1
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Galloway JG, Sung K, Minot SS, Garrett ME, Stoddard CI, Willcox AC, Yaffe ZA, Yucha R, Overbaugh J, Matsen FA. phippery: a software suite for PhIP-Seq data analysis. Bioinformatics 2023; 39:btad583. [PMID: 37740324 PMCID: PMC10547927 DOI: 10.1093/bioinformatics/btad583] [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: 09/28/2022] [Revised: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023] Open
Abstract
SUMMARY We present the phippery software suite for analyzing data from phage display methods that use immunoprecipitation and deep sequencing to capture antibody binding to peptides, often referred to as PhIP-Seq. It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner. AVAILABILITY AND IMPLEMENTATION All software packages are publicly available under the MIT License. The phip-flow pipeline: https://github.com/matsengrp/phip-flow. The phippery library: https://github.com/matsengrp/phippery. The phip-viz Streamlit application: https://github.com/matsengrp/phip-viz.
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Affiliation(s)
- Jared G Galloway
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kevin Sung
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Meghan E Garrett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Caitlin I Stoddard
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Alexandra C Willcox
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Zak A Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Ryan Yucha
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Julie Overbaugh
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
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2
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Stoddard CI, Sung K, Yaffe ZA, Weight H, Beaudoin-Bussières G, Galloway J, Gantt S, Adhiambo J, Begnel ER, Ojee E, Slyker J, Wamalwa D, Kinuthia J, Finzi A, Matsen FA, Lehman DA, Overbaugh J. Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers. Nat Commun 2023; 14:4864. [PMID: 37567924 PMCID: PMC10421871 DOI: 10.1038/s41467-023-40554-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. Here, we characterize antibody binding and functionality against Wuhan-Hu-1 (B lineage) strain SARS-CoV-2 in convalescent plasma from 36 postpartum women and 14 of their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. We find significantly higher antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels in infants versus mothers. Plasma antibodies from mothers and infants bind to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants display higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants have significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, Spike pseudovirus neutralization titers between infants and mothers are similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody activities and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.
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Affiliation(s)
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zak A Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Haidyn Weight
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montreal, QC, Canada
| | - Judith Adhiambo
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Emily R Begnel
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ednah Ojee
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Dara A Lehman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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3
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. Proc Natl Acad Sci U S A 2023; 120:e2220948120. [PMID: 37253011 PMCID: PMC10265947 DOI: 10.1073/pnas.2220948120] [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: 01/27/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor-binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are unique in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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Affiliation(s)
- Jamie Guenthoer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Michelle Lilly
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah, Salt Lake City, UT84112
| | | | - Klaus N. Lovendahl
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Jacob T. Croft
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | | | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
| | - Felicitas Ruiz
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Mackenzie S. Kopp
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QCH2X 0A9, Canada
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- HHMI, Seattle, WA98195
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA98195
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
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4
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Stoddard CI, Sung K, Yaffe ZA, Weight H, Beaudoin-Bussières G, Galloway J, Gantt S, Adhiambo J, Begnel ER, Ojee E, Slyker J, Wamalwa D, Kinuthia J, Finzi A, Matsen FA, Lehman DA, Overbaugh J. Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers. bioRxiv 2023:2023.02.06.527330. [PMID: 36798400 PMCID: PMC9934573 DOI: 10.1101/2023.02.06.527330] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. We characterized antibody binding and functionality in convalescent plasma from postpartum women and their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. Antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels were significantly higher in infants than in mothers. Plasma antibodies from mothers and infants bound to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants displayed higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants had significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, neutralization titers between infants and mothers were similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody repertoires and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.
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Affiliation(s)
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Zak A Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center
- Medical Scientist Training Program, University of Washington
| | - Haidyn Weight
- Human Biology Division, Fred Hutchinson Cancer Center
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Université de Montréal
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal
| | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal
- Centre de Recherche du CHU Sainte-Justine, Université de Montréal
| | - Judith Adhiambo
- Department of Pediatrics and Child Health, University of Nairobi
| | | | - Ednah Ojee
- Department of Pediatrics and Child Health, University of Nairobi
| | | | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi
| | - John Kinuthia
- Department of Global Health, University of Washington
- Department of Research and Programs, Kenyatta National Hospital
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Center
- Howard Hughes Medical Institute
| | - Dara A Lehman
- Human Biology Division, Fred Hutchinson Cancer Center
- Department of Global Health, University of Washington
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center
- Public Health Sciences Division, Fred Hutchinson Cancer Center
- Lead contact
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5
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Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. bioRxiv 2022:2022.12.15.520606. [PMID: 36561191 PMCID: PMC9774213 DOI: 10.1101/2022.12.15.520606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs, including recently circulating BA.4/BA.5, in both pseudovirus-based and live virus assays, and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
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6
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Stoddard CI, Sung K, Ojee E, Adhiambo J, Begnel ER, Slyker J, Gantt S, Matsen FA, Kinuthia J, Wamalwa D, Overbaugh J, Lehman DA. Distinct Antibody Responses to Endemic Coronaviruses Pre- and Post-SARS-CoV-2 Infection in Kenyan Infants and Mothers. Viruses 2022; 14:1517. [PMID: 35891497 PMCID: PMC9323260 DOI: 10.3390/v14071517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 01/21/2023] Open
Abstract
Pre-existing antibodies that bind endemic human coronaviruses (eHCoVs) can cross-react with SARS-CoV-2, which is the betacoronavirus that causes COVID-19, but whether these responses influence SARS-CoV-2 infection is still under investigation and is particularly understudied in infants. In this study, we measured eHCoV and SARS-CoV-1 IgG antibody titers before and after SARS-CoV-2 seroconversion in a cohort of Kenyan women and their infants. Pre-existing eHCoV antibody binding titers were not consistently associated with SARS-CoV-2 seroconversion in infants or mothers; however, we observed a very modest association between pre-existing HCoV-229E antibody levels and a lack of SARS-CoV-2 seroconversion in the infants. After seroconversion to SARS-CoV-2, antibody binding titers to the endemic betacoronaviruses HCoV-OC43 and HCoV-HKU1, and the highly pathogenic betacoronavirus SARS-CoV-1, but not the endemic alphacoronaviruses HCoV-229E and HCoV-NL63, increased in the mothers. However, eHCoV antibody levels did not increase following SARS-CoV-2 seroconversion in the infants, suggesting the increase seen in the mothers was not simply due to cross-reactivity to naively generated SARS-CoV-2 antibodies. In contrast, the levels of antibodies that could bind SARS-CoV-1 increased after SARS-CoV-2 seroconversion in both the mothers and infants, both of whom were unlikely to have had a prior SARS-CoV-1 infection, supporting prior findings that SARS-CoV-2 responses cross-react with SARS-CoV-1. In summary, we found evidence of increased eHCoV antibody levels following SARS-CoV-2 seroconversion in the mothers but not the infants, suggesting eHCoV responses can be boosted by SARS-CoV-2 infection when a prior memory response has been established, and that pre-existing cross-reactive antibodies are not strongly associated with SARS-CoV-2 infection risk in mothers or infants.
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Affiliation(s)
- Caitlin I. Stoddard
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.S.); (F.A.M.IV)
| | - Ednah Ojee
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi 00100, Kenya; (E.O.); (J.A.); (D.W.)
| | - Judith Adhiambo
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi 00100, Kenya; (E.O.); (J.A.); (D.W.)
| | - Emily R. Begnel
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; (E.R.B.); (J.S.); (J.K.)
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; (E.R.B.); (J.S.); (J.K.)
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada;
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC H3T 1C5, Canada
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.S.); (F.A.M.IV)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; (E.R.B.); (J.S.); (J.K.)
- Department of Research and Programs, Kenyatta National Hospital, Nairobi 00202, Kenya
| | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi 00100, Kenya; (E.O.); (J.A.); (D.W.)
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (K.S.); (F.A.M.IV)
| | - Dara A. Lehman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; (E.R.B.); (J.S.); (J.K.)
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7
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Stoddard CI, Sung K, Ojee E, Adhiambo J, Begnel ER, Slyker J, Gantt S, Matsen FA, Kinuthia J, Wamalwa D, Overbaugh J, Lehman DA. Distinct antibody responses to endemic coronaviruses pre- and post-SARS-CoV-2 infection in Kenyan infants and mothers. bioRxiv 2022:2022.06.02.493651. [PMID: 35677071 PMCID: PMC9176650 DOI: 10.1101/2022.06.02.493651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Pre-existing antibodies that bind endemic human coronaviruses (eHCoVs) can cross-react with SARS-CoV-2, the betacoronavirus that causes COVID-19, but whether these responses influence SARS-CoV-2 infection is still under investigation and is particularly understudied in infants. In this study, we measured eHCoV and SARS-CoV-1 IgG antibody titers before and after SARS-CoV-2 seroconversion in a cohort of Kenyan women and their infants. Pre-existing eHCoV antibody binding titers were not consistently associated with SARS-CoV-2 seroconversion in infants or mothers, though we observed a very modest association between pre-existing HCoV-229E antibody levels and lack of SARS-CoV-2 seroconversion in infants. After seroconversion to SARS-CoV-2, antibody binding titers to endemic betacoronaviruses HCoV-OC43 and HCoV-HKU1, and the highly pathogenic betacoronavirus SARS-CoV-1, but not endemic alphacoronaviruses HCoV-229E and HCoV-NL63, increased in mothers. However, eHCoV antibody levels did not increase following SARS-CoV-2 seroconversion in infants, suggesting the increase seen in mothers was not simply due to cross-reactivity to naively generated SARS-CoV-2 antibodies. In contrast, the levels of antibodies that could bind SARS-CoV-1 increased after SARS-CoV-2 seroconversion in both mothers and infants, both of whom are unlikely to have had a prior SARS-CoV-1 infection, supporting prior findings that SARS-CoV-2 responses cross-react with SARS-CoV-1. In summary, we find evidence for increased eHCoV antibody levels following SARS-CoV-2 seroconversion in mothers but not infants, suggesting eHCoV responses can be boosted by SARS-CoV-2 infection when a prior memory response has been established, and that pre-existing cross-reactive antibodies are not strongly associated with SARS-CoV-2 infection risk in mothers or infants.
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Affiliation(s)
- Caitlin I Stoddard
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ednah Ojee
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Judith Adhiambo
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Emily R Begnel
- Department of Global Health, University of Washington, Seattle, WA
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal
- Centre Hospitalier Universitaire Sainte-Justine
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Howard Hughes Medical Institute
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, WA
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Dara A Lehman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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8
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Stoddard CI, Galloway J, Chu HY, Shipley MM, Sung K, Itell HL, Wolf CR, Logue JK, Magedson A, Garrett ME, Crawford KHD, Laserson U, Matsen FA, Overbaugh J. Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs. Cell Rep 2021; 35:109164. [PMID: 33991511 PMCID: PMC8121454 DOI: 10.1016/j.celrep.2021.109164] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 11/04/2020] [Revised: 03/12/2021] [Accepted: 05/03/2021] [Indexed: 01/14/2023] Open
Abstract
A major goal of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine efforts is to elicit antibody responses that confer protection. Mapping the epitope targets of the SARS-CoV-2 antibody response is critical for vaccine design, diagnostics, and development of therapeutics. Here, we develop a pan-coronavirus phage display library to map antibody binding sites at high resolution within the complete viral proteomes of all known human-infecting coronaviruses in patients with mild or moderate/severe coronavirus disease 2019 (COVID-19). We find that the majority of immune responses to SARS-CoV-2 are targeted to the spike protein, nucleocapsid, and ORF1ab and include sites of mutation in current variants of concern. Some epitopes are identified in the majority of samples, while others are rare, and we find variation in the number of epitopes targeted between individuals. We find low levels of SARS-CoV-2 cross-reactivity in individuals with no exposure to the virus and significant cross-reactivity with endemic human coronaviruses (CoVs) in convalescent sera from patients with COVID-19.
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Affiliation(s)
- Caitlin I Stoddard
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Mackenzie M Shipley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Hannah L Itell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ariana Magedson
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Meghan E Garrett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Uri Laserson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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9
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Garrett ME, Galloway J, Chu HY, Itell HL, Stoddard CI, Wolf CR, Logue JK, McDonald D, Weight H, Matsen FA, Overbaugh J. High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. Cell 2021; 184:2927-2938.e11. [PMID: 34010620 PMCID: PMC8096189 DOI: 10.1016/j.cell.2021.04.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/26/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023]
Abstract
Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, spike (S). Here, we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using coronavirus disease 2019 (COVID-19) convalescent plasma. Antibody binding was common in two regions, the fusion peptide and the linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.
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Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Jared Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hannah L Itell
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Caitlin I Stoddard
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dylan McDonald
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Haidyn Weight
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA.
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10
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Garrett ME, Galloway J, Chu HY, Itell HL, Stoddard CI, Wolf CR, Logue JK, McDonald D, Matsen FA, Overbaugh J. High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. bioRxiv 2020:2020.11.16.385278. [PMID: 33236010 PMCID: PMC7685320 DOI: 10.1101/2020.11.16.385278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 11/25/2022]
Abstract
Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, Spike (S). Here we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using COVID-19 convalescent plasma. Antibody binding was common in two regions: the fusion peptide and linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.
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Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jared Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hannah L Itell
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Caitlin I Stoddard
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dylan McDonald
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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11
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Dumesic PA, Stoddard CI, Catania S, Narlikar GJ, Madhani HD. ATP Hydrolysis by the SNF2 Domain of Dnmt5 Is Coupled to Both Specific Recognition and Modification of Hemimethylated DNA. Mol Cell 2020; 79:127-139.e4. [PMID: 32437639 DOI: 10.1016/j.molcel.2020.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023]
Abstract
C.neoformans Dnmt5 is an unusually specific maintenance-type CpG methyltransferase (DNMT) that mediates long-term epigenome evolution. It harbors a DNMT domain and SNF2 ATPase domain. We find that the SNF2 domain couples substrate specificity to an ATPase step essential for DNA methylation. Coupling occurs independent of nucleosomes. Hemimethylated DNA preferentially stimulates ATPase activity, and mutating Dnmt5's ATP-binding pocket disproportionately reduces ATPase stimulation by hemimethylated versus unmethylated substrates. Engineered DNA substrates that stabilize a reaction intermediate by mimicking a "flipped-out" conformation of the target cytosine bypass the SNF2 domain's requirement for hemimethylation. This result implies that ATP hydrolysis by the SNF2 domain is coupled to the DNMT domain conformational changes induced by preferred substrates. These findings establish a new role for a SNF2 ATPase: controlling an adjoined enzymatic domain's substrate recognition and catalysis. We speculate that this coupling contributes to the exquisite specificity of Dnmt5 via mechanisms related to kinetic proofreading.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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12
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Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 2020; 180:816. [PMID: 32084344 PMCID: PMC7201975 DOI: 10.1016/j.cell.2020.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 2020; 180:263-277.e20. [PMID: 31955845 PMCID: PMC7197499 DOI: 10.1016/j.cell.2019.12.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022]
Abstract
Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 mya. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 million years through a process analogous to Darwinian evolution of the genome.
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Affiliation(s)
- Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Harold Pimentel
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ammar Nasif
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sophie Cook
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth Geinger
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert Lintner
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan K Pritchard
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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14
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Stoddard CI, Feng S, Campbell MG, Liu W, Wang H, Zhong X, Bernatavichute Y, Cheng Y, Jacobsen SE, Narlikar GJ. A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase. Mol Cell 2018; 73:73-83.e6. [PMID: 30415948 DOI: 10.1016/j.molcel.2018.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 07/21/2017] [Revised: 08/22/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is poorly understood. The maintenance DNA methyltransferase from Zea mays, ZMET2, recognizes dimethylation of H3K9 via a chromodomain (CD) and a bromo adjacent homology (BAH) domain, which flank the catalytic domain. Here, we show that dinucleosomes are the preferred ZMET2 substrate, with DNA methylation preferentially targeted to linker DNA. Electron microscopy shows one ZMET2 molecule bridging two nucleosomes within a dinucleosome. We find that the CD stabilizes binding, whereas the BAH domain enables allosteric activation by the H3K9me mark. ZMET2 further couples recognition of H3K9me to an increase in the specificity for hemimethylated versus unmethylated DNA. We propose a model in which synergistic coupling between recognition of nucleosome spacing, H3K9 methylation, and DNA modification allows ZMET2 to maintain DNA methylation in heterochromatin with high fidelity.
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Affiliation(s)
- Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Melody G Campbell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wanlu Liu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Haifeng Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Yana Bernatavichute
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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15
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Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep 2018; 19:2033-2044. [PMID: 28591576 DOI: 10.1016/j.celrep.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 04/01/2016] [Revised: 04/05/2017] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric AAA+ ATPases Rvb1 and Rvb2 (Rvbs) are essential for diverse processes ranging from metabolic signaling to chromatin remodeling, but their functions are unknown. While originally thought to act as helicases, recent proposals suggest that Rvbs act as protein assembly chaperones. However, experimental evidence for chaperone-like behavior is lacking. Here, we identify a potent protein activator of the Rvbs, a domain in the Ino80 ATPase subunit of the INO80 chromatin-remodeling complex, termed Ino80INS. Ino80INS stimulates Rvbs' ATPase activity by 16-fold while concomitantly promoting their dodecamerization. Using mass spectrometry, cryo-EM, and integrative modeling, we find that Ino80INS binds asymmetrically along the dodecamerization interface, resulting in a conformationally flexible dodecamer that collapses into hexamers upon ATP addition. Our results demonstrate the chaperone-like potential of Rvb1/Rvb2 and suggest a model where binding of multiple clients such as Ino80 stimulates ATP-driven cycling between hexamers and dodecamers, providing iterative opportunities for correct subunit assembly.
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Affiliation(s)
- Coral Y Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eugene Palovcak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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16
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Qin Y, Miranda JG, Stoddard CI, Dean KM, Galati DF, Palmer AE. Direct comparison of a genetically encoded sensor and small molecule indicator: implications for quantification of cytosolic Zn(2+). ACS Chem Biol 2013; 8:2366-71. [PMID: 23992616 DOI: 10.1021/cb4003859] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent sensors are powerful tools for visualizing and quantifying molecules and ions in living cells. A variety of small molecule and genetically encoded sensors have been developed for studying intracellular Zn(2+) homeostasis and signaling, but no direct comparisons exist, making it challenging for researchers to identify the appropriate sensor for a given application. Here we directly compare the widely used small molecule probe FluoZin-3 and a genetically encoded sensor, ZapCY2. We demonstrate that, in contrast to FluoZin-3, ZapCY2 exhibits a well-defined cytosolic localization, provides estimates of Zn(2+) concentration with little variability, does not perturb cytosolic Zn(2+) levels, and exhibits rapid Zn(2+) response dynamics. ZapCY2 was used to measure Zn(2+) concentrations in 5 different cell types, revealing higher cytosolic Zn(2+) levels in prostate cancer cells compared to normal prostate cells (although the total zinc is reduced in prostate cancer cells), suggesting distinct regulatory mechanisms.
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Affiliation(s)
- Yan Qin
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, UCB 596, Boulder, Colorado 80309, United States
| | - Jose G. Miranda
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, UCB 596, Boulder, Colorado 80309, United States
| | - Caitlin I. Stoddard
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, UCB 596, Boulder, Colorado 80309, United States
| | - Kevin M. Dean
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, UCB 596, Boulder, Colorado 80309, United States
| | - Domenico F. Galati
- Department
of Molecular, Cellular, and Developmental Biology, University of Colorado-Boulder, UCB
347, Boulder, Colorado 80309, United States
| | - Amy E. Palmer
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado-Boulder, UCB 596, Boulder, Colorado 80309, United States
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17
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Miranda JG, Weaver AL, Qin Y, Park JG, Stoddard CI, Lin MZ, Palmer AE. New alternately colored FRET sensors for simultaneous monitoring of Zn²⁺ in multiple cellular locations. PLoS One 2012; 7:e49371. [PMID: 23173058 PMCID: PMC3500285 DOI: 10.1371/journal.pone.0049371] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [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: 06/20/2012] [Accepted: 10/11/2012] [Indexed: 01/28/2023] Open
Abstract
Genetically encoded sensors based on fluorescence resonance energy transfer (FRET) are powerful tools for reporting on ions, molecules and biochemical reactions in living cells. Here we describe the development of new sensors for Zn²⁺based on alternate FRET-pairs that do not involve the traditional CFP and YFP. Zn²⁺ is an essential micronutrient and plays fundamental roles in cell biology. Consequently there is a pressing need for robust sensors to monitor Zn²⁺ levels and dynamics in cells with high spatial and temporal resolution. Here we develop a suite of sensors using alternate FRET pairs, including tSapphire/TagRFP, tSapphire/mKO, Clover/mRuby2, mOrange2/mCherry, and mOrange2/mKATE. These sensors were targeted to both the nucleus and cytosol and characterized and validated in living cells. Sensors based on the new FRET pair Clover/mRuby2 displayed a higher dynamic range and better signal-to-noise ratio than the remaining sensors tested and were optimal for monitoring changes in cytosolic and nuclear Zn²⁺. Using a green-red sensor targeted to the nucleus and cyan-yellow sensor targeted to either the ER, Golgi, or mitochondria, we were able to monitor Zn²⁺ uptake simultaneously in two compartments, revealing that nuclear Zn²⁺ rises quickly, whereas the ER, Golgi, and mitochondria all sequester Zn²⁺ more slowly and with a delay of 600-700 sec. Lastly, these studies provide the first glimpse of nuclear Zn²⁺ and reveal that nuclear Zn²⁺ is buffered at a higher level than cytosolic Zn²⁺.
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Affiliation(s)
- Jose G. Miranda
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Amanda L. Weaver
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Yan Qin
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - J. Genevieve Park
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Caitlin I. Stoddard
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Michael Z. Lin
- Department of Pediatrics and Engineering, Stanford Medical School, Stanford, California, United States of Americs
| | - Amy E. Palmer
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
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