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Fong Y, Shen X, Ashley VC, Deal A, Seaton KE, Yu C, Grant SP, Ferrari G, deCamp AC, Bailer RT, Koup RA, Montefiori D, Haynes BF, Sarzotti-Kelsoe M, Graham BS, Carpp LN, Hammer SM, Sobieszczyk M, Karuna S, Swann E, DeJesus E, Mulligan M, Frank I, Buchbinder S, Novak RM, McElrath MJ, Kalams S, Keefer M, Frahm NA, Janes HE, Gilbert PB, Tomaras GD. Modification of the Association Between T-Cell Immune Responses and Human Immunodeficiency Virus Type 1 Infection Risk by Vaccine-Induced Antibody Responses in the HVTN 505 Trial. J Infect Dis 2019; 217:1280-1288. [PMID: 29325070 PMCID: PMC6018910 DOI: 10.1093/infdis/jiy008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 10/19/2017] [Accepted: 01/06/2018] [Indexed: 11/13/2022] Open
Abstract
Background HVTN 505 was a human immunodeficiency virus type 1 (HIV-1) preventive vaccine efficacy trial of a DNA/recombinant adenovirus serotype 5 (rAd5) vaccine regimen. We assessed antibody responses measured 1 month after final vaccination (month 7) as correlates of HIV-1 acquisition risk. Methods Binding antibody responses were quantified in serum samples from 25 primary endpoint vaccine cases (diagnosed with HIV-1 infection between month 7 and month 24) and 125 randomly sampled frequency-matched vaccine controls (HIV-1 negative at month 24). We prespecified for a primary analysis tier 6 antibody response biomarkers that measure immunoglobulin G (IgG) and immunoglobulin A (IgA) binding to Env proteins and 2 previously assessed T-cell response biomarkers. Results Envelope-specific IgG responses were significantly correlated with decreased HIV-1 risk. Moreover, the interaction of IgG responses and Env-specific CD8+ T-cell polyfunctionality score had a highly significant association with HIV-1 risk after adjustment for multiple comparisons. Conclusions Vaccinees with higher levels of Env IgG have significantly decreased HIV-1 risk when CD8+ T-cell responses are low. Moreover, vaccinees with high CD8+ T-cell responses generally have low risk, and those with low CD8+ T-cell and low Env antibody responses have high risk. These findings suggest the critical importance of inducing a robust IgG Env response when the CD8+ T-cell response is low.
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Affiliation(s)
- Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle.,Department of Biostatistics, University of Washington, Seattle
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina
| | - Vicki C Ashley
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina
| | - Aaron Deal
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina
| | - Kelly E Seaton
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina
| | - Chenchen Yu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle
| | - Shannon P Grant
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Surgery, Duke University, Durham, North Carolina.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina
| | - Allan C deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryl
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryl
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Surgery, Duke University, Durham, North Carolina
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Medicine, Duke University, Durham, North Carolina.,Department of Immunology, Duke University, Durham, North Carolina
| | - Marcella Sarzotti-Kelsoe
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Surgery, Duke University, Durham, North Carolina.,Department of Immunology, Duke University, Durham, North Carolina
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryl
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle
| | - Scott M Hammer
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York
| | - Magda Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York
| | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle
| | - Edith Swann
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryl
| | | | - Mark Mulligan
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Ian Frank
- School of Medicine, University of Pennsylvania, Philadelphia
| | - Susan Buchbinder
- Departments of Medicine, Epidemiology and Biostatistics, University of California, San Francisco
| | - Richard M Novak
- Division of Infectious Diseases, University of Illinois at Chicago
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle
| | - Spyros Kalams
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee
| | - Michael Keefer
- University of Rochester Medical Center, Rochester, New York
| | - Nicole A Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle
| | - Holly E Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle.,Department of Biostatistics, University of Washington, Seattle
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, University of Washington, Seattle.,Department of Biostatistics, University of Washington, Seattle
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina.,Department of Surgery, Duke University, Durham, North Carolina.,Department of Immunology, Duke University, Durham, North Carolina.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina
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Eckels J, Nathe C, Nelson EK, Shoemaker SG, Nostrand EV, Yates NL, Ashley VC, Harris LJ, Bollenbeck M, Fong Y, Tomaras GD, Piehler B. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. BMC Bioinformatics 2013; 14:145. [PMID: 23631706 PMCID: PMC3671158 DOI: 10.1186/1471-2105-14-145] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 07/31/2012] [Accepted: 03/27/2013] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials. RESULTS The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. CONCLUSIONS Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license.
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Affiliation(s)
| | | | | | - Sara G Shoemaker
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Nicole L Yates
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Vicki C Ashley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Linda J Harris
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark Bollenbeck
- Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
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