1
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Itell HL, Humes D, Baumgarten NE, Overbaugh J. Host cell glycosylation selects for infection with CCR5- versus CXCR4-tropic HIV-1. bioRxiv 2023:2023.09.05.556399. [PMID: 37732222 PMCID: PMC10508750 DOI: 10.1101/2023.09.05.556399] [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: 09/22/2023]
Abstract
HIV-1 infection involves a selection bottleneck that leads to transmission of one or a few HIV variants, which nearly always use CCR5 as the coreceptor (R5 viruses) for viral entry as opposed to CXCR4 (X4 viruses). The host properties that drive this selection are not well understood and may hold keys to factors that govern HIV susceptibility. In this report, we identified SLC35A2, a transporter of UDP-galactose, as a candidate X4-specific restriction factor in CRISPR-knockout screens in primary target CD4+ T cells. SLC35A2 inactivation in CD4+ T cells, which resulted in truncation of glycans due to the absence of galactose, not only increased X4 infection levels, but also consistently decreased infection levels of R5 HIV strains. Single cycle infections demonstrated that the effect is host cell dependent. SLC35A2 is expressed in CD4+ T cells at different tissue sites, with high levels in the genital tract - the site of most HIV infections. These data support a role for a host cell protein that regulates glycan structure on HIV infection, with enhanced R5 infection but reduced X4 infection associated with SLC35A2-mediated glycosylation. Host cell glycosylation may therefore contribute to R5 selection and host susceptibility during HIV transmission.
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Affiliation(s)
- Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, 98109, USA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Present address: Tr1X Inc, La Jolla, CA, 92037, USA
| | - Nell E. Baumgarten
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
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2
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. Cell Rep 2023; 42:112556. [PMID: 37227817 PMCID: PMC10592456 DOI: 10.1016/j.celrep.2023.112556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4+ T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4+ T cells by performing CRISPR-knockout screens with a custom library that specifically targets ISGs expressed in CD4+ T cells. Our investigation identifies previously undescribed HIV-restricting ISGs (HM13, IGFBP2, LAP3) and finds that two factors characterized in other HIV infection models (IFI16 and UBE2L6) mediate IFN restriction in T cells. Inactivation of these five ISGs in combination further diminishes IFN's protective effect against diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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3
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. bioRxiv 2023:2023.02.07.527545. [PMID: 36798236 PMCID: PMC9934674 DOI: 10.1101/2023.02.07.527545] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4 + T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4 + T cells. We performed CRISPR-knockout screens using a custom library that specifically targets ISGs expressed in CD4 + T cells and validated top hits. Our investigation identified new HIV-restricting ISGs (HM13, IGFBP2, LAP3) and found that two previously studied factors (IFI16, UBE2L6) are IFN effectors in T cells. Inactivation of these five ISGs in combination further diminished IFN’s protective effect against six diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, 98109, USA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Present address: Tr1X Inc, La Jolla, CA, 92037, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
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4
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Fish CS, Owiti P, Begnel ER, Itell HL, Ojee E, Adhiambo J, Ogweno V, Holland LA, Richardson BA, Khan AK, Maqsood R, Gantt S, Lim ES, Slyker J, Kinuthia J, Overbaugh J, Wamalwa D, Lehman DA, Chohan BH. Comparison of nucleocapsid and spike antibody ELISAs for determining SARS-CoV-2 seropositivity in Kenyan women and infants. J Med Virol 2023; 95:e28221. [PMID: 36251533 PMCID: PMC9839577 DOI: 10.1002/jmv.28221] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 01/29/2023]
Abstract
A multitude of enzyme-linked immunosorbent assays (ELISAs) has been developed to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies since the coronavirus disease 2019 pandemic started in late 2019. Assessing the reliability of these assays in diverse global populations is critical. This study compares the use of the commercially available Platelia Total Ab Assay (Bio-Rad) nucleocapsid ELISA to the widely used Mount Sinai spike IgG ELISA in a Kenyan population seroprevalence study. Using longitudinal plasma specimens collected from a mother-infant cohort living in Nairobi, Kenya between May 2019 and December 2020, this study demonstrates that the two assays have a high qualitative agreement (92.7%) and strong correlation of antibody levels (R2 = 0.973) in repeated measures. Within this cohort, seroprevalence detected by either ELISA closely resembled previously published seroprevalence estimates for Kenya during the sampling period and no significant difference in the incidence of SARS-CoV-2 antibody detection by either assay was observed. Assay comparability was not affected by HIV exposure status. These data support the use of the Platelia SARS-CoV-2 Total Ab ELISA as a suitable high-throughput method for seroprevalence studies in Kenya.
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Affiliation(s)
- Carolyn S. Fish
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Prestone Owiti
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - Emily R. Begnel
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA
| | - Hannah L. Itell
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA,Molecular and Cellular Biology Graduate ProgramUniversity of Washington and Fred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Ednah Ojee
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - Judith Adhiambo
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - Vincent Ogweno
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State UniversityTempeArizonaUSA
| | - Barbra A. Richardson
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Adam K. Khan
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State UniversityTempeArizonaUSA
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du CHU St‐JustineUniversité de MontréalMontréalQuébecCanada
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State UniversityTempeArizonaUSA,School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Jennifer Slyker
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - John Kinuthia
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Department of Research and Programs, Kenyatta National HospitalNairobiKenya
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA,Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Dalton Wamalwa
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya,Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA
| | - Dara A. Lehman
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA,Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA
| | - Bhavna H. Chohan
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Kenya Medical Research InstituteNairobiKenya
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5
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Berendam SJ, Morgan-Asiedu PK, Mangan RJ, Li SH, Heimsath H, Luo K, Curtis AD, Eudailey JA, Fox CB, Tomai MA, Phillips B, Itell HL, Kunz E, Hudgens M, Cronin K, Wiehe K, Alam SM, Van Rompay KKA, De Paris K, Permar SR, Moody MA, Fouda GG. Different adjuvanted pediatric HIV envelope vaccines induced distinct plasma antibody responses despite similar B cell receptor repertoires in infant rhesus macaques. PLoS One 2022; 16:e0256885. [PMID: 34972105 PMCID: PMC8719683 DOI: 10.1371/journal.pone.0256885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022] Open
Abstract
Different HIV vaccine regimens elicit distinct plasma antibody responses in both human and nonhuman primate models. Previous studies in human and non-human primate infants showed that adjuvants influenced the quality of plasma antibody responses induced by pediatric HIV envelope vaccine regimens. We recently reported that use of the 3M052-SE adjuvant and longer intervals between vaccinations are associated with higher magnitude of antibody responses in infant rhesus macaques. However, the impact of different adjuvants in HIV vaccine regimens on the developing infant B cell receptor (BCR) repertoire has not been studied. This study evaluated whether pediatric HIV envelope vaccine regimens with different adjuvants induced distinct antigen-specific memory B cell repertoires and whether specific immunoglobulin (Ig) immunogenetic characteristics are associated with higher magnitude of plasma antibody responses in vaccinated infant rhesus macaques. We utilized archived preclinical pediatric HIV vaccine studies PBMCs and tissue samples from 19 infant rhesus macaques immunized either with (i) HIV Env protein with a squalene adjuvant, (ii) MVA-HIV and Env protein co-administered using a 3-week interval, (iii) MVA-HIV prime/ protein boost with an extended 6-week interval between immunizations, or (iv) with HIV Env administered with 3M-052-SE adjuvant. Frequencies of vaccine-elicited HIV Env-specific memory B cells from PBMCs and tissues were similar across vaccination groups (frequency range of 0.06–1.72%). There was no association between vaccine-elicited antigen-specific memory B cell frequencies and plasma antibody titer or avidity. Moreover, the epitope specificity and Ig immunogenetic features of vaccine-elicited monoclonal antibodies did not differ between the different vaccine regimens. These data suggest that pediatric HIV envelope vaccine candidates with different adjuvants that previously induced higher magnitude and quality of plasma antibody responses in infant rhesus macaques were not driven by distinct antigen-specific memory BCR repertoires.
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Affiliation(s)
- Stella J. Berendam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Papa K. Morgan-Asiedu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Riley J. Mangan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Shuk Hang Li
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Holly Heimsath
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Alan D. Curtis
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joshua A. Eudailey
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Weill Cornell College of Medicine, New York City, New York, United States of America
| | - Christopher B. Fox
- Infectious Disease Research Institute (IDRI), Seattle, Washington State, United States of America
- Department of Global Health, University of Washington, Seattle, Washington State, United States of America
| | - Mark A. Tomai
- 3M Center, 3 M Drug Delivery Systems, St. Paul, Minnesota, United States of America
| | - Bonnie Phillips
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hannah L. Itell
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Erika Kunz
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California at Davis, Davis, California, United States of America
| | - Kristina De Paris
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Weill Cornell College of Medicine, New York City, New York, United States of America
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Genevieve G. Fouda
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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6
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Itell HL, Weight H, Fish CS, Logue JK, Franko N, Wolf CR, McCulloch DJ, Galloway J, Matsen FA, Chu HY, Overbaugh J. SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma. Microbiol Spectr 2021; 9:e0129821. [PMID: 34668728 PMCID: PMC8528110 DOI: 10.1128/spectrum.01298-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/17/2021] [Indexed: 11/20/2022] Open
Abstract
Wide-scale assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies is critical to understanding population seroprevalence, correlates of protection, and the longevity of vaccine-elicited responses. Most SARS-CoV-2 studies characterize antibody responses in plasma/sera. While reliable and broadly used, these samples pose several logistical restrictions, such as requiring venipuncture for collection and a cold chain for transportation and storage. Dried blood spots (DBS) overcome these barriers as they can be self-collected by fingerstick and mailed and stored at ambient temperature. Here, we evaluate the suitability of DBS for SARS-CoV-2 antibody assays by comparing several antibody responses between paired plasma and DBS from SARS-CoV-2 convalescent and vaccinated individuals. We found that DBS not only reflected plasma antibody binding by enzyme-linked immunosorbent assay (ELISA) and epitope profiles using phage display, but also yielded SARS-CoV-2 neutralization titers that highly correlated with paired plasma. Neutralization measurement was further streamlined by adapting assays to a high-throughput 384-well format. This study supports the adoption of DBS for numerous SARS-CoV-2 binding and neutralization assays. IMPORTANCE Plasma and sera isolated from venous blood represent conventional sample types used for the evaluation of SARS-CoV-2 antibody responses after infection or vaccination. However, collection of these samples is invasive and requires trained personnel and equipment for immediate processing. Once collected, plasma and sera must be stored and shipped at cold temperatures. To define the risk of emerging SARS-CoV-2 variants and the longevity of immune responses to natural infection and vaccination, it will be necessary to measure various antibody features in populations around the world, including in resource-limited areas. A sampling method that is compatible with these settings and is suitable for a variety of SARS-CoV-2 antibody assays is therefore needed to continue to understand and curb the COVID-19 pandemic.
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Affiliation(s)
- Hannah L. Itell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Haidyn Weight
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Carolyn S. Fish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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7
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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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8
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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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9
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Kaufman DA, Berenz A, Itell HL, Conaway M, Blackman A, Nataro JP, Permar SR. Dose escalation study of bovine lactoferrin in preterm infants: getting the dose right. Biochem Cell Biol 2021; 99:7-13. [DOI: 10.1139/bcb-2020-0217] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Lactoferrin as a nutritional enteral supplement has emerged as a novel preventative therapy against serious infections in preterm infants, although neonatal studies have demonstrated variable results, in part due to the lack of pharmacokinetic data and differences in the products tested. We conducted a prospective, dose escalation (100, 200, and 300 mg·kg–1·day–1) safety study of bovine lactoferrin (Glanbia Nutritionals, USA) dissolved in sterile water (100 mg·mL–1) for 30 days in preterm infants with birth weight <1500 g. Safety related to adverse events (AEs), tolerability, and exposure-response of lactoferrin was assessed. We enrolled 31 patients [10, 10, and 11 patients, for the lactoferrin treatment groups (100, 200, and 300 mg·kg–1·day–1, respectively)] over a 10-month period. No AEs related to the study solution occurred, and lactoferrin was tolerated by each group. During lactoferrin supplementation, one bloodstream infection occurred in each group, but there were no incidences of urinary tract infections and no cases of necrotizing enterocolitis. Postnatal cytomegalovirus acquisition was detected in the group treated with 200 mg·kg–1·day–1 (n = 2). There were no adverse effects on hepatic, renal, or hematologic function. All of the patients survived to discharge. Bovine lactoferrin at doses up to 300 mg·kg–1·day–1 is safe in preterm infants. Future studies examining higher doses of lactoferrin, length of treatment, and potency of different products will aid in determining the optimal approach for the use of lactoferrin to prevent infections in preterm infants.
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Affiliation(s)
- David A. Kaufman
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - Andrew Berenz
- Department of Pediatrics, Rush University Medical Center, Chicago, Illinois, USA
| | - Hannah L. Itell
- Department of Molecular and Cellular Biology, University of Washington, Washington, USA
| | - Mark Conaway
- Department of Biostatistics, University of Virginia, Charlottesville, Virginia, USA
| | - Amy Blackman
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - James P. Nataro
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, 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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Itell HL, Berenz A, Mangan RJ, Permar SR, Kaufman DA. Systemic and mucosal levels of lactoferrin in very low birth weight infants supplemented with bovine lactoferrin. Biochem Cell Biol 2020; 99:25-34. [PMID: 32841570 DOI: 10.1139/bcb-2020-0238] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lactoferrin supplementation may help prevent infections in preterm infants, but the efficacy has varied with different doses and products. We assessed the absorption and excretion of bovine lactoferrin (bLF) in 31 infants receiving 100, 200, or 300 mg·kg-1·day-1 of enteral bLF for 30 days. bLF and human lactoferrin (hLF) in infant saliva, blood, urine, and stool, as well as expressed (EBM) or donor breast milk (DBM) that were collected (i) before the treatment was initiated, (ii) at study day 22, and (iii) one week after treatment cessation, were measured using ELISA. During treatment, bLF was absorbed from the gastrointestinal tract and detected in plasma, saliva, and urine, as well as excreted in stool. Levels of bLF in the saliva and stool began to decline within 12 h after dosing, and bLF was undetectable in all samples one week after treatment. The concentrations of hLF exceeded those of bLF across sample types and time-points. Infants receiving EBM demonstrated higher levels of hLF in the saliva and stool than those receiving DBM. Neither bLF nor hLF levels varied by patient characteristics, bLF dosage, or infection status. This is the first study demonstrating bLF absorption into the bloodstream and distribution to saliva and urine in preterm infants. Future studies should further explore LF pharmacokinetics because higher and more frequent dosing may improve the clinical benefit of LF supplementation.
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Affiliation(s)
- Hannah L Itell
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Andrew Berenz
- Department of Pediatrics, Rush University Medical Center, Chicago, IL, USA
| | - Riley J Mangan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Sallie R Permar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - David A Kaufman
- Division of Neonatology, University of Virginia, Charlottesville, VA, USA
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12
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Saccoccio FM, Jenks JA, Itell HL, Li SH, Berry M, Pollara J, Casper C, Gantt S, Permar SR. Humoral Immune Correlates for Prevention of Postnatal Cytomegalovirus Acquisition. J Infect Dis 2020; 220:772-780. [PMID: 31107951 DOI: 10.1093/infdis/jiz192] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/02/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Development of a cytomegalovirus (CMV) vaccine is a high priority. However, the ability of antibodies to protect against CMV infection is not well characterized. Studies of maternal antibodies in infants offer the potential to identify humoral correlates of protection against postnatal acquisition. METHODS This hypothesis-generating study analyzed 29 Ugandan mother-infant pairs that were followed weekly for CMV acquisition. Seventeen mothers and no infants were infected with human immunodeficiency virus (HIV). We evaluated the association between CMV-specific immunoglobulin G (IgG) responses in mothers at the time of delivery and their infants' CMV status at 6 months of age. We also assessed levels of CMV-specific IgG in infants at 6 weeks of age. CMV-specific IgG responses in the mother-infant pairs were then analyzed on the basis of perinatal HIV exposure. RESULTS We found similar levels of multiple CMV glycoprotein-specific IgG binding specificities and functions in mothers and infants, irrespective of perinatal HIV exposure or infant CMV status at 6 months of age. However, the glycoprotein B-specific IgG titer, measured by 2 distinct assays, was higher in infants without CMV infection and was moderately associated with delayed CMV acquisition. CONCLUSIONS These data suggest that high levels of glycoprotein B-specific IgG may contribute to the partial protection against postnatal CMV infection afforded by maternal antibodies, and they support the continued inclusion of glycoprotein B antigens in CMV vaccine candidates.
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Affiliation(s)
- Frances M Saccoccio
- Division of Pediatric Infectious Diseases, Duke University, Durham, North Carolina
| | - Jennifer A Jenks
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina
| | - Hannah L Itell
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina
| | - Shuk Hang Li
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina
| | - Justin Pollara
- Department of Surgery, Duke University Medical Center, Duke University, Durham, North Carolina
| | - Corey Casper
- Infectious Disease Research Institute, Seattle, Washington
| | - Soren Gantt
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Sallie R Permar
- Division of Pediatric Infectious Diseases, Duke University, Durham, North Carolina.,Duke Human Vaccine Institute, Duke University, Durham, North Carolina
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13
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Mangan RJ, Stamper L, Ohashi T, Eudailey JA, Go EP, Jaeger FH, Itell HL, Watts BE, Fouda GG, Erickson HP, Alam SM, Desaire H, Permar SR. Determinants of Tenascin-C and HIV-1 envelope binding and neutralization. Mucosal Immunol 2019; 12:1004-1012. [PMID: 30976088 PMCID: PMC6599478 DOI: 10.1038/s41385-019-0164-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 05/31/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 02/04/2023]
Abstract
Interactions between innate antiviral factors at mucosal surfaces and HIV-1 virions contribute to the natural inefficiency of HIV-1 transmission and are a platform to inform the development of vaccine and nonvaccine strategies to block mucosal HIV-1 transmission. Tenascin-C (TNC) is a large, hexameric extracellular matrix glycoprotein identified in breast milk and genital fluids that broadly neutralizes HIV-1 via interaction with the HIV-1 Envelope (Env) variable 3 (V3) loop. In this report, we characterize the specific determinants of the interaction between TNC and the HIV-1 Env. We observed that TNC binding and neutralization of HIV-1 is dependent on the TNC fibrinogen-like globe (fbg) and fibronectin-type III (fn) domains, oligomerization, and its newly-mapped glycan structure. Moreover, we observed that TNC-mediated neutralization is also dependent on Env V3 residues 321/322 and 326/327, which surround the IGDIR motif of the V3 loop, as well the N332 glycan, which is critical to the broadly neutralizing activity of glycan-dependent V3-specific antibodies such as PGT128. Our results demonstrate a striking parallel between innate and adaptive immune mechanisms of broad HIV neutralization and provide further insight into the host protein-virus interactions responsible for the natural inefficiency of mucosal HIV-1 transmission.
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Affiliation(s)
- Riley J. Mangan
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Lisa Stamper
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tomoo Ohashi
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Joshua A. Eudailey
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Frederick H. Jaeger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hannah L. Itell
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Brian E. Watts
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Genevieve G. Fouda
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA;,Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA;,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA,Address correspondence to Sallie R. Permar, MD., Ph.D.,
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14
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Kaur A, Itell HL, Ehlinger EP, Varner V, Gantt S, Permar SR. Natural history of postnatal rhesus cytomegalovirus shedding by dams and acquisition by infant rhesus monkeys. PLoS One 2018; 13:e0206330. [PMID: 30356332 PMCID: PMC6200253 DOI: 10.1371/journal.pone.0206330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 07/24/2018] [Accepted: 10/10/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Human infants frequently acquire human cytomegalovirus (HCMV) through breastfeeding, resulting in persistent high-level viral shedding in saliva and urine and infectivity to others, including pregnant women. Thus, vaccination to interrupt postnatal HCMV transmission is an attractive strategy to prevent HCMV spread and congenital infection. Rhesus CMV (RhCMV) in nonhuman primates is a valuable model for the study of immune strategies to prevent CMV transmission. Although rhesus monkeys typically acquire RhCMV before 1 year of age, the timing and mode of natural infant RhCMV transmission remain unknown. METHODS We followed 5 RhCMV-seropositive dams and their infants from birth until weaning, approximately 6 months later. RhCMV DNA levels in plasma, breast milk, saliva, and urine were measured every 2 weeks by quantitative PCR. RhCMV-specific T cell responses in peripheral blood and breast milk were measured by interferon gamma ELISpot assays. Serum IgG antibody levels were measured by ELISA. RESULTS Four of five postpartum RhCMV-seropositive mothers had intermittent, low-level RhCMV shedding in breast milk, whereas all had high-magnitude RhCMV shedding in saliva and urine. The kinetics of maternal blood RhCMV-specific T cell responses and viral shedding in urine and saliva did not strongly associate, though dams with consistently high systemic RhCMV-specific T cell responses tended to have undetectable RhCMV shedding in breast milk. All RhCMV-exposed infants had intermittent, low-level RhCMV shedding in saliva during the lactation period, with minimal systemic RhCMV-specific T cell responses. CONCLUSIONS Despite exposure to RhCMV shedding in breast milk and other maternal fluids, postnatal mother-to-child RhCMV transmission appears to be less efficient than that of HCMV. A greater understanding of the determinants of RhCMV transmission and its usefulness as a model of HCMV mucosal acquisition may provide insight into strategies to prevent HCMV infections in humans.
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Affiliation(s)
- Amitinder Kaur
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, Washington, United States of America
| | - E. Peek Ehlinger
- Alaska Family Medicine Residency, Anchorage, Alaska, United States of America
| | - Valerie Varner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Soren Gantt
- BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sallie R. Permar
- Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
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15
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Itell HL, McGuire EP, Muresan P, Cunningham CK, McFarland EJ, Borkowsky W, Permar SR, Fouda GG. Development and application of a multiplex assay for the simultaneous measurement of antibody responses elicited by common childhood vaccines. Vaccine 2018; 36:5600-5608. [PMID: 30087048 DOI: 10.1016/j.vaccine.2018.07.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 05/15/2018] [Revised: 07/10/2018] [Accepted: 07/18/2018] [Indexed: 11/18/2022]
Abstract
Because vaccine co-administration can affect elicited immune responses, it is important to evaluate new vaccines in the context of pre-existing vaccination schedules. This is particularly necessary for new pediatric vaccines, as the World Health Organization's infant immunization program already schedules several vaccines to be administered during the first months of life. To facilitate the assessment of inter-vaccine interference, we developed a pediatric vaccine multiplex assay (PVMA) to simultaneously measure antibodies against vaccines commonly administered to infants, including hepatitis B, Haemophilus influenzae type B, diphtheria, tetanus, pertussis, rubella, and respiratory syncytial virus (RSV). Comparison of antibody concentrations determined by enzyme-linked immunosorbent assays (ELISAs) and the PVMA demonstrated that the PVMA is highly sensitive, specific, reproducible, and accurate. Moreover, the PVMA requires half the time to assess a cohort compared to ELISAs, and only costs marginally more. Demonstrating the utility of the assay, we employed the PVMA to assess vaccine interference in the setting of a candidate vaccine, using the infant HIV vaccines from the completed Pediatric AIDS Clinical Trials Group (PACTG) protocols 230 and 326 as examples. There was no substantial difference in antibody concentrations between vaccine and placebo recipients, which suggests that HIV vaccination did not disrupt antibody responses elicited by routine pediatric vaccines. Thus, the PVMA is a reliable, high-throughput technique that requires minimal sample volume to measure multiple antibody concentrations concurrently, and is an efficient alternative to ELISAs for the measurement of vaccine-elicited antibody responses in large cohorts.
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Affiliation(s)
| | | | - Petronella Muresan
- Center for Biostatistics in AIDS Research, T.H. Chan Harvard School of Public Health, Boston, MA, USA
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16
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Ram DR, Manickam C, Hueber B, Itell HL, Permar SR, Varner V, Reeves RK. Tracking KLRC2 (NKG2C)+ memory-like NK cells in SIV+ and rhCMV+ rhesus macaques. PLoS Pathog 2018; 14:e1007104. [PMID: 29851983 PMCID: PMC5997355 DOI: 10.1371/journal.ppat.1007104] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 01/23/2018] [Revised: 06/12/2018] [Accepted: 05/15/2018] [Indexed: 01/25/2023] Open
Abstract
Natural killer (NK) cells classically typify the nonspecific effector arm of the innate immune system, but have recently been shown to possess memory-like properties against multiple viral infections, most notably CMV. Expression of the activating receptor NKG2C is elevated on human NK cells in response to infection with CMV as well as HIV, and may delineate cells with memory and memory-like functions. A better understanding of how NKG2C+ NK cells specifically respond to these pathogens could be significantly advanced using nonhuman primate (NHP) models but, to date, it has not been possible to distinguish NKG2C from its inhibitory counterpart, NKG2A, in NHP because of unfaithful antibody cross-reactivity. Using novel RNA-based flow cytometry, we identify for the first time true memory NKG2C+ NK cells in NHP by gene expression (KLRC2), and show that these cells have elevated frequencies and diversify their functional repertoire specifically in response to rhCMV and SIV infections.
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Affiliation(s)
- Daniel R. Ram
- Center for Virology and Vaccine Research (CVVR), Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, United States
| | - Cordelia Manickam
- Center for Virology and Vaccine Research (CVVR), Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, United States
| | - Brady Hueber
- Center for Virology and Vaccine Research (CVVR), Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, United States
| | - Hannah L. Itell
- Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Sallie R. Permar
- Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Valerie Varner
- Center for Virology and Vaccine Research (CVVR), Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, United States
| | - R. Keith Reeves
- Center for Virology and Vaccine Research (CVVR), Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, United States
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachusetts, United States
- * E-mail:
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17
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Itell HL, Nelson CS, Martinez DR, Permar SR. Maternal immune correlates of protection against placental transmission of cytomegalovirus. Placenta 2017; 60 Suppl 1:S73-S79. [PMID: 28456432 PMCID: PMC5650553 DOI: 10.1016/j.placenta.2017.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 02/02/2023]
Abstract
Human cytomegalovirus (HCMV) is the most common congenitally transmitted pathogen worldwide, impacting an estimated 1 million newborns annually. In a subset of infected infants, congenital HCMV causes severe, long-lasting sequelae, including deafness, microcephaly, neurodevelopmental delay, and even death. Accordingly, a maternal vaccine to prevent congenital HCMV infection continues to be a top public health priority. Nevertheless, all vaccines tested to date have failed to meet clinical trial endpoints. Maternal immunity provides partial protection against congenital HCMV transmission, as vertical transmission from seropositive mothers is relatively rare. Therefore, an understanding of the maternal immune correlates of protection against HCMV congenital infection will be critical to inform design of an efficacious maternal vaccine. This review summarizes our understanding of the innate and adaptive immune correlates of protection against congenital transmission of HCMV, and discusses the advantages and applications of a novel nonhuman primate model of congenital CMV transmission to aid in rational vaccine design and evaluation.
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Affiliation(s)
- Hannah L Itell
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Cody S Nelson
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - David R Martinez
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Sallie R Permar
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
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18
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Itell HL, Kaur A, Deere JD, Barry PA, Permar SR. Rhesus monkeys for a nonhuman primate model of cytomegalovirus infections. Curr Opin Virol 2017; 25:126-133. [PMID: 28888133 DOI: 10.1016/j.coviro.2017.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022]
Abstract
Human cytomegalovirus (HCMV) is the leading opportunistic viral infection in solid organ transplant patients and is the most common congenitally transmitted pathogen worldwide. Despite the significant burden of disease HCMV causes in immunosuppressed patients and infected newborns, there are no licensed preventative vaccines or effective immunotherapeutic treatments for HCMV, largely due to our incomplete understanding of the immune correlates of protection against HCMV infection and disease. Though CMV species-specificity imposes an additional challenge in defining a suitable animal model for HCMV, nonhuman primate (NHP) CMVs are the most genetically related to HCMV. In this review, we discuss the advantages and applicability of rhesus monkey models for studying HCMV infections and pathogenesis and ultimately informing vaccine development.
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Affiliation(s)
- Hannah L Itell
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Jesse D Deere
- Center for Comparative Medicine, Department of Pathology and Laboratory Medicine, University of California, Davis, CA, USA
| | - Peter A Barry
- Center for Comparative Medicine, Department of Pathology and Laboratory Medicine, University of California, Davis, CA, USA
| | - Sallie R Permar
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
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19
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Eckdahl TT, Campbell AM, Heyer LJ, Poet JL, Blauch DN, Snyder NL, Atchley DT, Baker EJ, Brown M, Brunner EC, Callen SA, Campbell JS, Carr CJ, Carr DR, Chadinha SA, Chester GI, Chester J, Clarkson BR, Cochran KE, Doherty SE, Doyle C, Dwyer S, Edlin LM, Evans RA, Fluharty T, Frederick J, Galeota-Sprung J, Gammon BL, Grieshaber B, Gronniger J, Gutteridge K, Henningsen J, Isom B, Itell HL, Keffeler EC, Lantz AJ, Lim JN, McGuire EP, Moore AK, Morton J, Nakano M, Pearson SA, Perkins V, Parrish P, Pierson CE, Polpityaarachchige S, Quaney MJ, Slattery A, Smith KE, Spell J, Spencer M, Taye T, Trueblood K, Vrana CJ, Whitesides ET. Programmed evolution for optimization of orthogonal metabolic output in bacteria. PLoS One 2015; 10:e0118322. [PMID: 25714374 PMCID: PMC4340930 DOI: 10.1371/journal.pone.0118322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 09/10/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in energy, pharmaceuticals, chemical commodities, biomining, and bioremediation.
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Affiliation(s)
- Todd T. Eckdahl
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
- * E-mail:
| | - A. Malcolm Campbell
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Laurie J. Heyer
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Jeffrey L. Poet
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - David N. Blauch
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America
| | - Nicole L. Snyder
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America
| | - Dustin T. Atchley
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erich J. Baker
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Micah Brown
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Elizabeth C. Brunner
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sean A. Callen
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jesse S. Campbell
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Caleb J. Carr
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - David R. Carr
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Spencer A. Chadinha
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Grace I. Chester
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Josh Chester
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Ben R. Clarkson
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kelly E. Cochran
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Shannon E. Doherty
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Catherine Doyle
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sarah Dwyer
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Linnea M. Edlin
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Rebecca A. Evans
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Taylor Fluharty
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Janna Frederick
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jonah Galeota-Sprung
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Betsy L. Gammon
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Brandon Grieshaber
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jessica Gronniger
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Katelyn Gutteridge
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Joel Henningsen
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Bradley Isom
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Hannah L. Itell
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erica C. Keffeler
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Andrew J. Lantz
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Jonathan N. Lim
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erin P. McGuire
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Alexander K. Moore
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jerrad Morton
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Meredith Nakano
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sara A. Pearson
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Virginia Perkins
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Phoebe Parrish
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Claire E. Pierson
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Sachith Polpityaarachchige
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Michael J. Quaney
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Abagael Slattery
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kathryn E. Smith
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Jackson Spell
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Morgan Spencer
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Telavive Taye
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kamay Trueblood
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Caroline J. Vrana
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - E. Tucker Whitesides
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
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