Kim PS. Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies. J Biol Chem 2023; 299:103062. [PMID: 36841484 PMCID: PMC10064241 DOI: 10.1016/j.jbc.2023.103062] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
The hydrophobic pocket found in the N-heptad repeat (NHR) region of HIV-1 gp41 is a highly conserved epitope that is the target of various HIV-1-neutralizing monoclonal antibodies. Although the high conservation of the pocket makes it an attractive vaccine candidate, it has been challenging to elicit potent anti-NHR antibodies via immunization. Here, we solved a high-resolution structure of the NHR mimetic IQN17, and, consistent with previous ligand-bound gp41 pocket structures, we observed remarkable conformational plasticity of the pocket. The high malleability of this pocket led us to test whether we could improve the immunogenicity of the gp41 pocket by stabilizing its conformation. We show that the addition of five amino acids at the C terminus of IQN17, to generate IQN22, introduces a stabilizing salt bridge at the base of the peptide that rigidifies the pocket. Mice immunized with IQN22 elicited higher avidity antibodies against the gp41 pocket and a more potent, albeit still weak, neutralizing response against HIV-1 compared with IQN17. Stabilized epitope-focused immunogens could serve as the basis for future HIV-1 fusion-inhibiting vaccines.
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Affiliation(s)
- Theodora U J Bruun
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Shaogeng Tang
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Graham Erwin
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Lindsay Deis
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel Fernandez
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Chem-H Macromolecular Structure Knowledge Center (MSKC), Stanford University, Stanford, California, USA
| | - Peter S Kim
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA.
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18
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Bell BN, Bruun TUJ, Friedland N, Kim PS. HIV-1 prehairpin intermediate inhibitors show efficacy independent of neutralization tier. Proc Natl Acad Sci U S A 2023; 120:e2215792120. [PMID: 36795752 PMCID: PMC9974412 DOI: 10.1073/pnas.2215792120] [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: 09/19/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
HIV-1 strains are categorized into one of three neutralization tiers based on the relative ease by which they are neutralized by plasma from HIV-1-infected donors not on antiretroviral therapy; tier-1 strains are particularly sensitive to neutralization while tier-2 and tier-3 strains are increasingly difficult to neutralize. Most broadly neutralizing antibodies (bnAbs) previously described target the native prefusion conformation of HIV-1 Envelope (Env), but the relevance of the tiered categories for inhibitors targeting another Env conformation, the prehairpin intermediate, is not well understood. Here, we show that two inhibitors targeting distinct highly conserved regions of the prehairpin intermediate have strikingly consistent neutralization potencies (within ~100-fold for a given inhibitor) against strains in all three neutralization tiers of HIV-1; in contrast, best-in-class bnAbs targeting diverse Env epitopes vary by more than 10,000-fold in potency against these strains. Our results indicate that antisera-based HIV-1 neutralization tiers are not relevant for inhibitors targeting the prehairpin intermediate and highlight the potential for therapies and vaccine efforts targeting this conformation.
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Affiliation(s)
- Benjamin N. Bell
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Theodora U. J. Bruun
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
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19
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Jenner AL, Kelly W, Dallaston M, Araujo R, Parfitt I, Steinitz D, Pooladvand P, Kim PS, Wade SJ, Vine KL. Examining the efficacy of localised gemcitabine therapy for the treatment of pancreatic cancer using a hybrid agent-based model. PLoS Comput Biol 2023; 19:e1010104. [PMID: 36649330 PMCID: PMC9891514 DOI: 10.1371/journal.pcbi.1010104] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 02/01/2023] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
The prognosis for pancreatic ductal adenocarcinoma (PDAC) patients has not significantly improved in the past 3 decades, highlighting the need for more effective treatment approaches. Poor patient outcomes and lack of response to therapy can be attributed, in part, to a lack of uptake of perfusion of systemically administered chemotherapeutic drugs into the tumour. Wet-spun alginate fibres loaded with the chemotherapeutic agent gemcitabine have been developed as a potential tool for overcoming the barriers in delivery of systemically administrated drugs to the PDAC tumour microenvironment by delivering high concentrations of drug to the tumour directly over an extended period. While exciting, the practicality, safety, and effectiveness of these devices in a clinical setting requires further investigation. Furthermore, an in-depth assessment of the drug-release rate from these devices needs to be undertaken to determine whether an optimal release profile exists. Using a hybrid computational model (agent-based model and partial differential equation system), we developed a simulation of pancreatic tumour growth and response to treatment with gemcitabine loaded alginate fibres. The model was calibrated using in vitro and in vivo data and simulated using a finite volume method discretisation. We then used the model to compare different intratumoural implantation protocols and gemcitabine-release rates. In our model, the primary driver of pancreatic tumour growth was the rate of tumour cell division. We were able to demonstrate that intratumoural placement of gemcitabine loaded fibres was more effective than peritumoural placement. Additionally, we quantified the efficacy of different release profiles from the implanted fibres that have not yet been tested experimentally. Altogether, the model developed here is a tool that can be used to investigate other drug delivery devices to improve the arsenal of treatments available for PDAC and other difficult-to-treat cancers in the future.
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Affiliation(s)
- Adrianne L. Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- * E-mail:
| | - Wayne Kelly
- School of Computer Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Michael Dallaston
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Robyn Araujo
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Isobelle Parfitt
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dominic Steinitz
- Tweag Software Innovation Lab, London, United Kingdom
- Kingston University, Kingston, United Kingdom
| | - Pantea Pooladvand
- School of Mathematics and Statistics, University of Sydney, Sydney, New South Wales, Australia
| | - Peter S. Kim
- School of Mathematics and Statistics, University of Sydney, Sydney, New South Wales, Australia
| | - Samantha J. Wade
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kara L. Vine
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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20
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Weidenbacher PAB, Sanyal M, Friedland N, Tang S, Arunachalam PS, Hu M, Kumru OS, Morris MK, Fontenot J, Shirreff L, Do J, Cheng YC, Vasudevan G, Feinberg MB, Villinger FJ, Hanson C, Joshi SB, Volkin DB, Pulendran B, Kim PS. A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates. bioRxiv 2022:2022.12.25.521784. [PMID: 36597527 PMCID: PMC9810210 DOI: 10.1101/2022.12.25.521784] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
While the rapid development of COVID-19 vaccines has been a scientific triumph, the need remains for a globally available vaccine that provides longer-lasting immunity against present and future SARS-CoV-2 variants of concern (VOCs). Here, we describe DCFHP, a ferritin-based, protein-nanoparticle vaccine candidate that, when formulated with aluminum hydroxide as the sole adjuvant (DCFHP-alum), elicits potent and durable neutralizing antisera in non-human primates against known VOCs, including Omicron BQ.1, as well as against SARS-CoV-1. Following a booster ∼one year after the initial immunization, DCFHP-alum elicits a robust anamnestic response. To enable global accessibility, we generated a cell line that can enable production of thousands of vaccine doses per liter of cell culture and show that DCFHP-alum maintains potency for at least 14 days at temperatures exceeding standard room temperature. DCFHP-alum has potential as a once-yearly booster vaccine, and as a primary vaccine for pediatric use including in infants.
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Affiliation(s)
- Payton A.-B. Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Ozan S. Kumru
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | | | - Jane Fontenot
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Lisa Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Jonathan Do
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Ya-Chen Cheng
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Francois J. Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - Sangeeta B. Joshi
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - David B. Volkin
- Vaccine Analytics and Formulation Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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21
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Abstract
A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A.B. Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Bali Pulendran
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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22
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Xu D, Li C, Utz A, Weidenbacher PAB, Tang S, Sanyal M, Pulendran B, Kim PS. Designing epitope-focused vaccines via antigen reorientation. bioRxiv 2022. [PMID: 36597536 DOI: 10.1101/2022.09.08.507187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
UNLABELLED A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates. GRAPHICAL ABSTRACT Seasonal influenza vaccines induce a biased antibody response against the variable head of hemagglutinin, whereas conserved epitopes on the stem are a target for universal vaccines. Here we show that reorienting HA in an "upside-down" configuration sterically occludes the head and redirects the antibody response to the more exposed stem, thereby inducing broad cross-reactivity against hemagglutinins from diverse influenza strains.
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23
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Weidenbacher PAB, Waltari E, de Los Rios Kobara I, Bell BN, Morris MK, Cheng YC, Hanson C, Pak JE, Kim PS. Converting non-neutralizing SARS-CoV-2 antibodies into broad-spectrum inhibitors. Nat Chem Biol 2022; 18:1270-1276. [PMID: 36076082 PMCID: PMC9596371 DOI: 10.1038/s41589-022-01140-1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/10/2022] [Indexed: 01/07/2023]
Abstract
Omicron and its subvariants have rendered most authorized monoclonal antibody-based treatments for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ineffective, highlighting the need for biologics capable of overcoming SARS-CoV-2 evolution. These mostly ineffective antibodies target variable epitopes. Here we describe broad-spectrum SARS-CoV-2 inhibitors developed by tethering the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), to known non-neutralizing antibodies that target highly conserved epitopes in the viral spike protein. These inhibitors, called receptor-blocking conserved non-neutralizing antibodies (ReconnAbs), potently neutralize all SARS-CoV-2 variants of concern (VOCs), including Omicron. Neutralization potency is lost when the linker joining the binding and inhibitory ReconnAb components is severed. In addition, a bi-functional ReconnAb, made by linking ACE2 to a bi-specific antibody targeting two non-overlapping conserved epitopes, defined here, shows sub-nanomolar neutralizing activity against all VOCs, including Omicron and BA.2. Given their conserved targets and modular nature, ReconnAbs have the potential to act as broad-spectrum therapeutics against SARS-CoV-2 and other emerging pandemic diseases. ![]()
SARS-CoV-2 spike-directed, non-neutralizing antibodies were converted into broad-spectrum inhibitors by conjugation to the SARS-CoV-2 receptor, ACE2, resulting in fusion proteins that target all SARS-CoV-2 variants of concern tested.
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Affiliation(s)
- Payton A-B Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - Benjamin N Bell
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Ya-Chen Cheng
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.,Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter S Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA. .,Department of Biochemistry, School of Medicine, Stanford University, Stanford, CA, USA.
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24
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Powell AE, Xu D, Roth GA, Zhang K, Chiu W, Appel EA, Kim PS. Multimerization of Ebola GPΔmucin on protein nanoparticle vaccines has minimal effect on elicitation of neutralizing antibodies. Front Immunol 2022; 13:942897. [PMID: 36091016 PMCID: PMC9449635 DOI: 10.3389/fimmu.2022.942897] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
Ebola virus (EBOV), a member of the Filoviridae family of viruses and a causative agent of Ebola Virus Disease (EVD), is a highly pathogenic virus that has caused over twenty outbreaks in Central and West Africa since its formal discovery in 1976. The only FDA-licensed vaccine against Ebola virus, rVSV-ZEBOV-GP (Ervebo®), is efficacious against infection following just one dose. However, since this vaccine contains a replicating virus, it requires ultra-low temperature storage which imparts considerable logistical challenges for distribution and access. Additional vaccine candidates could provide expanded protection to mitigate current and future outbreaks. Here, we designed and characterized two multimeric protein nanoparticle subunit vaccines displaying 8 or 20 copies of GPΔmucin, a truncated form of the EBOV surface protein GP. Single-dose immunization of mice with GPΔmucin nanoparticles revealed that neutralizing antibody levels were roughly equivalent to those observed in mice immunized with non-multimerized GPΔmucin trimers. These results suggest that some protein subunit antigens do not elicit enhanced antibody responses when displayed on multivalent scaffolds and can inform next-generation design of stable Ebola virus vaccine candidates.
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Affiliation(s)
- Abigail E. Powell
- Department of Biochemistry and Stanford ChEM-H, Stanford University, Stanford, CA, United States
| | - Duo Xu
- Department of Biochemistry and Stanford ChEM-H, Stanford University, Stanford, CA, United States
| | - Gillie A. Roth
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Menlo Park, CA, United States
| | - Eric A. Appel
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Peter S. Kim
- Department of Biochemistry and Stanford ChEM-H, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
- *Correspondence: Peter S. Kim,
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25
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Weidenbacher P, Musunuri S, Powell AE, Tang S, Do J, Sanyal M, Kim PS. Simplified Purification of Glycoprotein-Modified Ferritin Nanoparticles for Vaccine Development. Biochemistry 2022; 62:292-299. [PMID: 35960597 PMCID: PMC9850919 DOI: 10.1021/acs.biochem.2c00241] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ferritin-based, self-assembling protein nanoparticle vaccines are being developed against a range of viral pathogens, including SARS-CoV-2, influenza, HIV-1, and Epstein-Barr virus. However, purification of these nanoparticles is often laborious and requires customization for each potential nanoparticle vaccine. We propose that the simple insertion of a polyhistidine tag into exposed flexible loops on the ferritin surface (His-Fer) can mitigate the need for complex purifications and enable facile metal-chelate-based purification, thereby allowing for optimization of early stage vaccine candidates. Using sequence homology and computational modeling, we identify four sites that can accommodate insertion of a polyhistidine tag and demonstrate purification of both hemagglutinin-modified and SARS-CoV-2 spike-modified ferritins, highlighting the generality of the approach. A site at the 4-fold axis of symmetry enables optimal purification of both protein nanoparticles. We demonstrate improved purification through modulating the polyhistidine length and optimizing both the metal cation and the resin type. Finally, we show that purified His-Fer proteins remain multimeric and elicit robust immune responses similar to those of their wild-type counterparts. Collectively, this work provides a simplified purification scheme for ferritin-based vaccines.
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Affiliation(s)
- Payton Weidenbacher
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States,Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sriharshita Musunuri
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States,Department
of Biochemistry, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Abigail E. Powell
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States,Department
of Biochemistry, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Shaogeng Tang
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States,Department
of Biochemistry, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Jonathan Do
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States,Department
of Biochemistry, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States,Department
of Biochemistry, School of Medicine, Stanford
University, Stanford, California 94305, United States
| | - Peter S. Kim
- Stanford
ChEM-H, Stanford University, Stanford, California 94305, United States,Department
of Biochemistry, School of Medicine, Stanford
University, Stanford, California 94305, United States,Chan
Zuckerberg Biohub, San Francisco, California 94158, United States,)
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26
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Weidenbacher PAB, Rodriguez-Rivera FP, Sanyal M, Visser JA, Do J, Bertozzi CR, Kim PS. Chemically Modified Bacterial Sacculi as a Vaccine Microparticle Scaffold. ACS Chem Biol 2022; 17:1184-1196. [PMID: 35412807 PMCID: PMC9127789 DOI: 10.1021/acschembio.2c00140] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Vaccine scaffolds
and carrier proteins increase the immunogenicity
of subunit vaccines. Here, we developed, characterized, and demonstrated
the efficacy of a novel microparticle vaccine scaffold comprised of
bacterial peptidoglycan (PGN), isolated as an entire sacculi. The
PGN microparticles contain bio-orthogonal chemical handles allowing
for site-specific attachment of immunogens. We first evaluated the
purification, integrity, and immunogenicity of PGN microparticles
derived from a variety of bacterial species. We then optimized PGN
microparticle modification conditions; Staphylococcus
aureus PGN microparticles containing azido-d-alanine yielded robust conjugation to immunogens. We then demonstrated
that this vaccine scaffold elicits comparable immunostimulation to
the conventional carrier protein, keyhole limpet hemocyanin (KLH).
We further modified the S. aureus PGN
microparticle to contain the SARS-CoV-2 receptor-binding domain (RBD)—this
conjugate vaccine elicited neutralizing antibody titers comparable
to those elicited by the KLH-conjugated RBD. Collectively, these findings
suggest that chemically modified bacterial PGN microparticles are
a conjugatable and biodegradable microparticle scaffold capable of
eliciting a robust immune response toward an antigen of interest.
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Affiliation(s)
- Payton A.-B. Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Frances P. Rodriguez-Rivera
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Joshua A. Visser
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jonathan Do
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Carolyn R. Bertozzi
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter S. Kim
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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27
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Le A, Hawkes K, Kim PS. Male mating choices: The drive behind menopause? Theor Popul Biol 2022; 145:126-135. [PMID: 35525440 DOI: 10.1016/j.tpb.2022.04.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/29/2022] [Accepted: 04/24/2022] [Indexed: 11/28/2022]
Abstract
When we examine the life history of humans against our closest primate relatives, the other great apes, there is notably a greater longevity in humans which includes a distinctive postmenopausal life stage, leading to the question, "How did human females evolve to have old-age infertility?" In their paper "Mate choice and the origin of menopause" (Morton et al., 2013), Morton et al. developed an agent-based model (ABM) to investigate the novel hypothesis that ancestral male mating choices, particularly forgoing mating with older females, was the driving force behind the evolution of menopause. From their model, they concluded that indeed male preference for young female mates could have driven females to lose fertility at older ages through deleterious mutations, leading to menopause. In this work, we revisit their male-mate-choice hypothesis by formulating an analogous mathematical model using a system of ordinary differential equations (ODEs). We first show that our ODE model recreates the qualitative behaviour and hence conclusions of key scenarios in Morton et al. (2013). However, since our ODE system is less computationally demanding than their ABM, we also conduct a broader sensitivity analysis over a range of parameters and differing initial conditions to analyse the dependence on their conclusions to underlying assumptions. Our results challenge those of Morton et al. as we find that even the slightest deviation from an exclusive mating preference for younger females would counteract the evolution of menopause. Consequently, we propose that their male-mate-choice hypothesis is incomplete and needs further explanation of how a male strategy to exclusively mate with young females could have arisen in our common ancestors and remained evolutionary stable for long enough to drive the evolution of old-age female infertility.
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Affiliation(s)
- Anthia Le
- School of Mathematics and Physics, The University of Queensland, Brisbane, Australia.
| | - Kristen Hawkes
- Department of Anthropology, University of Utah, Salt Lake City, USA
| | - Peter S Kim
- School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
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28
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Gale EC, Powell AE, Roth GA, Meany EL, Yan J, Ou BS, Grosskopf AK, Adamska J, Picece VCTM, d'Aquino AI, Pulendran B, Kim PS, Appel EA. Hydrogel-Based Slow Release of a Receptor-Binding Domain Subunit Vaccine Elicits Neutralizing Antibody Responses Against SARS-CoV-2. Adv Mater 2021; 33:e2104362. [PMID: 34651342 PMCID: PMC8646307 DOI: 10.1002/adma.202104362] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/21/2021] [Indexed: 05/22/2023]
Abstract
The development of effective vaccines that can be rapidly manufactured and distributed worldwide is necessary to mitigate the devastating health and economic impacts of pandemics like COVID-19. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, which mediates host cell entry of the virus, is an appealing antigen for subunit vaccines because it is efficient to manufacture, highly stable, and a target for neutralizing antibodies. Unfortunately, RBD is poorly immunogenic. While most subunit vaccines are commonly formulated with adjuvants to enhance their immunogenicity, clinically-relevant adjuvants Alum, AddaVax, and CpG/Alum are found unable to elicit neutralizing responses following a prime-boost immunization. Here, it has been shown that sustained delivery of an RBD subunit vaccine comprising CpG/Alum adjuvant in an injectable polymer-nanoparticle (PNP) hydrogel elicited potent anti-RBD and anti-spike antibody titers, providing broader protection against SARS-CoV-2 variants of concern compared to bolus administration of the same vaccine and vaccines comprising other clinically-relevant adjuvant systems. Notably, a SARS-CoV-2 spike-pseudotyped lentivirus neutralization assay revealed that hydrogel-based vaccines elicited potent neutralizing responses when bolus vaccines did not. Together, these results suggest that slow delivery of RBD subunit vaccines with PNP hydrogels can significantly enhance the immunogenicity of RBD and induce neutralizing humoral immunity.
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MESH Headings
- Adjuvants, Immunologic/chemistry
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- COVID-19/prevention & control
- COVID-19/virology
- CpG Islands/genetics
- Female
- Humans
- Hydrogels/chemistry
- Immunity, Humoral
- Mice
- Mice, Inbred C57BL
- Nanoparticles/chemistry
- Polymers/chemistry
- Protein Domains/immunology
- SARS-CoV-2/chemistry
- SARS-CoV-2/immunology
- SARS-CoV-2/isolation & purification
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/isolation & purification
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
- Vaccines, Subunit/metabolism
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Affiliation(s)
- Emily C. Gale
- Department of BiochemistryStanford University School of MedicineStanfordCA94305USA
| | - Abigail E. Powell
- Department of BiochemistryStanford University School of MedicineStanfordCA94305USA
- Stanford ChEM‐HStanford UniversityStanfordCA94305USA
| | - Gillie A. Roth
- Department of BioengineeringStanford UniversityStanfordCA94305USA
| | - Emily L. Meany
- Department of BioengineeringStanford UniversityStanfordCA94305USA
| | - Jerry Yan
- Department of BioengineeringStanford UniversityStanfordCA94305USA
| | - Ben S. Ou
- Department of BioengineeringStanford UniversityStanfordCA94305USA
| | | | - Julia Adamska
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCA94305USA
- Institute for Immunity, Transplantation, & InfectionStanford University School of MedicineStanfordCA94305USA
| | - Vittoria C. T. M. Picece
- Department of Materials Science & EngineeringStanford UniversityStanfordCA94305USA
- Department of Chemistry and Applied BiosciencesETH ZurichZurich8093Switzerland
| | - Andrea I. d'Aquino
- Department of Materials Science & EngineeringStanford UniversityStanfordCA94305USA
| | - Bali Pulendran
- Stanford ChEM‐HStanford UniversityStanfordCA94305USA
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCA94305USA
- Institute for Immunity, Transplantation, & InfectionStanford University School of MedicineStanfordCA94305USA
- Department of PathologyStanford University School of MedicineStanfordCA94306USA
| | - Peter S. Kim
- Department of BiochemistryStanford University School of MedicineStanfordCA94305USA
- Stanford ChEM‐HStanford UniversityStanfordCA94305USA
- Chan Zuckerberg BiohubSan FranciscoCA94158USA
| | - Eric A. Appel
- Stanford ChEM‐HStanford UniversityStanfordCA94305USA
- Department of BioengineeringStanford UniversityStanfordCA94305USA
- Institute for Immunity, Transplantation, & InfectionStanford University School of MedicineStanfordCA94305USA
- Department of Materials Science & EngineeringStanford UniversityStanfordCA94305USA
- Department of Pediatrics–EndocrinologyStanford University School of MedicineStanfordCA94305USA
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29
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Loo SL, Rose D, Hawkes K, Kim PS. Mate guarding in primates arises due to partner scarcity, even if the father provides no paternal care at all. Theor Popul Biol 2021; 142:100-113. [PMID: 34648764 DOI: 10.1016/j.tpb.2021.09.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 10/20/2022]
Abstract
Paternal care is unusual among primates; in most species males compete with one another for the acquisition of mates and leave the raising of offspring to the mothers. Callitrichids defy this trend with both fathers and older siblings contributing to the care of offspring. We extend a two-strategy population model (paternal care versus male-male competition) to account for various mechanisms that could possibly explain why male callitrichids invest in paternal care over male-male competition, and compare results from callitrichid, chimpanzee and hunter-gatherer life history parameters. The survival benefit to offspring due to care is an insufficient explanation of callitrichid paternal care, and the additional inclusion of differences in lactation-related biology similarly do not change that picture. Instead, paternal care may arise in parallel with, or even as a result of, mate guarding, which in turn is only beneficial when partners are scarce as modelled by the birth sex ratio in callitrichids and menopause in hunter-gatherers. In that situation, care need not even provide any benefit to the young (in the form of a survival bonus) for guarding to out-compete multiple mating competition.
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Affiliation(s)
- Sara L Loo
- University of New South Wales, Sydney, NSW, Australia.
| | - Danya Rose
- University of Sydney, Sydney, NSW, Australia.
| | | | - Peter S Kim
- University of Sydney, Sydney, NSW, Australia.
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30
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Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro J, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James JA, Kim PS, Meyer NJ, Nadeau KC, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Luning Prak ET, Utz PJ. New-onset IgG autoantibodies in hospitalized patients with COVID-19. Nat Commun 2021; 12:5417. [PMID: 34521836 PMCID: PMC8440763 DOI: 10.1038/s41467-021-25509-3] [Citation(s) in RCA: 222] [Impact Index Per Article: 74.0] [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: 02/02/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
COVID-19 is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. Here we develop three protein arrays to measure IgG autoantibodies associated with connective tissue diseases, anti-cytokine antibodies, and anti-viral antibody responses in serum from 147 hospitalized COVID-19 patients. Autoantibodies are identified in approximately 50% of patients but in less than 15% of healthy controls. When present, autoantibodies largely target autoantigens associated with rare disorders such as myositis, systemic sclerosis and overlap syndromes. A subset of autoantibodies targeting traditional autoantigens or cytokines develop de novo following SARS-CoV-2 infection. Autoantibodies track with longitudinal development of IgG antibodies recognizing SARS-CoV-2 structural proteins and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
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Affiliation(s)
- Sarah Esther Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisabeth Mack
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Maja Artandi
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford CROWN Clinic, Stanford University School of Medicine, Stanford, CA, USA
| | - Linda Barman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Kate Bennett
- Molecular Pathology and Imaging Core, Department of Medicine, Gastroenterology Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Iris Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon Chinthrajah
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaurya Dhingra
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Evan Do
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Amanda Finck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Gaano
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Reinhard Geßner
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Heather M Giannini
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Joyce Gonzalez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Greib
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Margrit Gündisch
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Alex Ren Hsu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Kuo
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rong Mao
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andreas Neubauer
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Oluwatosin Oniyide
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abigail E Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Rajan Puri
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Harald Renz
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany
| | - Jeffrey Schapiro
- TPMG Regional Reference Laboratory, Kaiser Permanente Northern California, Berkeley, CA, USA
| | - Payton A Weidenbacher
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Richard Wittman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Neera Ahuja
- Department of Medicine, Division of Hospital Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ho-Ryun Chung
- Institute for Medical Bioinformatics and Biostatistics, Philipps University Marburg, Marburg, Germany
| | - Prasanna Jagannathan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Judith A James
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Peter S Kim
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nuala J Meyer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kari C Nadeau
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - William H Robinson
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Upinder Singh
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany.
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany.
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
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31
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Abstract
We introduce a set of ordinary differential equations (ODEs) that qualitatively reproduce delayed responses observed in immune checkpoint blockade therapy (e.g. anti-CTLA-4 ipilimumab). This type of immunotherapy has been at the forefront of novel and promising cancer treatments over the past decade and was recognised by the 2018 Nobel Prize in Medicine. Our model describes the competition between effector T cells and non-effector T cells in a tumour. By calibrating a small subset of parameters that control immune checkpoint expression along with the patient's immune-system cancer readiness, our model is able to simulate either a complete absence of patient response to treatment, a quick anti-tumour T cell response (within days) or a delayed response (within months). Notably, the parameter space that generates a delayed response is thin and must be carefully calibrated, reflecting the observation that a small subset of patients experience such reactions to checkpoint blockade therapies. Finally, simulations predict that the anti-tumour T cell storm that breaks the delay is very short-lived compared to the length of time the cancer is able to stay suppressed. This suggests the tumour may subsist off an environment hostile to effector T cells; however, these cells are-at rare times-able to break through the tumour immunosuppressive defences to neutralise the tumour for a prolonged period. Our simulations aim to qualitatively describe the delayed response phenomenon without making precise fits to particular datasets, which are limited. It is our hope that our foundational model will stimulate further interest within the immunology modelling field.
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Affiliation(s)
- Collin Y Zheng
- School of Mathematics and Statistics, University of Sydney, Sydney, Australia
| | - Peter S Kim
- School of Mathematics and Statistics, University of Sydney, Sydney, Australia.
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32
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Rubio AA, Filsinger Interrante MV, Bell BN, Brown CL, Bruun TUJ, LaBranche CC, Montefiori DC, Kim PS. A Derivative of the D5 Monoclonal Antibody That Targets the gp41 N-Heptad Repeat of HIV-1 with Broad Tier-2-Neutralizing Activity. J Virol 2021; 95:e0235020. [PMID: 33980592 PMCID: PMC8274607 DOI: 10.1128/jvi.02350-20] [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: 12/09/2020] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
HIV-1 infection is initiated by the viral glycoprotein Env, which, after interaction with cellular coreceptors, adopts a transient conformation known as the prehairpin intermediate (PHI). The N-heptad repeat (NHR) is a highly conserved region of gp41 exposed in the PHI; it is the target of the FDA-approved drug enfuvirtide and of neutralizing monoclonal antibodies (mAbs). However, to date, these mAbs have only been weakly effective against tier-1 HIV-1 strains, which are most sensitive to neutralizing antibodies. Here, we engineered and tested 11 IgG variants of D5, an anti-NHR mAb, by recombining previously described mutations in four of D5's six antibody complementarity-determining regions. One variant, D5_AR, demonstrated 6-fold enhancement in the 50% inhibitory dose (ID50) against lentivirus pseudotyped with HXB2 Env. D5_AR exhibited weak cross-clade neutralizing activity against a diverse set of tier-2 HIV-1 viruses, which are less sensitive to neutralizing antibodies than tier-1 viruses and are the target of current antibody-based vaccine efforts. In addition, the neutralization potency of D5_AR IgG was greatly enhanced in target cells expressing FcγRI, with ID50 values of <0.1 μg/ml; this immunoglobulin receptor is expressed on macrophages and dendritic cells, which are implicated in the early stages of HIV-1 infection of mucosal surfaces. D5 and D5_AR have equivalent neutralization potency in IgG, Fab, and single-chain variable-fragment (scFv) formats, indicating that neutralization is not impacted by steric hindrance. Taken together, these results provide support for vaccine strategies that target the PHI by eliciting antibodies against the gp41 NHR and support investigation of anti-NHR mAbs in nonhuman primate passive immunization studies. IMPORTANCE Despite advances in antiretroviral therapy, HIV remains a global epidemic and has claimed more than 32 million lives. Accordingly, developing an effective HIV vaccine remains an urgent public health need. The gp41 N-heptad repeat (NHR) of the HIV-1 prehairpin intermediate (PHI) is highly conserved (>90%) and is inhibited by the FDA-approved drug enfuvirtide, making it an attractive vaccine target. However, to date, anti-NHR antibodies have not been potent. Here, we engineered D5_AR, a more potent variant of the anti-NHR antibody D5, and established its ability to inhibit HIV-1 strains that are more difficult to neutralize and are more representative of circulating strains (tier-2 strains). The neutralizing activity of D5_AR was greatly potentiated in cells expressing FcγRI; FcγRI is expressed on cells that are implicated at the earliest stages of sexual HIV-1 transmission. Taken together, these results bolster efforts to target the gp41 NHR and the PHI for vaccine development.
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Affiliation(s)
- Adonis A. Rubio
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University School of Humanities & Sciences, Stanford, California, USA
| | - Maria V. Filsinger Interrante
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin N. Bell
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
| | - Clayton L. Brown
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Theodora U. J. Bruun
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Celia C. LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Peter S. Kim
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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33
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Gale EC, Powell AE, Roth GA, Ou BS, Meany EL, Grosskopf AK, Adamska J, Picece VCTM, d'Aquino AI, Pulendran B, Kim PS, Appel E. Hydrogel-based slow release of a receptor-binding domain subunit vaccine elicits neutralizing antibody responses against SARS-CoV-2. bioRxiv 2021. [PMID: 33821276 DOI: 10.1101/2021.03.31.437792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of effective vaccines that can be rapidly manufactured and distributed worldwide is necessary to mitigate the devastating health and economic impacts of pandemics like COVID-19. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, which mediates host cell entry of the virus, is an appealing antigen for subunit vaccines because it is efficient to manufacture, highly stable, and a target for neutralizing antibodies. Unfortunately, RBD is poorly immunogenic. While most subunit vaccines are commonly formulated with adjuvants to enhance their immunogenicity, we found that clinically-relevant adjuvants Alum, AddaVax, and CpG/Alum were unable to elicit neutralizing responses following a prime-boost immunization. Here we show that sustained delivery of an RBD/CpG/Alum subunit vaccine in an injectable polymer-nanoparticle (PNP) hydrogel depot increased total anti-RBD antibody titers and elicited potent anti-spike titers, providing broader protection against SARS-CoV-2 variants of concern compared to bolus administration of the same vaccine and vaccines comprising other clinically-relevant adjuvant systems. Notably, a SARS-CoV-2 spike-pseudotyped lentivirus neutralization assay revealed that hydrogel-based vaccines elicited potent neutralizing responses when bolus vaccines did not. Together, these results suggest that slow delivery of RBD subunit vaccines with PNP hydrogels can significantly enhance the immunogenicity of RBD and induce neutralizing humoral immunity.
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34
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Pooladvand P, Kim PS, Fazekas de St Groth B. The Role of Antigen-Competitive Dynamics in Regulating the Immune Response. Bull Math Biol 2021; 83:40. [PMID: 33730201 DOI: 10.1007/s11538-021-00867-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/10/2021] [Indexed: 10/21/2022]
Abstract
The clonal expansion of T cells during an infection is tightly regulated to ensure an appropriate immune response against invading pathogens. Although experiments have mapped the trajectory from expansion to contraction, the interplay between mechanisms that control this response is not fully understood. Based on experimental data, we propose a model in which the dynamics of CD4+ T cell expansion is controlled through the interactions between T cells and antigen-presenting cells, where T cell stimulation is proportional to antigen availability, and antigen availability is regulated through downregulation of antigen by T cells. This antigen-dependent-feedback mechanism operates alongside an intrinsic reduction in cell proliferation rate that may also be responsible for slowing expansion. Our model can successfully predict T cell recruitment rates into division, expansion, and clonal burst size per cell when initial precursors are varied or when T cells are introduced late into an ongoing immune response. Importantly, the findings demonstrate that a feedback mechanism between T cells and antigen-presenting cells, along with a reduction in cell proliferation rate, can explain the ability of the immune system to adapt its response to variations in initial conditions or changes that occur later in the response, ensuring a robust yet controlled line of defence against pathogens.
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Affiliation(s)
- Pantea Pooladvand
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Peter S Kim
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Barbara Fazekas de St Groth
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
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35
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Brigger D, Horn MP, Pennington LF, Powell AE, Siegrist D, Weber B, Engler O, Piezzi V, Damonti L, Iseli P, Hauser C, Froehlich TK, Villiger PM, Bachmann MF, Leib SL, Bittel P, Fiedler M, Largiadèr CR, Marschall J, Stalder H, Kim PS, Jardetzky TS, Eggel A, Nagler M. Accuracy of serological testing for SARS-CoV-2 antibodies: First results of a large mixed-method evaluation study. Allergy 2021; 76:853-865. [PMID: 32997812 PMCID: PMC7537154 DOI: 10.1111/all.14608] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 08/03/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Serological immunoassays that can identify protective immunity against SARS-CoV-2 are needed to adapt quarantine measures, assess vaccination responses, and evaluate donor plasma. To date, however, the utility of such immunoassays remains unclear. In a mixed-design evaluation study, we compared the diagnostic accuracy of serological immunoassays that are based on various SARS-CoV-2 proteins and assessed the neutralizing activity of antibodies in patient sera. METHODS Consecutive patients admitted with confirmed SARS-CoV-2 infection were prospectively followed alongside medical staff and biobank samples from winter 2018/2019. An in-house enzyme-linked immunosorbent assay utilizing recombinant receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was developed and compared to three commercially available enzyme-linked immunosorbent assays (ELISAs) targeting the nucleoprotein (N), the S1 domain of the spike protein (S1), and a lateral flow immunoassay (LFI) based on full-length spike protein. Neutralization assays with live SARS-CoV-2 were performed. RESULTS One thousand four hundred and seventy-seven individuals were included comprising 112 SARS-CoV-2 positives (defined as a positive real-time PCR result; prevalence 7.6%). IgG seroconversion occurred between day 0 and day 21. While the ELISAs showed sensitivities of 88.4% for RBD, 89.3% for S1, and 72.9% for N protein, the specificity was above 94% for all tests. Out of 54 SARS-CoV-2 positive individuals, 96.3% showed full neutralization of live SARS-CoV-2 at serum dilutions ≥ 1:16, while none of the 6 SARS-CoV-2-negative sera revealed neutralizing activity. CONCLUSIONS ELISAs targeting RBD and S1 protein of SARS-CoV-2 are promising immunoassays which shall be further evaluated in studies verifying diagnostic accuracy and protective immunity against SARS-CoV-2.
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Affiliation(s)
- Daniel Brigger
- Department of Rheumatology, Immunology, and AllergologyInselspital University HospitalBernSwitzerland
- Department of BioMedical ResearchUniversity of BernBernSwitzerland
| | - Michael P. Horn
- University Institute of Clinical ChemistryInselspital University HospitalBernSwitzerland
| | - Luke F. Pennington
- Department of Structural BiologyStanford University School of MedicineStanfordCAUSA
| | - Abigail E. Powell
- Standford Chem‐H and Department of BiochemistryStanford University School of MedicineStanfordCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Denise Siegrist
- Spiez LaboratoryFederal Office for Civil ProtectionSpiezSwitzerland
| | - Benjamin Weber
- Spiez LaboratoryFederal Office for Civil ProtectionSpiezSwitzerland
| | - Olivier Engler
- Spiez LaboratoryFederal Office for Civil ProtectionSpiezSwitzerland
| | - Vanja Piezzi
- Department of Infectious DiseasesBern University HospitalUniversity of BernBernSwitzerland
| | - Lauro Damonti
- Department of Infectious DiseasesBern University HospitalUniversity of BernBernSwitzerland
| | - Patricia Iseli
- Occupational MedicineInselspital University HospitalBernSwitzerland
| | - Christoph Hauser
- Department of Infectious DiseasesBern University HospitalUniversity of BernBernSwitzerland
| | - Tanja K. Froehlich
- University Institute of Clinical ChemistryInselspital University HospitalBernSwitzerland
| | - Peter M. Villiger
- Department of Rheumatology, Immunology, and AllergologyInselspital University HospitalBernSwitzerland
| | - Martin F. Bachmann
- Department of Rheumatology, Immunology, and AllergologyInselspital University HospitalBernSwitzerland
- Department of BioMedical ResearchUniversity of BernBernSwitzerland
| | - Stephen L. Leib
- Institute for Infectious DiseasesUniversity of BernBernSwitzerland
| | - Pascal Bittel
- Institute for Infectious DiseasesUniversity of BernBernSwitzerland
| | - Martin Fiedler
- University Institute of Clinical ChemistryInselspital University HospitalBernSwitzerland
| | - Carlo R. Largiadèr
- University Institute of Clinical ChemistryInselspital University HospitalBernSwitzerland
| | - Jonas Marschall
- Department of Infectious DiseasesBern University HospitalUniversity of BernBernSwitzerland
| | - Hanspeter Stalder
- Vetsuisse FacultyInstitute of Virology and ImmunologyUniversity of BernBernSwitzerland
| | - Peter S. Kim
- Standford Chem‐H and Department of BiochemistryStanford University School of MedicineStanfordCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | | | - Alexander Eggel
- Department of Rheumatology, Immunology, and AllergologyInselspital University HospitalBernSwitzerland
- Department of BioMedical ResearchUniversity of BernBernSwitzerland
| | - Michael Nagler
- University Institute of Clinical ChemistryInselspital University HospitalBernSwitzerland
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36
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Affiliation(s)
- Peter S Kim
- Division of AIDSNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
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37
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Bell BN, Powell AE, Rodriguez C, Cochran JR, Kim PS. Neutralizing antibodies targeting the SARS-CoV-2 receptor binding domain isolated from a naïve human antibody library. Protein Sci 2021; 30:716-727. [PMID: 33586288 PMCID: PMC7980507 DOI: 10.1002/pro.4044] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022]
Abstract
Infection with SARS‐CoV‐2 elicits robust antibody responses in some patients, with a majority of the response directed at the receptor binding domain (RBD) of the spike surface glycoprotein. Remarkably, many patient‐derived antibodies that potently inhibit viral infection harbor few to no mutations from the germline, suggesting that naïve antibody libraries are a viable means for discovery of novel SARS‐CoV‐2 neutralizing antibodies. Here, we used a yeast surface‐display library of human naïve antibodies to isolate and characterize three novel neutralizing antibodies that target the RBD: one that blocks interaction with angiotensin‐converting enzyme 2 (ACE2), the human receptor for SARS‐CoV‐2, and two that target other epitopes on the RBD. These three antibodies neutralized SARS‐CoV‐2 spike‐pseudotyped lentivirus with IC50 values as low as 60 ng/ml in vitro. Using a biolayer interferometry‐based binding competition assay, we determined that these antibodies have distinct but overlapping epitopes with antibodies elicited during natural COVID‐19 infection. Taken together, these analyses highlight how in vitro selection of naïve antibodies can mimic the humoral response in vivo, yielding neutralizing antibodies and various epitopes that can be effectively targeted on the SARS‐CoV‐2 RBD.
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Affiliation(s)
- Benjamin N Bell
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA.,Stanford ChEM-H, Stanford University, Stanford, California, USA
| | - Abigail E Powell
- Stanford ChEM-H, Stanford University, Stanford, California, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | | | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - Peter S Kim
- Stanford ChEM-H, Stanford University, Stanford, California, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
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38
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Kumbhari A, Rose D, Lee PP, Kim PS. A minimal model of T cell avidity may identify subtherapeutic vaccine schedules. Math Biosci 2021; 334:108556. [PMID: 33539903 DOI: 10.1016/j.mbs.2021.108556] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022]
Abstract
T cells protect the body from cancer by recognising tumour-associated antigens. Recognising these antigens depends on multiple factors, one of which is T cell avidity, i.e., the total interaction strength between a T cell and a cancer cell. While both high- and low-avidity T cells can kill cancer cells, durable anti-cancer immune responses require the selection of high-avidity T cells. Previous experimentation with anti-cancer vaccines, however, has shown that most vaccines elicit low-avidity T cells. Optimising vaccine schedules may remedy this by preferentially selecting high-avidity T cells. Here, we use mathematical modelling to develop a simple, phenomenological model of avidity selection that may identify vaccine schedules that disproportionately favour low-avidity T cells. We calibrate our model to our prior, more complex model, and then validate it against several experimental data sets. We find that the sensitivity of the model's parameters change with vaccine dosage, which allows us to use a patient's data and clinical history to screen for suitable vaccine strategies.
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Affiliation(s)
- Adarsh Kumbhari
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
| | - Danya Rose
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
| | - Peter P Lee
- Department of Immuno-Oncology, City of Hope and Beckman Research Institute, Duarte, CA, USA
| | - Peter S Kim
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia.
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39
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Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro JM, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James J, Kim PS, Meyer NJ, Nadeau K, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Prak ETL, Utz PJ. New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19. medRxiv 2021. [PMID: 33532787 DOI: 10.1101/2021.01.27.21250559] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. We developed three different protein arrays to measure hallmark IgG autoantibodies associated with Connective Tissue Diseases (CTDs), Anti-Cytokine Antibodies (ACA), and anti-viral antibody responses in 147 hospitalized COVID-19 patients in three different centers. Autoantibodies were identified in approximately 50% of patients, but in <15% of healthy controls. When present, autoantibodies largely targeted autoantigens associated with rare disorders such as myositis, systemic sclerosis and CTD overlap syndromes. Anti-nuclear antibodies (ANA) were observed in ∼25% of patients. Patients with autoantibodies tended to demonstrate one or a few specificities whereas ACA were even more prevalent, and patients often had antibodies to multiple cytokines. Rare patients were identified with IgG antibodies against angiotensin converting enzyme-2 (ACE-2). A subset of autoantibodies and ACA developed de novo following SARS-CoV-2 infection while others were transient. Autoantibodies tracked with longitudinal development of IgG antibodies that recognized SARS-CoV-2 structural proteins such as S1, S2, M, N and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. COVID-19 patients with one or more autoantibodies tended to have higher levels of antibodies against SARS-CoV-2 Nonstructural Protein 1 (NSP1) and Methyltransferase (ME). We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
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40
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Powell A, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice. ACS Cent Sci 2021; 7:183-199. [PMID: 33527087 PMCID: PMC7805605 DOI: 10.1021/acscentsci.0c01405] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 05/05/2023]
Abstract
The development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines, and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
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Affiliation(s)
- Abigail
E. Powell
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Kaiming Zhang
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Shaogeng Tang
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Payton A. Weidenbacher
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Shanshan Li
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Tho D. Pham
- Department
of Pathology, Stanford University, Stanford, California 94305, United States
- Stanford
Blood Center, Palo Alto, California 94304, United States
| | - John E. Pak
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
| | - Wah Chiu
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Peter S. Kim
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
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41
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Röltgen K, Powell AE, Wirz OF, Stevens BA, Hogan CA, Najeeb J, Hunter M, Wang H, Sahoo MK, Huang C, Yamamoto F, Manohar M, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Jardetzky TS, Zehnder JL, Wang TT, Narasimhan B, Gombar S, Tibshirani R, Nadeau KC, Kim PS, Pinsky BA, Boyd SD. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Sci Immunol 2020; 5:eabe0240. [PMID: 33288645 PMCID: PMC7857392 DOI: 10.1126/sciimmunol.abe0240] [Citation(s) in RCA: 325] [Impact Index Per Article: 81.3] [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: 07/27/2020] [Revised: 10/05/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, can neutralize the virus. It is, however, unknown which features of the serological response may affect clinical outcomes of COVID-19 patients. We analyzed 983 longitudinal plasma samples from 79 hospitalized COVID-19 patients and 175 SARS-CoV-2-infected outpatients and asymptomatic individuals. Within this cohort, 25 patients died of their illness. Higher ratios of IgG antibodies targeting S1 or RBD domains of spike compared to nucleocapsid antigen were seen in outpatients who had mild illness versus severely ill patients. Plasma antibody increases correlated with decreases in viral RNAemia, but antibody responses in acute illness were insufficient to predict inpatient outcomes. Pseudovirus neutralization assays and a scalable ELISA measuring antibodies blocking RBD-ACE2 interaction were well correlated with patient IgG titers to RBD. Outpatient and asymptomatic individuals' SARS-CoV-2 antibodies, including IgG, progressively decreased during observation up to five months post-infection.
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Affiliation(s)
- Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Abigail E Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver F Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, USA
| | | | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Justin Manalac
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tho D Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Blood Center, Palo Alto, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Angela J Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
| | - Nigam H Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Balasubramanian Narasimhan
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Kari C Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Peter S Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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42
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Pooladvand P, Yun CO, Yoon AR, Kim PS, Frascoli F. The role of viral infectivity in oncolytic virotherapy outcomes: A mathematical study. Math Biosci 2020; 334:108520. [PMID: 33290764 DOI: 10.1016/j.mbs.2020.108520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/15/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
A model capturing the dynamics between virus and tumour cells in the context of oncolytic virotherapy is presented and analysed. The ability of the virus to be internalised by uninfected cells is described by an infectivity parameter, which is inferred from available experimental data. The parameter is also able to describe the effects of changes in the tumour environment that affect viral uptake from tumour cells. Results show that when a virus is inoculated inside a growing tumour, strategies for enhancing infectivity do not lead to a complete eradication of the tumour. Within typical times of experiments and treatments, we observe the onset of oscillations, which always prevent a full destruction of the tumour mass. These findings are in good agreement with available laboratory results. Further analysis shows why a fully successful therapy cannot exist for the proposed model and that care must be taken when designing and engineering viral vectors with enhanced features. In particular, bifurcation analysis reveals that creating longer lasting virus particles or using strategies for reducing infected cell lifespan can cause unexpected and unwanted surges in the overall tumour load over time. Our findings suggest that virotherapy alone seems unlikely to be effective in clinical settings unless adjuvant strategies are included.
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Affiliation(s)
- Pantea Pooladvand
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Chae-Ok Yun
- Department of Bioengineering, Collage of Engineering, Hanyang University, Seoul, South Korea; Institute of Nano Science and Technology (INST), Hanyang University, Seoul, South Korea
| | - A-Rum Yoon
- Department of Bioengineering, Collage of Engineering, Hanyang University, Seoul, South Korea; Institute of Nano Science and Technology (INST), Hanyang University, Seoul, South Korea
| | - Peter S Kim
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Federico Frascoli
- Department of Mathematics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, VIC 3122, Australia
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43
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Affiliation(s)
- Peter S Kim
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sarah W Read
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Anthony S Fauci
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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44
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Kumbhari A, Egelston CA, Lee PP, Kim PS. Mature Dendritic Cells May Promote High-Avidity Tuning of Vaccine T Cell Responses. Front Immunol 2020; 11:584680. [PMID: 33193401 PMCID: PMC7662095 DOI: 10.3389/fimmu.2020.584680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
Therapeutic vaccines can elicit tumor-specific cytotoxic T lymphocytes (CTLs), but durable reductions in tumor burden require vaccines that stimulate high-avidity CTLs. Recent advances in immunotherapy responses have led to renewed interest in vaccine approaches, including dendritic cell vaccine strategies. However, dendritic cell requirements for vaccines that generate potent anti-tumor T-cell responses are unclear. Here we use mathematical modeling to show that, counterintuitively, increasing levels of immature dendritic cells may lead to selective expansion of high-avidity CTLs. This finding is in contrast with traditional dendritic cell vaccine approaches that have sought to harness ex vivo generated mature dendritic cells. We show that the injection of vaccine antigens in the context of increased numbers of immature dendritic cells results in a decreased overall peptide:MHC complex load that favors high-avidity CTL activation and expansion. Overall, our results provide a firm basis for further development of this approach, both alone and in combination with other immunotherapies such as checkpoint blockade.
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Affiliation(s)
- Adarsh Kumbhari
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
| | - Colt A Egelston
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Peter P Lee
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Peter S Kim
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
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45
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Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Jean GH, Stevens BA, Lee JY, Rustagi A, Rogers AJ, Powell AE, Hunter M, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Nadeau KC, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2. Cell Host Microbe 2020; 28:516-525.e5. [PMID: 32941787 PMCID: PMC7470783 DOI: 10.1016/j.chom.2020.09.002] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [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: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
B cells are critical for the production of antibodies and protective immunity to viruses. Here we show that patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who develop coronavirus disease 2019 (COVID-19) display early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify convergence of antibody sequences across SARS-CoV-2-infected patients, highlighting stereotyped naive responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and SARS-CoV.
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Affiliation(s)
| | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Grace H Jean
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela J Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Abigail E Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kari C Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Theodore S Jardetzky
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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46
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Loo SL, Rose D, Weight M, Hawkes K, Kim PS. Why Males Compete Rather Than Care, with an Application to Supplying Collective Goods. Bull Math Biol 2020; 82:125. [PMID: 32939621 DOI: 10.1007/s11538-020-00800-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 08/31/2020] [Indexed: 11/30/2022]
Abstract
The question of why males invest more into competition than offspring care is an age-old problem in evolutionary biology. On the one hand, paternal care could increase the fraction of offspring surviving to maturity. On the other hand, competition could increase the likelihood of more paternities and thus the relative number of offspring produced. While drivers of these behaviours are often intertwined with a wide range of other constraints, here we present a simple dynamic model to investigate the benefits of these two alternative fitness-enhancing pathways. Using this framework, we evaluate the sensitivity of equilibrium dynamics to changes in payoffs for male allocation to mating versus parenting. Even with strong effects of care on offspring survivorship, small competitive benefits can outweigh benefits from care. We consider an application of the model that includes men's competition for hunting reputations where big game supplies a benefit to all and find a frequency-dependent parameter region within which, depending on initial population proportions, either strategy may outperform the other. Results demonstrate that allocation to competition gives males greater fitness than offspring care for a range of circumstances that are dependent on life-history parameters and, for the large-game hunting application, frequency dependent. The greater the collective benefit, the more individuals can be selected to supply it.
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Affiliation(s)
- Sara L Loo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Danya Rose
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, 2006, Australia
| | - Michael Weight
- Department of Anthropology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Kristen Hawkes
- Department of Anthropology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Peter S Kim
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, 2006, Australia
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47
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Parikh RV, Tan TC, Salyer AS, Auron A, Kim PS, Ku E, Go AS. Community-Based Epidemiology of Hospitalized Acute Kidney Injury. Pediatrics 2020; 146:peds.2019-2821. [PMID: 32784225 PMCID: PMC7461200 DOI: 10.1542/peds.2019-2821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Acute kidney injury (AKI) may lead to short- and long-term consequences in children, but its epidemiology has not been well described at a population level and outside of ICU settings. METHODS In a large, diverse pediatric population receiving care within an integrated health care delivery system between 2008 and 2016, we calculated age- and sex-adjusted incidences of hospitalized AKI using consensus serum creatinine (SCr)-based diagnostic criteria. We also investigated the proportion of AKI detected in non-ICU settings and the rates of follow-up outpatient SCr testing after AKI hospitalization. RESULTS Among 1 500 546 children, the mean age was 9.8 years, 49.0% were female, and 33.1% were minorities. Age- and sex-adjusted incidence of hospitalized AKI among the entire pediatric population did not change significantly across the study period, averaging 0.70 (95% confidence interval: 0.68-0.73) cases per 1000 person-years. Among the subset of hospitalized children, the adjusted incidence of AKI increased from 6.0% of hospitalizations in 2008 to 8.8% in 2016. Approximately 66.7% of AKI episodes were not associated with an ICU stay, and 54.3% of confirmed, unresolved Stage 2 or 3 AKI episodes did not have outpatient follow-up SCr testing within 30 days postdischarge. CONCLUSIONS Community-based pediatric AKI incidence was ∼1 per 1000 per year, with two-thirds of cases not associated with an ICU stay and more than one-half not receiving early outpatient follow-up kidney function testing. Further efforts are needed to increase the systematic recognition of AKI in all inpatient settings with appropriate, targeted postdischarge kidney function monitoring and associated management.
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Affiliation(s)
- Rishi V. Parikh
- Division of Research, Kaiser Permanente Northern
California, Oakland, California
| | - Thida C. Tan
- Division of Research, Kaiser Permanente Northern
California, Oakland, California
| | - Anne S. Salyer
- Department of Pediatric Nephrology, Oakland Medical
Center, Kaiser Permanente, Oakland, California
| | - Ari Auron
- Department of Pediatric Nephrology, Roseville Medical
Center, Kaiser Permanente, Roseville, California
| | - Peter S. Kim
- Department of Pediatric Nephrology, Santa Clara
Medical Center, Kaiser Permanente, Santa Clara, California
| | - Elaine Ku
- Divisions of Nephrology and Pediatric Nephrology,
Departments of Medicine and Pediatrics, University of California San Francisco,
San Francisco, California
| | - Alan S. Go
- Division of Research, Kaiser Permanente Northern
California, Oakland, California;,Departments of Epidemiology and Biostatistics and
Medicine, School of Medicine, University of California, San Francisco, San
Francisco, California; and,Division of Nephrology, Department of Medicine and
Department of Health Research and Policy, Stanford Medicine, Stanford
University, Palo Alto, California
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48
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Powell AE, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice. bioRxiv 2020:2020.08.28.272518. [PMID: 32869030 PMCID: PMC7457616 DOI: 10.1101/2020.08.28.272518] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
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Affiliation(s)
- Abigail E. Powell
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Kaiming Zhang
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Shaogeng Tang
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Payton A. Weidenbacher
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Shanshan Li
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Tho D. Pham
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Stanford Blood Center, Palo Alto, CA 94304, USA
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Wah Chiu
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Peter S. Kim
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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49
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Röltgen K, Wirz OF, Stevens BA, Powell AE, Hogan CA, Najeeb J, Hunter M, Sahoo MK, Huang C, Yamamoto F, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Nadeau KC, Jardetzky TS, Zehnder JL, Wang TT, Kim PS, Gombar S, Tibshirani R, Pinsky BA, Boyd SD. SARS-CoV-2 Antibody Responses Correlate with Resolution of RNAemia But Are Short-Lived in Patients with Mild Illness. medRxiv 2020:2020.08.15.20175794. [PMID: 32839786 PMCID: PMC7444305 DOI: 10.1101/2020.08.15.20175794] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, could offer protective immunity, and may affect clinical outcomes of COVID-19 patients. We analyzed 625 serial plasma samples from 40 hospitalized COVID-19 patients and 170 SARS-CoV-2-infected outpatients and asymptomatic individuals. Severely ill patients developed significantly higher SARS-CoV-2-specific antibody responses than outpatients and asymptomatic individuals. The development of plasma antibodies was correlated with decreases in viral RNAemia, consistent with potential humoral immune clearance of virus. Using a novel competition ELISA, we detected antibodies blocking RBD-ACE2 interactions in 68% of inpatients and 40% of outpatients tested. Cross-reactive antibodies recognizing SARS-CoV RBD were found almost exclusively in hospitalized patients. Outpatient and asymptomatic individuals' serological responses to SARS-CoV-2 decreased within 2 months, suggesting that humoral protection may be short-lived.
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Affiliation(s)
- Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A. Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Abigail E. Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A. Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, USA
| | | | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin Manalac
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tho D. Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Blood Center, Palo Alto, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
| | - Nigam H. Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Kari C. Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | | | - James L. Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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50
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Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Stevens B, Lee JY, Rustagi A, Rogers AJ, Powell AE, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2. bioRxiv 2020:2020.07.08.194456. [PMID: 32676593 PMCID: PMC7359515 DOI: 10.1101/2020.07.08.194456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
During virus infection B cells are critical for the production of antibodies and protective immunity. Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify extensive convergence of antibody sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses.
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Affiliation(s)
- Sandra C. A. Nielsen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Katherine J. L. Jackson
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- These authors contributed equally
| | - Ramona A. Hoh
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Abigail E. Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Theodore S. Jardetzky
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Peter S. Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | | | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
- Lead Contact
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