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Gilbert PB, Excler JL, Tomaras GD, Carpp LN, Haynes BF, Liao HX, Montefiori DC, Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Kijak GH, Tovanabutra S, Francis DP, Lee C, Sinangil F, Berman PW, Premsri N, Kunasol P, O’Connell RJ, Michael NL, Robb ML, Morrow R, Corey L, Kim JH. Antibody to HSV gD peptide induced by vaccination does not protect against HSV-2 infection in HSV-2 seronegative women. PLoS One 2017; 12:e0176428. [PMID: 28493891 PMCID: PMC5426618 DOI: 10.1371/journal.pone.0176428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 04/11/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In the HIV-1 vaccine trial RV144, ALVAC-HIV prime with an AIDSVAX® B/E boost reduced HIV-1 acquisition by 31% at 42 months post first vaccination. The bivalent AIDSVAX® B/E vaccine contains two gp120 envelope glycoproteins, one from the subtype B HIV-1 MN isolate and one from the subtype CRF01_AE A244 isolate. Each envelope glycoprotein harbors a highly conserved 27-amino acid HSV-1 glycoprotein D (gD) tag sequence that shares 93% sequence identity with the HSV-2 gD sequence. We assessed whether vaccine-induced anti-gD antibodies protected females against HSV-2 acquisition in RV144. METHODS Of the women enrolled in RV144, 777 vaccine and 807 placebo recipients were eligible and randomly selected according to their pre-vaccination HSV-1 and HSV-2 serostatus for analysis. Immunoglobulin G (IgG) and IgA responses to gD were determined by a binding antibody multiplex assay and HSV-2 serostatus was determined by Western blot analysis. Ninety-three percent and 75% of the vaccine recipients had anti-gD IgG and IgA responses two weeks post last vaccination, respectively. There was no evidence of reduction in HSV-2 infection by vaccination compared to placebo recipients over 78 weeks of follow-up. The annual incidence of HSV-2 infection in individuals who were HSV-2 negative at baseline or HSV-1 positive and HSV-2 indeterminate at baseline were 4.38/100 person-years (py) and 3.28/100 py in the vaccine and placebo groups, respectively. Baseline HSV-1 status did not affect subsequent HSV-2 acquisition. Specifically, the estimated odds ratio of HSV-2 infection by Week 78 for female placebo recipients who were baseline HSV-1 positive (n = 422) vs. negative (n = 1120) was 1.14 [95% confidence interval 0.66 to 1.94, p = 0.64)]. No evidence of reduction in the incidence of HSV-2 infection by vaccination was detected. CONCLUSIONS AIDSVAX® B/E containing gD did not confer protection from HSV-2 acquisition in HSV-2 seronegative women, despite eliciting anti-gD serum antibodies.
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Affiliation(s)
- Peter B. Gilbert
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Jean-Louis Excler
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail: ,
| | - Georgia D. Tomaras
- Duke University Human Vaccine Institute and the Center for HIV/AIDS Vaccine Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Lindsay N. Carpp
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barton F. Haynes
- Duke University Human Vaccine Institute and the Center for HIV/AIDS Vaccine Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hua-Xin Liao
- Duke University Human Vaccine Institute and the Center for HIV/AIDS Vaccine Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Punnee Pitisuttithum
- Vaccine Trial Center, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Jaranit Kaewkungwal
- Center of Excellence for Biomedical and Public Health Informatics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Gustavo H. Kijak
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sodsai Tovanabutra
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Donald P. Francis
- Global Solutions for Infectious Diseases, South San Francisco, California, United States of America
| | - Carter Lee
- Global Solutions for Infectious Diseases, South San Francisco, California, United States of America
| | - Faruk Sinangil
- Global Solutions for Infectious Diseases, South San Francisco, California, United States of America
| | - Phillip W. Berman
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California, United States of America
| | - Nakorn Premsri
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Prayura Kunasol
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Robert J. O’Connell
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Nelson L. Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Rhoda Morrow
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Lawrence Corey
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- HIV Vaccine Trials Network, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jerome H. Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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Janes HE, Cohen KW, Frahm N, De Rosa SC, Sanchez B, Hural J, Magaret CA, Karuna S, Bentley C, Gottardo R, Finak G, Grove D, Shen M, Graham BS, Koup RA, Mulligan MJ, Koblin B, Buchbinder SP, Keefer MC, Adams E, Anude C, Corey L, Sobieszczyk M, Hammer SM, Gilbert PB, McElrath MJ. Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial. J Infect Dis 2017; 215:1376-1385. [PMID: 28199679 PMCID: PMC5853653 DOI: 10.1093/infdis/jix086] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/08/2017] [Indexed: 12/15/2022] Open
Abstract
Background It is important to identify vaccine-induced immune responses that predict the preventative efficacy of a human immunodeficiency virus (HIV)-1 vaccine. We assessed T-cell response markers as correlates of risk in the HIV Vaccine Trials Network (HVTN) 505 HIV-1 vaccine efficacy trial. Methods 2504 participants were randomized to DNA/rAd5 vaccine or placebo, administered at weeks 0, 4, 8, and 24. Peripheral blood mononuclear cells were obtained at week 26 from all 25 primary endpoint vaccine cases and 125 matched vaccine controls, and stimulated with vaccine-insert-matched peptides. Primary variables were total HIV-1-specific CD4+ T-cell magnitude and Env-specific CD4+ polyfunctionality. Four secondary variables were also assessed. Immune responses were evaluated as predictors of HIV-1 infection among vaccinees using Cox proportional hazards models. Machine learning analyses identified immune response combinations best predicting HIV-1 infection. Results We observed an unexpectedly strong inverse correlation between Env-specific CD8+ immune response magnitude and HIV-1 infection risk (hazard ratio [HR] = 0.18 per SD increment; P = .04) and between Env-specific CD8+ polyfunctionality and infection risk (HR = 0.34 per SD increment; P < .01). Conclusions Further research is needed to determine if these immune responses are predictors of vaccine efficacy or markers of natural resistance to HIV-1 infection.
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Affiliation(s)
- Holly E Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Brittany Sanchez
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Carter Bentley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Douglas Grove
- The Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mingchao Shen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | | | - Beryl Koblin
- Laboratory of Infectious Disease Prevention, New York Blood Center, New York
| | - Susan P Buchbinder
- Departments of Medicine and Epidemiology/Biostatistics, University of California San Francisco
| | - Michael C Keefer
- University of Rochester Medical Center, School of Medicine and Dentistry, New York
| | - Elizabeth Adams
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
| | - Chuka Anude
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland; and
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - Magdalena Sobieszczyk
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York
| | - Scott M Hammer
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and
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153
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Huang Y, Zhang L, Ledgerwood J, Grunenberg N, Bailer R, Isaacs A, Seaton K, Mayer KH, Capparelli E, Corey L, Gilbert PB. Population pharmacokinetics analysis of VRC01, an HIV-1 broadly neutralizing monoclonal antibody, in healthy adults. MAbs 2017; 9:792-800. [PMID: 28368743 DOI: 10.1080/19420862.2017.1311435] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The monoclonal antibody VRC01 targets the CD4 binding site of the human immunodeficiency virus (HIV)-1 envelope. In the clinical study HVTN 104 (NCT02165267), 84 HIV-uninfected adults received multiple-dose intravenous (IV) VRC01 (10, 20, 30 or 40 mg/kg) every 4 or 8 weeks or subcutaneous (SC) VRC01 (5 mg/kg) every 2 weeks, and were followed for 32 weeks. We conducted a population pharmacokinetics (popPK) analysis based on 1117 VRC01 serum concentrations using a 2-compartment PK model with first-order elimination; for SC VRC01 a depot compartment with a first-order absorption rate constant was also included. All PK parameters were estimated with acceptable precision. Estimated bioavailability of SC VRC01 was 74%, with peak concentrations occurring 2-3 d after administration. For both IV and SC VRC01, population mean estimates for clearance (CL), central volume of distribution (Vc), inter-compartmental distribution clearance (Q) and peripheral volume of distribution (Vp) were 0.40 L/day, 1.94 L, 0.84 L/day and 4.90 L, respectively; the estimated terminal half-life was 15 d and these were independent of VRC01 dose. Body weight significantly influenced CL (1.2% fold/kg), Vc (1.0% fold/kg), Q (0.69 log(L/day)/kg) and Vp (0.82 log(L)/kg). The developed popPK model, supporting weight-dependent dosing regimens, projected positive trough levels, 5.54 (95% prediction interval: 1.69, 14.5) mcg/mL and 15.9 (5.29, 46.63) mcg/mL, respectively, for the 10 mg/kg and 30 mg/kg 8-weekly regimens being evaluated in ongoing HIV prevention efficacy studies of IV VRC01. These results are critical for future dose-regimen selection and modeling research to identify VRC01 serum concentration levels sufficient for protection against HIV infection.
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Affiliation(s)
- Yunda Huang
- a Vaccine and Infectious Disease Division, Public Health Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA.,b Department of Global Health , University of Washington , Seattle , WA , USA
| | - Lily Zhang
- c Vaccine And Infectious Disease Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Julie Ledgerwood
- d Vaccine Research Center, National Institute of Allergy and Infectious Diseases , Bethesda , MD , USA
| | - Nicole Grunenberg
- c Vaccine And Infectious Disease Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Robert Bailer
- e Vaccine Research Center, National Institute of Allergy and Infectious Diseases , Bethesda , MD , USA
| | - Abby Isaacs
- c Vaccine And Infectious Disease Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Kelly Seaton
- f Duke Human Vaccine Institute, Duke University Medical Center , Durham , NC , USA
| | | | | | - Larry Corey
- c Vaccine And Infectious Disease Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Peter B Gilbert
- a Vaccine and Infectious Disease Division, Public Health Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA.,i Department of Biostatistics , University of Washington , Seattle , WA , USA
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154
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Huang Y, Zhang L, Janes H, Frahm N, Isaacs A, Kim JH, Montefiori D, McElrath MJ, Tomaras GD, Gilbert PB. Predictors of durable immune responses six months after the last vaccination in preventive HIV vaccine trials. Vaccine 2017; 35:1184-1193. [PMID: 28131393 DOI: 10.1016/j.vaccine.2016.09.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 06/09/2016] [Revised: 08/04/2016] [Accepted: 09/21/2016] [Indexed: 11/29/2022]
Abstract
BACKGROUND The evaluation of durable immune responses is important in HIV vaccine research and development. The efficiency of such evaluation could be increased by incorporating predictors of the responses in the statistical analysis. In this paper, we investigated whether and how baseline demographic variables and immune responses measured two weeks after vaccination predicted durable immune responses measured six months later. METHODS We included data from seven preventive HIV vaccine regimens evaluated in three clinical trials: a Phase 1 study of four DNA, NYVAC and/or AIDSVAX vaccine regimens (HVTN096), a Phase 2 study of two DNA and/or MVA vaccine regimens (HVTN205), and a Phase 3 study of a single ALVAC/AIDSVAX regimen (RV144). Regularized random forests and linear regression models were used to identify and evaluate predictors of the positivity and magnitude of durable immune responses. RESULTS We analyzed 201 vaccine recipients with data from 10 to 127 immune response biomarkers, and 3-5 demographic variables. The best prediction of participants' durable response positivity based on two-week responses rendered up to close-to-perfect accuracy; the best prediction of participants' durable response magnitude rendered correlation coefficients between the observed and predicted responses ranging up to 0.91. Though prediction performances differed among biomarkers, durable immune responses were best predicted by the two-week response level of the same biomarker. Adding demographic information and two-week response levels of different biomarkers provided little or no improvement in the predictions. CONCLUSIONS For some biomarkers and for the vaccines we studied, two-week post-vaccination responses can well predict durable responses six months later. Therefore, if immune response durability is only assessed in a sub-sample of vaccine recipients, statistical analyses of durable responses will have increased efficiency by incorporating two-week response data. Further research is needed to generalize the findings to other vaccine regimens and biomarkers. Clinicaltrials.gov identifiers: NCT01799954, NCT00820846, NCT00223080.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Department of Global Health, University of Washington, 1510 San Juan Rd., Seattle, WA 98195, USA.
| | - Lily Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA.
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, 1705 NE Pacific St., Seattle, WA 98195, USA.
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Department of Global Health, University of Washington, 1510 San Juan Rd., Seattle, WA 98195, USA.
| | - Abby Isaacs
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA.
| | - Jerome H Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, MD 20910, USA; International Vaccine Institute, 1 Gwanak-ro, Gwanak-gu, Seoul, South Korea.
| | - David Montefiori
- Duke Human Vaccine Institute, Genome Court, MSRB II, Durham, NC 27710, USA.
| | - M Julie McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Department of Global Health, University of Washington, 1510 San Juan Rd., Seattle, WA 98195, USA; Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA; Department of Medicine, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA.
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Genome Court, MSRB II, Durham, NC 27710, USA.
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, 1705 NE Pacific St., Seattle, WA 98195, USA.
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155
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Aiyegbo MS, Shmelkov E, Dominguez L, Goger M, Battacharya S, deCamp AC, Gilbert PB, Berman PW, Cardozo T. Peptide Targeted by Human Antibodies Associated with HIV Vaccine-Associated Protection Assumes a Dynamic α-Helical Structure. PLoS One 2017; 12:e0170530. [PMID: 28107435 PMCID: PMC5249078 DOI: 10.1371/journal.pone.0170530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 11/14/2016] [Accepted: 01/05/2017] [Indexed: 02/02/2023] Open
Abstract
The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide. α–helical folding was strongly preferred by part of the peptide. A high-throughput structure prediction of this segment in all circulating HIV strains demonstrated that α–helical conformations are preferred by this segment almost universally across all subtypes. Notably, α–helical conformations of this segment of the V2 loop cluster cross-subtype-conserved amino acids on one face of the helix and the variable amino acid positions on the other in a semblance of an amphipathic α–helix. Accordingly, some Abs that protected against HIV in RV144 may have targeted a specific, conserved α–helical peptide epitope in the V2 loop of HIV’s surface envelope glycoprotein.
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Affiliation(s)
- Mohammed S. Aiyegbo
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Evgeny Shmelkov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Lorenzo Dominguez
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Michael Goger
- The New York Structural Biology Center, New York, New York, United States of America
| | - Shibani Battacharya
- The New York Structural Biology Center, New York, New York, United States of America
| | - Allan C. deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Phillip W. Berman
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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156
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Fu R, Gilbert PB. Joint modeling of longitudinal and survival data with the Cox model and two-phase sampling. Lifetime Data Anal 2017; 23:136-159. [PMID: 27007859 PMCID: PMC5035179 DOI: 10.1007/s10985-016-9364-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 03/12/2016] [Indexed: 06/05/2023]
Abstract
A common objective of cohort studies and clinical trials is to assess time-varying longitudinal continuous biomarkers as correlates of the instantaneous hazard of a study endpoint. We consider the setting where the biomarkers are measured in a designed sub-sample (i.e., case-cohort or two-phase sampling design), as is normative for prevention trials. We address this problem via joint models, with underlying biomarker trajectories characterized by a random effects model and their relationship with instantaneous risk characterized by a Cox model. For estimation and inference we extend the conditional score method of Tsiatis and Davidian (Biometrika 88(2):447-458, 2001) to accommodate the two-phase biomarker sampling design using augmented inverse probability weighting with nonparametric kernel regression. We present theoretical properties of the proposed estimators and finite-sample properties derived through simulations, and illustrate the methods with application to the AIDS Clinical Trials Group 175 antiretroviral therapy trial. We discuss how the methods are useful for evaluating a Prentice surrogate endpoint, mediation, and for generating hypotheses about biological mechanisms of treatment efficacy.
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Affiliation(s)
- Rong Fu
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA.
| | - Peter B Gilbert
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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157
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Gilbert PB, Juraska M, deCamp AC, Karuna S, Edupuganti S, Mgodi N, Donnell DJ, Bentley C, Sista N, Andrew P, Isaacs A, Huang Y, Zhang L, Capparelli E, Kochar N, Wang J, Eshleman SH, Mayer KH, Magaret CA, Hural J, Kublin JG, Gray G, Montefiori DC, Gomez MM, Burns DN, McElrath J, Ledgerwood J, Graham BS, Mascola JR, Cohen M, Corey L. Basis and Statistical Design of the Passive HIV-1 Antibody Mediated Prevention (AMP) Test-of-Concept Efficacy Trials. Stat Commun Infect Dis 2017; 9:20160001. [PMID: 29218117 PMCID: PMC5714515 DOI: 10.1515/scid-2016-0001] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Anti-HIV-1 broadly neutralizing antibodies (bnAbs) have been developed as potential agents for prevention of HIV-1 infection. The HIV Vaccine Trials Network and the HIV Prevention Trials Network are conducting the Antibody Mediated Prevention (AMP) trials to assess whether, and how, intravenous infusion of the anti-CD4 binding site bnAb, VRC01, prevents HIV-1 infection. These are the first test-of-concept studies to assess HIV-1 bnAb prevention efficacy in humans. METHODS The AMP trials are two parallel phase 2b HIV-1 prevention efficacy trials conducted in two cohorts: 2700 HIV-uninfected men and transgender persons who have sex with men in the United States, Peru, Brazil, and Switzerland; and 1500 HIV-uninfected sexually active women in seven countries in sub-Saharan Africa. Participants are randomized 1:1:1 to receive an intravenous infusion of 10 mg/kg VRC01, 30 mg/kg VRC01, or a control preparation every 8 weeks for a total of 10 infusions. Each trial is designed (1) to assess overall prevention efficacy (PE) pooled over the two VRC01 dose groups vs. control and (2) to assess VRC01 dose and laboratory markers as correlates of protection (CoPs) against overall and genotype- and phenotype-specific infection. RESULTS Each AMP trial is designed to have 90% power to detect PE > 0% if PE is ≥ 60%. The AMP trials are also designed to identify VRC01 properties (i.e., concentration and effector functions) that correlate with protection and to provide insight into mechanistic CoPs. CoPs are assessed using data from breakthrough HIV-1 infections, including genetic sequences and sensitivities to VRC01-mediated neutralization and Fc effector functions. CONCLUSIONS The AMP trials test whether VRC01 can prevent HIV-1 infection in two study populations. If affirmative, they will provide information for estimating the optimal dosage of VRC01 (or subsequent derivatives) and identify threshold levels of neutralization and Fc effector functions associated with high-level protection, setting a benchmark for future vaccine evaluation and constituting a bridge to other bnAb approaches for HIV-1 prevention.
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Affiliation(s)
- Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Allan C. deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Nyaradzo Mgodi
- University of Zimbabwe – University of California San Francisco Research Program, Harare, Zimbabwe
| | - Deborah J. Donnell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Carter Bentley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Abby Isaacs
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lily Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Edmund Capparelli
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Nidhi Kochar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jing Wang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenneth H. Mayer
- The Fenway Institute, Boston, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Craig A. Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Glenda Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- South African Medical Research Council, Cape Town, South Africa; Perinatal HIV Research Unit, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | | | - Margarita M. Gomez
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - David N. Burns
- Prevention Sciences Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Julie McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Julie Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Myron Cohen
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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158
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Qi L, Sun Y, Gilbert PB. Generalized semiparametric varying-coefficient model for longitudinal data with applications to adaptive treatment randomizations. Biometrics 2016; 73:441-451. [PMID: 27918612 DOI: 10.1111/biom.12626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 09/01/2016] [Accepted: 09/01/2016] [Indexed: 11/30/2022]
Abstract
This article investigates a generalized semiparametric varying-coefficient model for longitudinal data that can flexibly model three types of covariate effects: time-constant effects, time-varying effects, and covariate-varying effects. Different link functions can be selected to provide a rich family of models for longitudinal data. The model assumes that the time-varying effects are unspecified functions of time and the covariate-varying effects are parametric functions of an exposure variable specified up to a finite number of unknown parameters. The estimation procedure is developed using local linear smoothing and profile weighted least squares estimation techniques. Hypothesis testing procedures are developed to test the parametric functions of the covariate-varying effects. The asymptotic distributions of the proposed estimators are established. A working formula for bandwidth selection is discussed and examined through simulations. Our simulation study shows that the proposed methods have satisfactory finite sample performance. The proposed methods are applied to the ACTG 244 clinical trial of HIV infected patients being treated with Zidovudine to examine the effects of antiretroviral treatment switching before and after HIV develops the T215Y/F drug resistance mutation. Our analysis shows benefits of treatment switching to the combination therapies as compared to continuing with ZDV monotherapy before and after developing the 215-mutation.
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Affiliation(s)
- Li Qi
- Biostatistics and Programming, Sanofi, Bridgewater, New Jersey 08807, USA
| | - Yanqing Sun
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, USA
| | - Peter B Gilbert
- Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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159
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Fong Y, Di C, Huang Y, Gilbert PB. Model-robust inference for continuous threshold regression models. Biometrics 2016; 73:452-462. [PMID: 27858965 DOI: 10.1111/biom.12623] [Citation(s) in RCA: 22] [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: 01/01/2016] [Revised: 10/01/2016] [Accepted: 10/01/2016] [Indexed: 11/30/2022]
Abstract
We study threshold regression models that allow the relationship between the outcome and a covariate of interest to change across a threshold value in the covariate. In particular, we focus on continuous threshold models, which experience no jump at the threshold. Continuous threshold regression functions can provide a useful summary of the association between outcome and the covariate of interest, because they offer a balance between flexibility and simplicity. Motivated by collaborative works in studying immune response biomarkers of transmission of infectious diseases, we study estimation of continuous threshold models in this article with particular attention to inference under model misspecification. We derive the limiting distribution of the maximum likelihood estimator, and propose both Wald and test-inversion confidence intervals. We evaluate finite sample performance of our methods, compare them with bootstrap confidence intervals, and provide guidelines for practitioners to choose the most appropriate method in real data analysis. We illustrate the application of our methods with examples from the HIV-1 immune correlates studies.
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Affiliation(s)
- Youyi Fong
- Fred Hutchinson Cancer Research Center, Seattle Washington 98109, U.S.A
| | - Chongzhi Di
- Fred Hutchinson Cancer Research Center, Seattle Washington 98109, U.S.A
| | - Ying Huang
- Fred Hutchinson Cancer Research Center, Seattle Washington 98109, U.S.A
| | - Peter B Gilbert
- Fred Hutchinson Cancer Research Center, Seattle Washington 98109, U.S.A
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160
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Abstract
An objective of randomized placebo-controlled preventive HIV vaccine efficacy (VE) trials is to assess the relationship between vaccine effects to prevent HIV acquisition and continuous genetic distances of the exposing HIVs to multiple HIV strains represented in the vaccine. The set of genetic distances, only observed in failures, is collectively termed the 'mark.' The objective has motivated a recent study of a multivariate mark-specific hazard ratio model in the competing risks failure time analysis framework. Marks of interest, however, are commonly subject to substantial missingness, largely due to rapid post-acquisition viral evolution. In this article, we investigate the mark-specific hazard ratio model with missing multivariate marks and develop two inferential procedures based on (i) inverse probability weighting (IPW) of the complete cases, and (ii) augmentation of the IPW estimating functions by leveraging auxiliary data predictive of the mark. Asymptotic properties and finite-sample performance of the inferential procedures are presented. This research also provides general inferential methods for semiparametric density ratio/biased sampling models with missing data. We apply the developed procedures to data from the HVTN 502 'Step' HIV VE trial.
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Affiliation(s)
- Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mail Stop M2-C200, Seattle, WA, 98109, USA.
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, and Department of Biostatistics, University of Washington, 1100 Fairview Avenue North, Mail Stop M2-C200, Seattle, WA, 98109, USA
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161
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Churchyard G, Mlisana K, Karuna S, Williamson AL, Williamson C, Morris L, Tomaras GD, De Rosa SC, Gilbert PB, Gu N, Yu C, Mkhize NN, Hermanus T, Allen M, Pensiero M, Barnett SW, Gray G, Bekker LG, Montefiori DC, Kublin J, Corey L. Sequential Immunization with gp140 Boosts Immune Responses Primed by Modified Vaccinia Ankara or DNA in HIV-Uninfected South African Participants. PLoS One 2016; 11:e0161753. [PMID: 27583368 PMCID: PMC5008759 DOI: 10.1371/journal.pone.0161753] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 02/16/2016] [Accepted: 08/08/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The safety and immunogenicity of SAAVI DNA-C2 (4 mg IM), SAAVI MVA-C (2.9 x 109 pfu IM) and Novartis V2-deleted subtype C gp140 (100 mcg) with MF59 adjuvant in various vaccination regimens was evaluated in HIV-uninfected adults in South Africa. METHODS Participants at three South African sites were randomized (1:1:1:1) to one of four vaccine regimens: MVA prime, sequential gp140 protein boost (M/M/P/P); concurrent MVA/gp140 (MP/MP); DNA prime, sequential MVA boost (D/D/M/M); DNA prime, concurrent MVA/gp140 boost (D/D/MP/MP) or placebo. Peak HIV specific humoral and cellular responses were measured. RESULTS 184 participants were enrolled: 52% were female, all were Black/African, median age was 23 years (range, 18-42 years) and 79% completed all vaccinations. 159 participants reported at least one adverse event, 92.5% were mild or moderate. Five, unrelated, serious adverse events were reported. The M/M/P/P and D/D/MP/MP regimens induced the strongest peak neutralizing and binding antibody responses and the greatest CD4+ T-cell responses to Env. All peak neutralizing and binding antibody responses decayed with time. The MVA, but not DNA, prime contributed to the humoral and cellular immune responses. The D/D/M/M regimen was poorly immunogenic overall but did induce modest CD4+ T-cell responses to Gag and Pol. CD8+ T-cell responses to any antigen were low for all regimens. CONCLUSIONS The SAAVI DNA-C2, SAAVI MVA-C and Novartis gp140 with MF59 adjuvant in various combinations were safe and induced neutralizing and binding antibodies and cellular immune responses. Sequential immunization with gp140 boosted immune responses primed by MVA or DNA. The best overall immune responses were seen with the M/M/P/P regimen. TRIAL REGISTRATION ClinicalTrials.gov NCT01418235.
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Affiliation(s)
- Gavin Churchyard
- Aurum Institute for Health Research, Klerksdorp, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa
- Advancing Care and Treatment for TB and HIV, Medical Research Council Collaborating Centre, Klerksdorp, South Africa
| | | | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Services, Observatory, Cape Town, South Africa
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Services, Observatory, Cape Town, South Africa
| | - Lynn Morris
- National Institute for Communicable Diseases, National Health Laboratory Services, Sandringham, Johannesburg, South Africa
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Niya Gu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Chenchen Yu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Nonhlanhla N. Mkhize
- National Institute for Communicable Diseases, National Health Laboratory Services, Sandringham, Johannesburg, South Africa
| | - Tandile Hermanus
- National Institute for Communicable Diseases, National Health Laboratory Services, Sandringham, Johannesburg, South Africa
| | - Mary Allen
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Michael Pensiero
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Susan W. Barnett
- Novartis Vaccines and Diagnostics, Cambridge, MA, United States of America
| | - Glenda Gray
- South African Medical Research Council, Cape Town, South Africa
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David C. Montefiori
- Laboratory for AIDS Vaccine Research and Development, Duke University Medical Center, Durham, NC, United States of America
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States of America
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162
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Prentice HA, Tomaras GD, Geraghty DE, Apps R, Fong Y, Ehrenberg PK, Rolland M, Kijak GH, Krebs SJ, Nelson W, DeCamp A, Shen X, Yates NL, Zolla-Pazner S, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Ferrari G, McElrath MJ, Montefiori DC, Bailer RT, Koup RA, O'Connell RJ, Robb ML, Michael NL, Gilbert PB, Kim JH, Thomas R. HLA class II genes modulate vaccine-induced antibody responses to affect HIV-1 acquisition. Sci Transl Med 2016; 7:296ra112. [PMID: 26180102 DOI: 10.1126/scitranslmed.aab4005] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [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]
Abstract
In the RV144 vaccine trial, two antibody responses were found to correlate with HIV-1 acquisition. Because human leukocyte antigen (HLA) class II-restricted CD4(+) T cells are involved in antibody production, we tested whether HLA class II genotypes affected HIV-1-specific antibody levels and HIV-1 acquisition in 760 individuals. Indeed, antibody responses correlated with acquisition only in the presence of single host HLA alleles. Envelope (Env)-specific immunoglobulin A (IgA) antibodies were associated with increased risk of acquisition specifically in individuals with DQB1*06. IgG antibody responses to Env amino acid positions 120 to 204 were higher and were associated with decreased risk of acquisition and increased vaccine efficacy only in the presence of DPB1*13. Screening IgG responses to overlapping peptides spanning Env 120-204 and viral sequence analysis of infected individuals defined differences in vaccine response that were associated with the presence of DPB1*13 and could be responsible for the protection observed. Overall, the underlying genetic findings indicate that HLA class II modulated the quantity, quality, and efficacy of antibody responses in the RV144 trial.
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Affiliation(s)
- Heather A Prentice
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard Apps
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Wyatt Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Allan DeCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicole L Yates
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Susan Zolla-Pazner
- Veterans Affairs New York Harbor Healthcare System and the Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Sorachai Nitayaphan
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute Medical Sciences, Bangkok 10400, Thailand
| | - Supachai Rerks-Ngarm
- Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Jaranit Kaewkungwal
- Center of Excellence for Biomedical and Public Health Informatics (BIOPHICS), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Punnee Pitisuttithum
- Vaccine Trial Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert J O'Connell
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute Medical Sciences, Bangkok 10400, Thailand
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20818, USA.
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163
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Gilbert PB, Janes HE, Huang Y. Power/sample size calculations for assessing correlates of risk in clinical efficacy trials. Stat Med 2016; 35:3745-59. [PMID: 27037797 DOI: 10.1002/sim.6952] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 11/07/2022]
Abstract
In a randomized controlled clinical trial that assesses treatment efficacy, a common objective is to assess the association of a measured biomarker response endpoint with the primary study endpoint in the active treatment group, using a case-cohort, case-control, or two-phase sampling design. Methods for power and sample size calculations for such biomarker association analyses typically do not account for the level of treatment efficacy, precluding interpretation of the biomarker association results in terms of biomarker effect modification of treatment efficacy, with detriment that the power calculations may tacitly and inadvertently assume that the treatment harms some study participants. We develop power and sample size methods accounting for this issue, and the methods also account for inter-individual variability of the biomarker that is not biologically relevant (e.g., due to technical measurement error). We focus on a binary study endpoint and on a biomarker subject to measurement error that is normally distributed or categorical with two or three levels. We illustrate the methods with preventive HIV vaccine efficacy trials and include an R package implementing the methods. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Peter B Gilbert
- Vaccine and Infectious Disease and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, 98109, Washington, U.S.A
| | - Holly E Janes
- Vaccine and Infectious Disease and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, 98109, Washington, U.S.A
| | - Yunda Huang
- Vaccine and Infectious Disease and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, 98109, Washington, U.S.A
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164
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Peng X, Li SS, Gilbert PB, Geraghty DE, Katze MG. FCGR2C Polymorphisms Associated with HIV-1 Vaccine Protection Are Linked to Altered Gene Expression of Fc-γ Receptors in Human B Cells. PLoS One 2016; 11:e0152425. [PMID: 27015273 PMCID: PMC4807760 DOI: 10.1371/journal.pone.0152425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 01/02/2016] [Accepted: 03/14/2016] [Indexed: 11/19/2022] Open
Abstract
The phase III Thai RV144 vaccine trial showed an estimated vaccine efficacy (VE) to prevent HIV-1 infection of 31.2%, which has motivated the search for immune correlates of vaccine protection. In a recent report, several single nucleotide polymorphisms (SNPs) in FCGR2C were identified to associate with the level of VE in the RV144 trial. To investigate the functional significance of these SNPs, we utilized a large scale B cell RNA sequencing database of 462 individuals from the 1000 Genomes Project to examine associations between FCGR2C SNPs and gene expression. We found that the FCGR2C SNPs that associated with vaccine efficacy in RV144 also strongly associated with the expression of FCGR2A/C and one of them also associated with the expression of Fc receptor-like A (FCRLA), another Fc-γ receptor (FcγR) gene that was not examined in the previous report. These results suggest that the expression of FcγR genes is influenced by these SNPs either directly or in linkage with other causal variants. More importantly, these results motivate further investigations into the potential for a causal association of expression and alternative splicing of FCGR2C and other FcγR genes with the HIV-1 vaccine protection in the RV144 trial and other similar studies.
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Affiliation(s)
- Xinxia Peng
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Shuying S. Li
- Department of Biostatistics, Bioinformatics, and Epidemiology, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Department of Biostatistics, Bioinformatics, and Epidemiology, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael G. Katze
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, United States of America
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165
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Fiore-Gartland A, Manso BA, Friedrich DP, Gabriel EE, Finak G, Moodie Z, Hertz T, De Rosa SC, Frahm N, Gilbert PB, McElrath MJ. Pooled-Peptide Epitope Mapping Strategies Are Efficient and Highly Sensitive: An Evaluation of Methods for Identifying Human T Cell Epitope Specificities in Large-Scale HIV Vaccine Efficacy Trials. PLoS One 2016; 11:e0147812. [PMID: 26863315 PMCID: PMC4749288 DOI: 10.1371/journal.pone.0147812] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 09/04/2015] [Accepted: 11/22/2015] [Indexed: 11/19/2022] Open
Abstract
The interferon gamma, enzyme-linked immunospot (IFN-γ ELISpot) assay is widely used to identify viral antigen-specific T cells is frequently employed to quantify T cell responses in HIV vaccine studies. It can be used to define T cell epitope specificities using panels of peptide antigens, but with sample and cost constraints there is a critical need to improve the efficiency of epitope mapping for large and variable pathogens. We evaluated two epitope mapping strategies, based on group testing, for their ability to identify vaccine-induced T-cells from participants in the Step HIV-1 vaccine efficacy trial, and compared the findings to an approach of assaying each peptide individually. The group testing strategies reduced the number of assays required by >7-fold without significantly altering the accuracy of T-cell breadth estimates. Assays of small pools containing 7–30 peptides were highly sensitive and effective at detecting single positive peptides as well as summating responses to multiple peptides. Also, assays with a single 15-mer peptide, containing an identified epitope, did not always elicit a response providing validation that 15-mer peptides are not optimal antigens for detecting CD8+ T cells. Our findings further validate pooling-based epitope mapping strategies, which are critical for characterizing vaccine-induced T-cell responses and more broadly for informing iterative vaccine design. We also show ways to improve their application with computational peptide:MHC binding predictors that can accurately identify the optimal epitope within a 15-mer peptide and within a pool of 15-mer peptides.
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Affiliation(s)
- Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
- * E-mail:
| | - Bryce A. Manso
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - David P. Friedrich
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - Erin E. Gabriel
- Biostatistics Research Branch, National Institute of Allergy and Infectious Disease, Rockville, Maryland, 20852, United States of America
| | - Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - Tomer Hertz
- Shraga Segal Department of Microbiology, Immunology and Genetics, Ben Gurion Institute of the Negev, Beer-Sheva, 84105, Israel
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, United States of America
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166
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Huang Y, DiazGranados C, Janes H, Huang Y, deCamp AC, Metch B, Grant S, Sanchez B, Phogat S, Koutsoukos M, Kanesa-Thasan N, Bourguignon P, Collard A, Buchbinder S, Tomaras GD, McElrath J, Gray G, Kublin JG, Corey L, Gilbert PB. Selection of HIV vaccine candidates for concurrent testing in an efficacy trial. Curr Opin Virol 2016; 17:57-65. [PMID: 26827165 DOI: 10.1016/j.coviro.2016.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/22/2015] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
Abstract
Phase IIb or III HIV-1 vaccine efficacy trials are generally large and operationally challenging. To mitigate this challenge, the HIV Vaccine Trials Network is designing a Phase IIb efficacy trial accommodating the evaluation of multiple vaccine regimens concurrently. As this efficacy trial would evaluate a limited number of vaccine regimens, there is a need to develop a framework for optimizing the strategic selection of regimens from the large number of vaccine candidates tested in Phase I/IIa trials. In this paper we describe the approaches for the selection process, including the choice of immune response endpoints and the statistical criteria and algorithms. We illustrate the selection approaches using data from HIV-1 vaccine trials.
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Affiliation(s)
- Ying Huang
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
| | | | - Holly Janes
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yunda Huang
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Allan C deCamp
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Barbara Metch
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Shannon Grant
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Brittany Sanchez
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | | | | | | | | | | | - Susan Buchbinder
- Department of Medicine and Epidemiology/Biostatistics, UCSF, San Francisco, CA, United States
| | - Georgia D Tomaras
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | - Julie McElrath
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Glenda Gray
- Perinatnal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - James G Kublin
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Lawrence Corey
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Peter B Gilbert
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
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Gilbert PB, Huang Y. Predicting Overall Vaccine Efficacy in a New Setting by Re-Calibrating Baseline Covariate and Intermediate Response Endpoint Effect Modifiers of Type-Specific Vaccine Efficacy. ACTA ACUST UNITED AC 2016; 5:93-112. [PMID: 28154793 DOI: 10.1515/em-2015-0007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We develop a transport formula for predicting overall cumulative vaccine efficacy through time t (VE(t)) to prevent clinically significant infection with a genetically diverse pathogen (e.g., HIV infection) in a new setting for which a Phase III preventive vaccine efficacy trial that would directly estimate VE(t) has not yet been conducted. The formula integrates data from (1) a previous Phase III trial, (2) a Phase I/II immune response biomarker endpoint trial in the new setting where a follow-up Phase III trial is planned, (3) epidemiological data on background HIV infection incidence in the new setting; and (4) genomic epidemiological data on HIV sequence distributions in the previous and new settings. For (1), the randomized vaccine versus placebo Phase III trial yields estimates of vaccine efficacy to prevent particular genotypes of HIV in participant subgroups defined by baseline covariates X and immune responses to vaccination S(1) measured at a fixed time point τ (potential outcomes if assigned vaccine); often one or more immune responses to vaccination are available that modify genotype-specific vaccine efficacy. The formula focuses on subgroups defined by X and S(1) and being at-risk for HIV infection at τ under both the vaccine and placebo treatment assignments. For (2), the Phase I/II trial tests the same vaccine in a new setting, or a refined new vaccine in the same or new setting, and measures the same baseline covariates and immune responses as the original Phase III trial. For (3), epidemiological data in the new setting are used to project overall background HIV infection rates in the baseline covariate subgroups in the planned Phase III trial, hence re-calibrating for HIV incidence differences in the two settings; whereas for (4), data bases of HIV sequences measured from HIV infected individuals are used to re-calibrate for differences in the distributions of the circulating HIV genotypes in the two settings. The transport formula incorporates a user-specified bridging assumption function that measures differences in HIV genotype-specific conditional biological-susceptibility vaccine efficacies in the two settings, facilitating a sensitivity analysis. We illustrate the transport formula with application to HIV Vaccine Trials Network (HVTN) research. One application of the transport formula is to use predicted VE(t) as a rational criterion for ranking a set of candidate vaccines being studied in Phase I/II trials for their priority for down-selection into the follow-up Phase III trial.
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Affiliation(s)
- Peter B Gilbert
- Vaccine and Infectious Disease and Public Health Science Divisions, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, U.S.A; Department of Biostatistics, University of Washington, Seattle, Washington, 98105, U.S.A
| | - Ying Huang
- Vaccine and Infectious Disease and Public Health Science Divisions, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, U.S.A; Department of Biostatistics, University of Washington, Seattle, Washington, 98105, U.S.A
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168
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Abstract
Motivated by the need to assess HIV vaccine efficacy, previous studies proposed an extension of the discrete competing risks proportional hazards model, in which the cause of failure is replaced by a continuous mark only observed at the failure time. However the model assumptions may fail in several ways, and no diagnostic testing procedure for this situation has been proposed. A goodness-of-fit test procedure for the stratified mark-specific proportional hazards model in which the regression parameters depend nonparametrically on the mark and the baseline hazards depends nonparametrically on both time and the mark is proposed. The test statistics are constructed based on the weighted cumulative mark-specific martingale residuals. The critical values of the proposed test statistics are approximated using the Gaussian multiplier method. The performance of the proposed tests are examined extensively in simulations for a variety of the models under the null hypothesis and under different types of alternative models. An analysis of the 'Step' HIV vaccine efficacy trial using the proposed method is presented. The analysis suggests that the HIV vaccine candidate may increase susceptibility to HIV acquisition.
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Affiliation(s)
- Yanqing Sun
- Department of Mathematics and Statistics University of North Carolina at Charlotte, Charlotte, NC 28223
| | - Mei Li
- School of Public Health Zhejiang University, Hangzhou, China
| | - Peter B Gilbert
- Department of Biostatistics, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98109
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169
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Affiliation(s)
- Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; University of Washington, Seattle, WA, USA.
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; University of Washington, Seattle, WA, USA
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170
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Neafsey DE, Juraska M, Bedford T, Benkeser D, Valim C, Griggs A, Lievens M, Abdulla S, Adjei S, Agbenyega T, Agnandji ST, Aide P, Anderson S, Ansong D, Aponte JJ, Asante KP, Bejon P, Birkett AJ, Bruls M, Connolly KM, D'Alessandro U, Dobaño C, Gesase S, Greenwood B, Grimsby J, Tinto H, Hamel MJ, Hoffman I, Kamthunzi P, Kariuki S, Kremsner PG, Leach A, Lell B, Lennon NJ, Lusingu J, Marsh K, Martinson F, Molel JT, Moss EL, Njuguna P, Ockenhouse CF, Ogutu BR, Otieno W, Otieno L, Otieno K, Owusu-Agyei S, Park DJ, Pellé K, Robbins D, Russ C, Ryan EM, Sacarlal J, Sogoloff B, Sorgho H, Tanner M, Theander T, Valea I, Volkman SK, Yu Q, Lapierre D, Birren BW, Gilbert PB, Wirth DF. Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine. N Engl J Med 2015; 373:2025-2037. [PMID: 26488565 PMCID: PMC4762279 DOI: 10.1056/nejmoa1505819] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND The RTS,S/AS01 vaccine targets the circumsporozoite protein of Plasmodium falciparum and has partial protective efficacy against clinical and severe malaria disease in infants and children. We investigated whether the vaccine efficacy was specific to certain parasite genotypes at the circumsporozoite protein locus. METHODS We used polymerase chain reaction-based next-generation sequencing of DNA extracted from samples from 4985 participants to survey circumsporozoite protein polymorphisms. We evaluated the effect that polymorphic positions and haplotypic regions within the circumsporozoite protein had on vaccine efficacy against first episodes of clinical malaria within 1 year after vaccination. RESULTS In the per-protocol group of 4577 RTS,S/AS01-vaccinated participants and 2335 control-vaccinated participants who were 5 to 17 months of age, the 1-year cumulative vaccine efficacy was 50.3% (95% confidence interval [CI], 34.6 to 62.3) against clinical malaria in which parasites matched the vaccine in the entire circumsporozoite protein C-terminal (139 infections), as compared with 33.4% (95% CI, 29.3 to 37.2) against mismatched malaria (1951 infections) (P=0.04 for differential vaccine efficacy). The vaccine efficacy based on the hazard ratio was 62.7% (95% CI, 51.6 to 71.3) against matched infections versus 54.2% (95% CI, 49.9 to 58.1) against mismatched infections (P=0.06). In the group of infants 6 to 12 weeks of age, there was no evidence of differential allele-specific vaccine efficacy. CONCLUSIONS These results suggest that among children 5 to 17 months of age, the RTS,S vaccine has greater activity against malaria parasites with the matched circumsporozoite protein allele than against mismatched malaria. The overall vaccine efficacy in this age category will depend on the proportion of matched alleles in the local parasite population; in this trial, less than 10% of parasites had matched alleles. (Funded by the National Institutes of Health and others.).
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171
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Gilbert PB, Gabriel EE, Hudgens MG, Miao X, Li X, Su SC, Parrino J, Chan ISF. Reply to Dunning. J Infect Dis 2015; 212:1521-3. [PMID: 25985906 DOI: 10.1093/infdis/jiv287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/12/2022] Open
Affiliation(s)
- Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center and Department of Biostatistics, University of Washington
| | - Erin E Gabriel
- National Institute of Allergy and Infectious Diseases, Biostatistics Research Branch, Bethesda, Maryland
| | - Michael G Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | | | - Xiaoming Li
- Biostatistics, Gilead Sciences, Seattle, Washington
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172
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Abstract
The partial efficacy reported in the RV144 HIV vaccine trial in 2009 has driven the HIV vaccine field to define correlates of risk associated with HIV-1 acquisition and connect these functionally to preventing HIV infection. Immunological correlates, mainly including CD4(+) T cell responses to the HIV envelope and Fc-mediated antibody effector function, have been connected to reduced acquisition. These immunological correlates place immunological and genetic pressure on the virus. Indeed, antibodies directed at conserved regions of the V1V2 loop and antibodies that mediate antibody-dependent cellular cytotoxicity to HIV envelope in the absence of inhibiting serum immunoglobulin A antibodies correlated with decreased HIV risk. More recently, researchers have expanded their search with nonhuman primate studies using vaccine regimens that differ from that used in RV144; these studies indicate that non-neutralizing antibodies are associated with protection from experimental lentivirus challenge as well. These immunological correlates have provided the basis for the design of a next generation of vaccine regimens to improve upon the qualitative and quantitative degree of magnitude of these immune responses on HIV acquisition.
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Affiliation(s)
- Lawrence Corey
- HIV Vaccine Trials Network, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Peter B Gilbert
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Giuseppe Pantaleo
- Lausanne University Hospital and Swiss Vaccine Research Institute, Lausanne 1011, Switzerland
| | - Anthony S Fauci
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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173
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Moodie Z, Metch B, Bekker LG, Churchyard G, Nchabeleng M, Mlisana K, Laher F, Roux S, Mngadi K, Innes C, Mathebula M, Allen M, Bentley C, Gilbert PB, Robertson M, Kublin J, Corey L, Gray GE. Continued Follow-Up of Phambili Phase 2b Randomized HIV-1 Vaccine Trial Participants Supports Increased HIV-1 Acquisition among Vaccinated Men. PLoS One 2015; 10:e0137666. [PMID: 26368824 PMCID: PMC4569275 DOI: 10.1371/journal.pone.0137666] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 06/02/2015] [Accepted: 08/19/2015] [Indexed: 12/14/2022] Open
Abstract
Background The Phase 2b double-blinded, randomized Phambili/HVTN 503 trial evaluated safety and efficacy of the MRK Ad5 gag/pol/nef subtype B HIV-1 preventive vaccine vs placebo in sexually active HIV-1 seronegative participants in South Africa. Enrollment and vaccinations stopped and participants were unblinded but continued follow-up when the Step study evaluating the same vaccine in the Americas, Caribbean, and Australia was unblinded for non-efficacy. Final Phambili analyses found more HIV-1 infections amongst vaccine than placebo recipients, impelling the HVTN 503-S recall study. Methods HVTN 503-S sought to enroll all 695 HIV-1 uninfected Phambili participants, provide HIV testing, risk reduction counseling, physical examination, risk behavior assessment and treatment assignment recall. After adding HVTN 503-S data, HIV-1 infection hazard ratios (HR vaccine vs. placebo) were estimated by Cox models. Results Of the 695 eligible, 465 (67%) enrolled with 230 from the vaccine group and 235 from the placebo group. 38% of the 184 Phambili dropouts were enrolled. Enrollment did not differ by treatment group, gender, or baseline HSV-2. With the additional 1286 person years of 503-S follow-up, the estimated HR over Phambili and HVTN 503-S follow-up was 1.52 (95% CI 1.08–2.15, p = 0.02, 82 vaccine/54 placebo infections). The HR was significant for men (HR = 2.75, 95% CI 1.49, 5.06, p = 0.001) but not for women (HR = 1.12, 95% CI 0.73, 1.72, p = 0.62). Conclusion The additional follow-up from HVTN 503-S supported the Phambili finding of increased HIV-1 acquisition among vaccinated men and strengthened the evidence of lack of vaccine effect among women. Trial Registration clinicaltrials.gov NCT00413725 SA National Health Research Database DOH-27-0207-1539
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Affiliation(s)
- Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Barbara Metch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Linda-Gail Bekker
- Desmond Tutu HIV Foundation, University of Cape Town, Cape Town, South Africa
| | - Gavin Churchyard
- Aurum Institute for Health Research, Johannesburg, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Maphoshane Nchabeleng
- Mecru Clinical Research Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Koleka Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, Durban, South Africa
| | - Fatima Laher
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Surita Roux
- Desmond Tutu HIV Foundation, University of Cape Town, Cape Town, South Africa
| | - Kathryn Mngadi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal and National Health Laboratory Service, Durban, South Africa
| | - Craig Innes
- Aurum Institute Clinical Research Site, Klerksdorp, South Africa
| | - Matsontso Mathebula
- Mecru Clinical Research Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Mary Allen
- Vaccine Research Program, Division of AIDS, NIAID, NIH, Rockville, United States of America
| | - Carter Bentley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Robertson
- Merck Research Laboratories, West Point, Pennsylvania, United States of America
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Glenda E. Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Cape Town, South Africa
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174
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Huang Y, Follmann D, Nason M, Zhang L, Huang Y, Mehrotra DV, Moodie Z, Metch B, Janes H, Keefer MC, Churchyard G, Robb ML, Fast PE, Duerr A, McElrath MJ, Corey L, Mascola JR, Graham BS, Sobieszczyk ME, Kublin JG, Robertson M, Hammer SM, Gray GE, Buchbinder SP, Gilbert PB. Effect of rAd5-Vector HIV-1 Preventive Vaccines on HIV-1 Acquisition: A Participant-Level Meta-Analysis of Randomized Trials. PLoS One 2015; 10:e0136626. [PMID: 26332672 PMCID: PMC4558095 DOI: 10.1371/journal.pone.0136626] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/05/2015] [Indexed: 11/28/2022] Open
Abstract
Background Three phase 2b, double-blind, placebo-controlled, randomized efficacy trials have tested recombinant Adenovirus serotype-5 (rAd5)-vector preventive HIV-1 vaccines: MRKAd5 HIV-1 gag/pol/nef in Step and Phambili, and DNA/rAd5 HIV-1 env/gag/pol in HVTN505. Due to efficacy futility observed at the first interim analysis in Step and HVTN505, participants of all three studies were unblinded to their vaccination assignments during the study but continued follow–up. Rigorous meta-analysis can provide crucial information to advise the future utility of rAd5-vector vaccines. Methods We included participant-level data from all three efficacy trials, and three Phase 1–2 trials evaluating the HVTN505 vaccine regimen. We predefined two co-primary analysis cohorts for assessing the vaccine effect on HIV-1 acquisition. The modified-intention-to-treat (MITT) cohort included all randomly assigned participants HIV-1 uninfected at study entry, who received at least the first vaccine/placebo, and the Ad5 cohort included MITT participants who received at least one dose of rAd5-HIV vaccine or rAd5-placebo. Multivariable Cox regression models were used to estimate hazard ratios (HRs) of HIV-1 infection (vaccine vs. placebo) and evaluate HR variation across vaccine regimens, time since vaccination, and subgroups using interaction tests. Findings Results are similar for the MITT and Ad5 cohorts; we summarize MITT cohort results. Pooled across the efficacy trials, over all follow-up time 403 (n = 224 vaccine; n = 179 placebo) of 6266 MITT participants acquired HIV-1, with a non-significantly higher incidence in vaccine recipients (HR 1.21, 95% CI 0.99–1.48, P = 0.06). The HRs significantly differed by vaccine regimen (interaction P = 0.03; MRKAd5 HR 1.41, 95% CI 1.11–1.78, P = 0.005 vs. DNA/rAd5 HR 0.88, 95% CI 0.61–1.26, P = 0.48). Results were similar when including the Phase 1–2 trials. Exploratory analyses based on the efficacy trials supported that the MRKAd5 vaccine-increased risk was concentrated in Ad5-positive or uncircumcised men early in follow-up, and in Ad5-negative or circumcised men later. Overall, MRKAd5 vaccine-increased risk was evident across subgroups except in circumcised Ad5-negative men (HR 0.97, 95% CI 0.58−1.63, P = 0.91); there was little evidence that the DNA/rAd5 vaccine, that was tested in this subgroup, increased risk (HR 0.88, 95% CI 0.61–1.26, P = 0.48). When restricting the analysis of Step and Phambili to follow-up time before unblinding, 114 (n = 65 vaccine; n = 49 placebo) of 3770 MITT participants acquired HIV-1, with a non-significantly higher incidence in MRKAd5 vaccine recipients (HR 1.30, 95% CI 0.89–1.14, P = 0.18). Interpretation and Significance The data support increased risk of HIV-1 infection by MRKAd5 over all follow-up time, but do not support increased risk of HIV-1 infection by DNA/rAd5. This study provides a rationale for including monitoring plans enabling detection of increased susceptibility to infection in HIV-1 at-risk populations.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Dean Follmann
- National Institute of Allergy and Infectious Diseases and Biostatistics Research Branch, National Institutes of Health, Bethesda, MD, United States of America
| | - Martha Nason
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Lily Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Devan V. Mehrotra
- Merck Research Laboratories, North Wales, PA, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barbara Metch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael C. Keefer
- Infectious Disease Division, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| | | | - Merlin L. Robb
- HJF HIV Program, US Military HIV Research Program, Bethesda, MD, United States of America
| | - Patricia E. Fast
- Research and Development, International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Ann Duerr
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Barney S. Graham
- Viral Pathogenesis Laboratory, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Magdalena E. Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Robertson
- Infectious Disease Clinical Research, Merck, Philadelphia, Pennsylvania, United States of America
| | - Scott M. Hammer
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
| | - Glenda E. Gray
- University of the Witwatersrand, Johannesburg, South Africa
| | - Susan P. Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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175
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Gilbert PB, Gabriel EE, Huang Y, Chan IS. Surrogate Endpoint Evaluation: Principal Stratification Criteria and the Prentice Definition. J Causal Inference 2015; 3:157-175. [PMID: 26722639 PMCID: PMC4692254 DOI: 10.1515/jci-2014-0007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A common problem of interest within a randomized clinical trial is the evaluation of an inexpensive response endpoint as a valid surrogate endpoint for a clinical endpoint, where a chief purpose of a valid surrogate is to provide a way to make correct inferences on clinical treatment effects in future studies without needing to collect the clinical endpoint data. Within the principal stratification framework for addressing this problem based on data from a single randomized clinical efficacy trial, a variety of definitions and criteria for a good surrogate endpoint have been proposed, all based on or closely related to the "principal effects" or "causal effect predictiveness (CEP)" surface. We discuss CEP-based criteria for a useful surrogate endpoint, including (1) the meaning and relative importance of proposed criteria including average causal necessity (ACN), average causal sufficiency (ACS), and large clinical effect modification; (2) the relationship between these criteria and the Prentice definition of a valid surrogate endpoint; and (3) the relationship between these criteria and the consistency criterion (i.e., assurance against the "surrogate paradox"). This includes the result that ACN plus a strong version of ACS generally do not imply the Prentice definition nor the consistency criterion, but they do have these implications in special cases. Moreover, the converse does not hold except in a special case with a binary candidate surrogate. The results highlight that assumptions about the treatment effect on the clinical endpoint before the candidate surrogate is measured are influential for the ability to draw conclusions about the Prentice definition or consistency. In addition, we emphasize that in some scenarios that occur commonly in practice, the principal strata sub-populations for inference are identifiable from the observable data, in which cases the principal stratification framework has relatively high utility for the purpose of effect modification analysis, and is closely connected to the treatment marker selection problem. The results are illustrated with application to a vaccine efficacy trial, where ACN and ACS for an antibody marker are found to be consistent with the data and hence support the Prentice definition and consistency.
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Affiliation(s)
- Peter B. Gilbert
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, U.S.A
- Department of Biostatistics, University of Washington, Seattle, Washington, 98105, U.S.A
| | - Erin E. Gabriel
- Biostatistics Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, 20817, U.S.A
| | - Ying Huang
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, U.S.A
- Department of Biostatistics, University of Washington, Seattle, Washington, 98105, U.S.A
| | - Ivan S.F. Chan
- Merck & Co., Whitehouse Station, New Jersey, 08889, U.S.A
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176
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Fuchs JD, Bart PA, Frahm N, Morgan C, Gilbert PB, Kochar N, DeRosa SC, Tomaras GD, Wagner TM, Baden LR, Koblin BA, Rouphael NG, Kalams SA, Keefer MC, Goepfert PA, Sobieszczyk ME, Mayer KH, Swann E, Liao HX, Haynes BF, Graham BS, McElrath MJ. Safety and Immunogenicity of a Recombinant Adenovirus Serotype 35-Vectored HIV-1 Vaccine in Adenovirus Serotype 5 Seronegative and Seropositive Individuals. ACTA ACUST UNITED AC 2015; 6. [PMID: 26587311 DOI: 10.4172/2155-6113.1000461] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Recombinant adenovirus serotype 5 (rAd5)-vectored HIV-1 vaccines have not prevented HIV-1 infection or disease and pre-existing Ad5 neutralizing antibodies may limit the clinical utility of Ad5 vectors globally. Using a rare Ad serotype vector, such as Ad35, may circumvent these issues, but there are few data on the safety and immunogenicity of rAd35 directly compared to rAd5 following human vaccination. METHODS HVTN 077 randomized 192 healthy, HIV-uninfected participants into one of four HIV-1 vaccine/placebo groups: rAd35/rAd5, DNA/rAd5, and DNA/rAd35 in Ad5-seronegative persons; and DNA/rAd35 in Ad5-seropositive persons. All vaccines encoded the HIV-1 EnvA antigen. Antibody and T-cell responses were measured 4 weeks post boost immunization. RESULTS All vaccines were generally well tolerated and similarly immunogenic. As compared to rAd5, rAd35 was equally potent in boosting HIV-1-specific humoral and cellular immunity and responses were not significantly attenuated in those with baseline Ad5 seropositivity. Like DNA, rAd35 efficiently primed rAd5 boosting. All vaccine regimens tested elicited cross-clade antibody responses, including Env V1/V2-specific IgG responses. CONCLUSIONS Vaccine antigen delivery by rAd35 is well-tolerated and immunogenic as a prime to rAd5 immunization and as a boost to prior DNA immunization with the homologous insert. Further development of rAd35-vectored prime-boost vaccine regimens is warranted.
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Affiliation(s)
- Jonathan D Fuchs
- Population Health Division, San Francisco Department of Public Health, San Francisco, CA, USA ; Department of Medicine, University of California, San Francisco, San Francisco, USA
| | | | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cecilia Morgan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nidhi Kochar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen C DeRosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Theresa M Wagner
- Population Health Division, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Lindsey R Baden
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA, USA
| | - Beryl A Koblin
- Laboratory of Infectious Disease Prevention, New York Blood Center, New York, NY, USA
| | - Nadine G Rouphael
- The Hope Clinic, Division of Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Spyros A Kalams
- Infectious Diseases Division, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael C Keefer
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Magdalena E Sobieszczyk
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Kenneth H Mayer
- Fenway Health and the Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, USA
| | - Edith Swann
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Hua-Xin Liao
- Human Vaccine Institute, Duke University, Durham, NC, USA
| | | | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Bose M, Arroyo MA, O’Connell RJ, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, Kirys T, Georgiev IS, Kwong PD, Scheffler K, Pond SLK, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB. Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Comput Biol 2015; 11:e1003973. [PMID: 25646817 PMCID: PMC4315437 DOI: 10.1371/journal.pcbi.1003973] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [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: 07/24/2014] [Accepted: 10/08/2014] [Indexed: 01/25/2023] Open
Abstract
The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or "signatures" and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.
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Affiliation(s)
- Paul T. Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Morgane Rolland
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- The Shraga Segal Dept. of Microbiology, Immunology and Genetics, Faculty of Health Sciences, and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Andrew J. Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Allan C. deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Craig A. Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Hasan Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Connor McCoy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Brendan B. Larsen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Eric Sanders-Buell
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Chris Carrico
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sergey Menis
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
| | - Meera Bose
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | | | | | | | | | | | | | | | - Merlin L. Robb
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Tatsiana Kirys
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Ivelin S. Georgiev
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Konrad Scheffler
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Sergei L. Kosakovsky Pond
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan M. Carlson
- eSience Research Group, Microsoft Research, Redmond, Washington, United States of America
| | - Nelson L. Michael
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jerome H. Kim
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Yates NL, Liao HX, Fong Y, deCamp A, Vandergrift NA, Williams WT, Alam SM, Ferrari G, Yang ZY, Seaton KE, Berman PW, Alpert MD, Evans DT, O'Connell RJ, Francis D, Sinangil F, Lee C, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Pinter A, Zolla-Pazner S, Gilbert PB, Nabel GJ, Michael NL, Kim JH, Montefiori DC, Haynes BF, Tomaras GD. Vaccine-induced Env V1-V2 IgG3 correlates with lower HIV-1 infection risk and declines soon after vaccination. Sci Transl Med 2014; 6:228ra39. [PMID: 24648342 DOI: 10.1126/scitranslmed.3007730] [Citation(s) in RCA: 368] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-1-specific immunoglobulin G (IgG) subclass antibodies bind to distinct cellular Fc receptors. Antibodies of the same epitope specificity but of a different subclass therefore can have different antibody effector functions. The study of IgG subclass profiles between different vaccine regimens used in clinical trials with divergent efficacy outcomes can provide information on the quality of the vaccine-induced B cell response. We show that HIV-1-specific IgG3 distinguished two HIV-1 vaccine efficacy studies (RV144 and VAX003 clinical trials) and correlated with decreased risk of HIV-1 infection in a blinded follow-up case-control study with the RV144 vaccine. HIV-1-specific IgG3 responses were not long-lived, which was consistent with the waning efficacy of the RV144 vaccine. These data suggest that specific vaccine-induced HIV-1 IgG3 should be tested in future studies of immune correlates in HIV-1 vaccine efficacy trials.
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Huang Y, Duerr A, Frahm N, Zhang L, Moodie Z, De Rosa S, McElrath MJ, Gilbert PB. Immune-correlates analysis of an HIV-1 vaccine efficacy trial reveals an association of nonspecific interferon-γ secretion with increased HIV-1 infection risk: a cohort-based modeling study. PLoS One 2014; 9:e108631. [PMID: 25369172 PMCID: PMC4219669 DOI: 10.1371/journal.pone.0108631] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Elevated risk of HIV-1 infection among recipients of an adenovirus serotype 5 (Ad5)-vectored HIV-1 vaccine was previously reported in the Step HIV-1 vaccine efficacy trial. We assessed pre-infection cellular immune responses measured at 4 weeks after the second vaccination to determine their roles in HIV-1 infection susceptibility among Step study male participants. METHODS We examined ex vivo interferon-γ (IFN-γ) secretion from peripheral blood mononuclear cells (PBMC) using an ELISpot assay in 112 HIV-infected and 962 uninfected participants. In addition, we performed flow cytometric assays to examine T-cell activation, and ex vivo IFN-γ and interleukin-2 secretion from CD4(+) and CD8(+) T cells. We accounted for the sub-sampling design in Cox proportional hazards models to estimate hazard ratios (HRs) of HIV-1 infection per 1-log(e) increase of the immune responses. FINDINGS We found that HIV-specific immune responses were not associated with risk of HIV-1 infection. However, each 1-log(e) increase of mock responses measured by the ELISpot assay (i.e., IFN-γ secretion in the absence of antigen-specific stimulation) was associated with a 62% increase of HIV-1 infection risk among vaccine recipients (HR = 1.62, 95% CI: (1.28, 2.04), p<0.001). This association remains after accounting for CD4(+) or CD8(+) T-cell activation. We observed a moderate correlation between ELISpot mock responses and CD4(+) T-cells secreting IFN-γ (ρ = 0.33, p = 0.007). In addition, the effect of the Step vaccine on infection risk appeared to vary with ELISpot mock response levels, especially among participants who had pre-existing anti-Ad5 antibodies (interaction p = 0.04). CONCLUSIONS The proportion of cells, likely CD4(+) T-cells, producing IFN-γ without stimulation by exogenous antigen appears to carry information beyond T-cell activation and baseline characteristics that predict risk of HIV-1 infection. These results motivate additional investigation to understand the potential link between IFN-γ secretion and underlying causes of elevated HIV-1 infection risk among vaccine recipients in the Step study.
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MESH Headings
- AIDS Vaccines/immunology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cohort Studies
- Follow-Up Studies
- HIV Infections/pathology
- HIV Infections/prevention & control
- HIV-1/metabolism
- Humans
- Immunoassay
- Interferon-gamma/metabolism
- Interleukin-2/metabolism
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Lymphocyte Activation
- Male
- Proportional Hazards Models
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Risk
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/immunology
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- nef Gene Products, Human Immunodeficiency Virus/genetics
- nef Gene Products, Human Immunodeficiency Virus/immunology
- nef Gene Products, Human Immunodeficiency Virus/metabolism
- pol Gene Products, Human Immunodeficiency Virus/genetics
- pol Gene Products, Human Immunodeficiency Virus/immunology
- pol Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Ann Duerr
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Lily Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Steve De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
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180
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Abstract
This paper considers conducting inference about the effect of a treatment (or exposure) on an outcome of interest. In the ideal setting where treatment is assigned randomly, under certain assumptions the treatment effect is identifiable from the observable data and inference is straightforward. However, in other settings such as observational studies or randomized trials with noncompliance, the treatment effect is no longer identifiable without relying on untestable assumptions. Nonetheless, the observable data often do provide some information about the effect of treatment, that is, the parameter of interest is partially identifiable. Two approaches are often employed in this setting: (i) bounds are derived for the treatment effect under minimal assumptions, or (ii) additional untestable assumptions are invoked that render the treatment effect identifiable and then sensitivity analysis is conducted to assess how inference about the treatment effect changes as the untestable assumptions are varied. Approaches (i) and (ii) are considered in various settings, including assessing principal strata effects, direct and indirect effects and effects of time-varying exposures. Methods for drawing formal inference about partially identified parameters are also discussed.
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Affiliation(s)
- Amy Richardson
- Quantitative Analyst, Google Inc., Mountain View, California 94043, USA
| | - Michael G Hudgens
- Associate Professor, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Peter B Gilbert
- Member, Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
| | - Jason P Fine
- Professor, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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181
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Gabriel EE, Sachs MC, Gilbert PB. Comparing and combining biomarkers as principal surrogates for time-to-event clinical endpoints. Stat Med 2014; 34:381-95. [PMID: 25352131 DOI: 10.1002/sim.6349] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 10/08/2014] [Indexed: 01/28/2023]
Abstract
Principal surrogate endpoints are useful as targets for phase I and II trials. In many recent trials, multiple post-randomization biomarkers are measured. However, few statistical methods exist for comparison of or combination of biomarkers as principal surrogates, and none of these methods to our knowledge utilize time-to-event clinical endpoint information. We propose a Weibull model extension of the semi-parametric estimated maximum likelihood method that allows for the inclusion of multiple biomarkers in the same risk model as multivariate candidate principal surrogates. We propose several methods for comparing candidate principal surrogates and evaluating multivariate principal surrogates. These include the time-dependent and surrogate-dependent true and false positive fraction, the time-dependent and the integrated standardized total gain, and the cumulative distribution function of the risk difference. We illustrate the operating characteristics of our proposed methods in simulations and outline how these statistics can be used to evaluate and compare candidate principal surrogates. We use these methods to investigate candidate surrogates in the Diabetes Control and Complications Trial.
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Affiliation(s)
- Erin E Gabriel
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, U.S.A
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182
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Huang Y, Karuna ST, Janes H, Frahm N, Nason M, Edlefsen PT, Kublin JG, Corey L, McElrath MJ, Gilbert PB. Use of placebos in Phase 1 preventive HIV vaccine clinical trials. Vaccine 2014; 33:749-52. [PMID: 25454855 DOI: 10.1016/j.vaccine.2014.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 06/19/2014] [Revised: 09/29/2014] [Accepted: 10/08/2014] [Indexed: 11/25/2022]
Abstract
Phase 1 preventive HIV vaccine trials are often designed as randomized, double-blind studies with the inclusion of placebo recipients. Careful consideration is needed to determine when the inclusion of placebo recipients is highly advantageous and when it is optional for achieving the study objectives of assessing vaccine safety, tolerability and immunogenicity. The inclusion of placebo recipients is generally important to form a reference group that ensures fair evaluation and interpretation of subjective study endpoints, or endpoints whose levels may change due to exposures besides vaccination. In some settings, however, placebo recipients are less important because other data sources and tools are available to achieve the study objectives.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Shelly T Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Martha Nason
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paul T Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
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183
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Bart PA, Huang Y, Karuna ST, Chappuis S, Gaillard J, Kochar N, Shen X, Allen MA, Ding S, Hural J, Liao HX, Haynes BF, Graham BS, Gilbert PB, McElrath MJ, Montefiori DC, Tomaras GD, Pantaleo G, Frahm N. HIV-specific humoral responses benefit from stronger prime in phase Ib clinical trial. J Clin Invest 2014; 124:4843-56. [PMID: 25271627 DOI: 10.1172/jci75894] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/26/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND. Vector prime-boost immunization strategies induce strong cellular and humoral immune responses. We examined the priming dose and administration order of heterologous vectors in HIV Vaccine Trials Network 078 (HVTN 078), a randomized, double-blind phase Ib clinical trial to evaluate the safety and immunogenicity of heterologous prime-boost regimens, with a New York vaccinia HIV clade B (NYVAC-B) vaccine and a recombinant adenovirus 5-vectored (rAd5-vectored) vaccine. METHODS. NYVAC-B included HIV-1 clade B Gag-Pol-Nef and gp120, while rAd5 included HIV-1 clade B Gag-Pol and clades A, B, and C gp140. Eighty Ad5-seronegative subjects were randomized to receive 2 × NYVAC-B followed by 1 × 1010 PFU rAd5 (NYVAC/Ad5hi); 1 × 108 PFU rAd5 followed by 2 × NYVAC-B (Ad5lo/NYVAC); 1 × 109 PFU rAd5 followed by 2 × NYVAC-B (Ad5med/NYVAC); 1 × 1010 PFU rAd5 followed by 2 × NYVAC-B (Ad5hi/NYVAC); or placebo. Immune responses were assessed 2 weeks after the final vaccination. Intracellular cytokine staining measured T cells producing IFN-γ and/or IL-2; cross-clade and epitope-specific binding antibodies were determined; and neutralizing antibodies (nAbs) were assessed with 6 tier 1 viruses. RESULTS. CD4+ T cell response rates ranged from 42.9% to 93.3%. NYVAC/Ad5hi response rates (P ≤ 0.01) and magnitudes (P ≤ 0.03) were significantly lower than those of other groups. CD8+ T cell response rates ranged from 65.5% to 85.7%. NYVAC/Ad5hi magnitudes were significantly lower than those of other groups (P ≤ 0.04). IgG response rates to the group M consensus gp140 were 89.7% for NYVAC/Ad5hi and 21.4%, 84.6%, and 100% for Ad5lo/NYVAC, Ad5med/NYVAC, and Ad5hi/NYVAC, respectively, and were similar for other vaccine proteins. Overall nAb responses were low, but aggregate responses appeared stronger for Ad5med/NYVAC and Ad5hi/NYVAC than for NYVAC/Ad5hi. CONCLUSIONS. rAd5 prime followed by NYVAC boost is superior to the reverse regimen for both vaccine-induced cellular and humoral immune responses. Higher Ad5 priming doses significantly increased binding and nAbs. These data provide a basis for optimizing the design of future clinical trials testing vector-based heterologous prime-boost strategies. TRIAL REGISTRATION. ClinicalTrials.gov NCT00961883. FUNDING. NIAID, NIH UM1AI068618, AI068635, AI068614, and AI069443.
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184
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Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Bose M, Arroyo MA, O'Connell RJ, deSouza MS, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, McLellan JS, Georgiev IS, Kirys T, Kwong PD, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB. Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5036.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Paul T. Edlefsen
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | - Morgane Rolland
- US Military HIV Research Program, Silver Spring, MD, United States
| | - Tomer Hertz
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | | | - Andrew J. Gartland
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | - Allan C. deCamp
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | - Craig A. Magaret
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | - Hasan Ahmed
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | - Michal Juraska
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
| | - Connor McCoy
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, United States
| | - Brendan B. Larsen
- University of Washington, Department of Microbiology, Seattle, WA, United States
| | | | - Chris Carrico
- University of Washington, Department of Biochemistry, Seattle, WA, United States
- The Scripps Research Institute, IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, La Jolla, CA, United States
| | - Sergey Menis
- University of Washington, Department of Biochemistry, Seattle, WA, United States
- The Scripps Research Institute, IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, La Jolla, CA, United States
| | - Meera Bose
- US Military HIV Research Program, Silver Spring, MD, United States
| | | | | | | | | | | | | | | | - Merlin L. Robb
- US Military HIV Research Program, Silver Spring, MD, United States
| | | | | | - Tatsiana Kirys
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, United States
| | - Peter D. Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, United States
| | | | | | - William R. Schief
- University of Washington, Department of Biochemistry, Seattle, WA, United States
- The Scripps Research Institute, IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, La Jolla, CA, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - James I. Mullins
- University of Washington, Department of Microbiology, Seattle, WA, United States
| | - Jerome H. Kim
- US Military HIV Research Program, Silver Spring, MD, United States
| | - Peter B. Gilbert
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, United States
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Scott JM, deCamp A, Juraska M, Fay MP, Gilbert PB. Finite-sample corrected generalized estimating equation of population average treatment effects in stepped wedge cluster randomized trials. Stat Methods Med Res 2014; 26:583-597. [PMID: 25267551 DOI: 10.1177/0962280214552092] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [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: 11/15/2022]
Abstract
Stepped wedge designs are increasingly commonplace and advantageous for cluster randomized trials when it is both unethical to assign placebo, and it is logistically difficult to allocate an intervention simultaneously to many clusters. We study marginal mean models fit with generalized estimating equations for assessing treatment effectiveness in stepped wedge cluster randomized trials. This approach has advantages over the more commonly used mixed models that (1) the population-average parameters have an important interpretation for public health applications and (2) they avoid untestable assumptions on latent variable distributions and avoid parametric assumptions about error distributions, therefore, providing more robust evidence on treatment effects. However, cluster randomized trials typically have a small number of clusters, rendering the standard generalized estimating equation sandwich variance estimator biased and highly variable and hence yielding incorrect inferences. We study the usual asymptotic generalized estimating equation inferences (i.e., using sandwich variance estimators and asymptotic normality) and four small-sample corrections to generalized estimating equation for stepped wedge cluster randomized trials and for parallel cluster randomized trials as a comparison. We show by simulation that the small-sample corrections provide improvement, with one correction appearing to provide at least nominal coverage even with only 10 clusters per group. These results demonstrate the viability of the marginal mean approach for both stepped wedge and parallel cluster randomized trials. We also study the comparative performance of the corrected methods for stepped wedge and parallel designs, and describe how the methods can accommodate interval censoring of individual failure times and incorporate semiparametric efficient estimators.
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Affiliation(s)
- JoAnna M Scott
- 1 Department of Pediatric Dentistry, University of Washington, Seattle, Washington, USA
| | - Allan deCamp
- 2 Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,3 Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Michal Juraska
- 2 Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael P Fay
- 4 Division of Biostatistics, National Institute of Allergies and Infectious Diseases, Bethesda, USA
| | - Peter B Gilbert
- 2 Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,3 Department of Biostatistics, University of Washington, Seattle, Washington, USA
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186
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Li SS, Gilbert PB, Tomaras GD, Kijak G, Ferrari G, Thomas R, Pyo CW, Zolla-Pazner S, Montefiori D, Liao HX, Nabel G, Pinter A, Evans DT, Gottardo R, Dai JY, Janes H, Morris D, Fong Y, Edlefsen PT, Li F, Frahm N, Alpert MD, Prentice H, Rerks-Ngarm S, Pitisuttithum P, Kaewkungwal J, Nitayaphan S, Robb ML, O'Connell RJ, Haynes BF, Michael NL, Kim JH, McElrath MJ, Geraghty DE. FCGR2C polymorphisms associate with HIV-1 vaccine protection in RV144 trial. J Clin Invest 2014; 124:3879-90. [PMID: 25105367 DOI: 10.1172/jci75539] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/19/2014] [Indexed: 02/02/2023] Open
Abstract
The phase III RV144 HIV-1 vaccine trial estimated vaccine efficacy (VE) to be 31.2%. This trial demonstrated that the presence of HIV-1-specific IgG-binding Abs to envelope (Env) V1V2 inversely correlated with infection risk, while the presence of Env-specific plasma IgA Abs directly correlated with risk of HIV-1 infection. Moreover, Ab-dependent cellular cytotoxicity responses inversely correlated with risk of infection in vaccine recipients with low IgA; therefore, we hypothesized that vaccine-induced Fc receptor-mediated (FcR-mediated) Ab function is indicative of vaccine protection. We sequenced exons and surrounding areas of FcR-encoding genes and found one FCGR2C tag SNP (rs114945036) that associated with VE against HIV-1 subtype CRF01_AE, with lysine at position 169 (169K) in the V2 loop (CRF01_AE 169K). Individuals carrying CC in this SNP had an estimated VE of 15%, while individuals carrying CT or TT exhibited a VE of 91%. Furthermore, the rs114945036 SNP was highly associated with 3 other FCGR2C SNPs (rs138747765, rs78603008, and rs373013207). Env-specific IgG and IgG3 Abs, IgG avidity, and neutralizing Abs inversely correlated with CRF01_AE 169K HIV-1 infection risk in the CT- or TT-carrying vaccine recipients only. These data suggest a potent role of Fc-γ receptors and Fc-mediated Ab function in conferring protection from transmission risk in the RV144 VE trial.
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187
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Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, Sidney J, Sette A, Zolla-Pazner S, Montefiori D, McElrath MJ, Mullins JI, Kim JH, Gilbert PB, Hertz T. Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial. J Virol 2014; 88:8242-55. [PMID: 24829343 PMCID: PMC4135964 DOI: 10.1128/jvi.01164-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [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: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The RV144 HIV-1 vaccine trial demonstrated partial efficacy of 31% against HIV-1 infection. Studies into possible correlates of protection found that antibodies specific to the V1 and V2 (V1/V2) region of envelope correlated inversely with infection risk and that viruses isolated from trial participants contained genetic signatures of vaccine-induced pressure in the V1/V2 region. We explored the hypothesis that the genetic signatures in V1 and V2 could be partly attributed to selection by vaccine-primed T cells. We performed a T-cell-based sieve analysis of breakthrough viruses in the RV144 trial and found evidence of predicted HLA binding escape that was greater in vaccine versus placebo recipients. The predicted escape depended on class I HLA A*02- and A*11-restricted epitopes in the MN strain rgp120 vaccine immunogen. Though we hypothesized that this was indicative of postacquisition selection pressure, we also found that vaccine efficacy (VE) was greater in A*02-positive (A*02(+)) participants than in A*02(-) participants (VE = 54% versus 3%, P = 0.05). Vaccine efficacy against viruses with a lysine residue at site 169, important to antibody binding and implicated in vaccine-induced immune pressure, was also greater in A*02(+) participants (VE = 74% versus 15%, P = 0.02). Additionally, a reanalysis of vaccine-induced immune responses that focused on those that were shown to correlate with infection risk suggested that the humoral responses may have differed in A*02(+) participants. These exploratory and hypothesis-generating analyses indicate there may be an association between a class I HLA allele and vaccine efficacy, highlighting the importance of considering HLA alleles and host immune genetics in HIV vaccine trials. IMPORTANCE The RV144 trial was the first to show efficacy against HIV-1 infection. Subsequently, much effort has been directed toward understanding the mechanisms of protection. Here, we conducted a T-cell-based sieve analysis, which compared the genetic sequences of viruses isolated from infected vaccine and placebo recipients. Though we hypothesized that the observed sieve effect indicated postacquisition T-cell selection, we also found that vaccine efficacy was greater for participants who expressed HLA A*02, an allele implicated in the sieve analysis. Though HLA alleles have been associated with disease progression and viral load in HIV-1 infection, these data are the first to suggest the association of a class I HLA allele and vaccine efficacy. While these statistical analyses do not provide mechanistic evidence of protection in RV144, they generate testable hypotheses for the HIV vaccine community and they highlight the importance of assessing the impact of host immune genetics in vaccine-induced immunity and protection. (This study has been registered at ClinicalTrials.gov under registration no. NCT00223080.).
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Affiliation(s)
- Andrew J Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sue Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John McNevin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daryl Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Paul T Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Brendan B Larsen
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | | | | | - Allan C deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hasan Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Lennie Chen
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Philip Konopa
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Snehal Nariya
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Julia N Stoddard
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Kim Wong
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Hong Zhao
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Brandon S Maust
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Meera Bose
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Shana Howell
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Adam Bates
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Michelle Lazzaro
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | | | - Esther Lei
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Andrea Bradfield
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Grace Ibitamuno
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | | | | | | | | | | | - Merlin L Robb
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | | | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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188
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Gilbert PB, Sun Y. Inferences on relative failure rates in stratified mark-specific proportional hazards models with missing marks, with application to HIV vaccine efficacy trials. J R Stat Soc Ser C Appl Stat 2014; 64:49-73. [PMID: 25641990 DOI: 10.1111/rssc.12067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 11/29/2022]
Abstract
This article develops hypothesis testing procedures for the stratified mark-specific proportional hazards model in the presence of missing marks. The motivating application is preventive HIV vaccine efficacy trials, where the mark is the genetic distance of an infecting HIV sequence to an HIV sequence represented inside the vaccine. The test statistics are constructed based on two-stage efficient estimators, which utilize auxiliary predictors of the missing marks. The asymptotic properties and finite-sample performances of the testing procedures are investigated, demonstrating double-robustness and effectiveness of the predictive auxiliaries to recover efficiency. The methods are applied to the RV144 vaccine trial.
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Affiliation(s)
- Peter B Gilbert
- Department of Biostatistics, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yanqing Sun
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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189
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Gilbert PB, Gabriel EE, Miao X, Li X, Su SC, Parrino J, Chan ISF. Fold rise in antibody titers by measured by glycoprotein-based enzyme-linked immunosorbent assay is an excellent correlate of protection for a herpes zoster vaccine, demonstrated via the vaccine efficacy curve. J Infect Dis 2014; 210:1573-81. [PMID: 24823623 DOI: 10.1093/infdis/jiu279] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The phase III Zostavax Efficacy and Safety Trial of 1 dose of licensed zoster vaccine (ZV; Zostavax; Merck) in 50-59-year-olds showed approximately 70% vaccine efficacy (VE) to reduce the incidence of herpes zoster (HZ). An objective of the trial was to assess immune response biomarkers measuring antibodies to varicella zoster virus (VZV) by glycoprotein-based enzyme-linked immunosorbent assay as correlates of protection (CoPs) against HZ. METHODS The principal stratification vaccine efficacy curve framework for statistically evaluating immune response biomarkers as CoPs was applied. The VE curve describes how VE against the clinical end point (HZ) varies across participant subgroups defined by biomarker readout measuring vaccine-induced immune response. The VE curve was estimated using several subgroup definitions. RESULTS The fold rise in VZV antibody titers from the time before immunization to 6 weeks after immunization was an excellent CoP, with VE increasing sharply with fold rise: VE was estimated at 0% for the subgroup with no rise and at 90% for the subgroup with 5.26-fold rise. In contrast, VZV antibody titers measured 6 weeks after immunization did not predict VE, with similar estimated VEs across titer subgroups. CONCLUSIONS The analysis illustrates the value of the VE curve framework for assessing immune response biomarkers as CoPs in vaccine efficacy trials. CLINICAL TRIALS REGISTRATION NCT00534248.
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Affiliation(s)
- Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center and Department of Biostatistics, University of Washington
| | - Erin E Gabriel
- National Institute of Allergy and Infectious Diseases, Biostatistics Research Branch, Bethesda, Maryland
| | - Xiaopeng Miao
- Department of Biometrics, Biogen Idec, Cambridge, Massachusetts
| | - Xiaoming Li
- Biostatistics, Gilead Sciences, Seattle, Washington
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190
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Gray GE, Moodie Z, Metch B, Gilbert PB, Bekker LG, Churchyard G, Nchabeleng M, Mlisana K, Laher F, Roux S, Mngadi K, Innes C, Mathebula M, Allen M, McElrath MJ, Robertson M, Kublin J, Corey L. Recombinant adenovirus type 5 HIV gag/pol/nef vaccine in South Africa: unblinded, long-term follow-up of the phase 2b HVTN 503/Phambili study. Lancet Infect Dis 2014; 14:388-96. [PMID: 24560541 DOI: 10.1016/s1473-3099(14)70020-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The HVTN 503/Phambili study, which assessed the efficacy of the Merck Ad5 gag/pol/nef subtype B HIV-1 preventive vaccine in South Africa, was stopped when futility criteria in the Step study (assessing the same vaccine in the Americas, Caribbean, and Australia) were met. Here we report long-term follow-up data. METHODS HVTN 503/Phambili was a double-blind, placebo-controlled, randomised trial that recruited HIV-1 uninfected, sexually active adults aged 18-35 years from five sites in South Africa. Eligible participants were randomly assigned (1:1) by computer-generated random numbers to either vaccine or placebo, stratified by site and sex. Cox proportional hazards models were used to estimate HIV-1 infection in the modified intention-to-treat cohort, all of whom were unmasked early in follow-up. The trial is registered with ClinicalTrials.gov, number NCT00413725 and the South African National Health Research Database, number DOH-27-0207-1539. FINDINGS Between Jan 24, 2007, and Sept 19, 2007, 801 participants (26·7%) of a planned 3000 were randomly assigned (400 to vaccine, 401 to placebo); 216 (27%) received only one injection, 529 (66%) received only two injections, and 56 (7%) received three injections. At a median follow-up of 42 months (IQR 31-42), 63 vaccine recipients (16%) had HIV-1 infection compared with 37 placebo recipients (9%; adjusted HR 1·70, 95% CI 1·13-2·55; p=0·01). Risk for HIV-1 infection did not differ according to the number of vaccinations received, sex, circumcision, or adenovirus type 5 (Ad5) serostatus. Differences in risk behaviour at baseline or during the study, or annualised dropout rate (7·7% [95% CI 6·2-9·5] for vaccine recipients vs 8·8% [7·1-10·7] for placebo recipients; p=0·40) are unlikely explanations for the increased rate of HIV-1 infections seen in vaccine recipients. INTERPRETATION The increased risk of HIV-1 acquisition in vaccine recipients, irrespective of number of doses received, warrants further investigation to understand the biological mechanism. We caution against further use of the Ad5 vector for HIV vaccines. FUNDING National Institute of Allergy and Infectious Diseases, Merck, and South African Medical Research Council.
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Affiliation(s)
- Glenda E Gray
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa; South African Medical Research Council, Cape Town, South Africa.
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Barbara Metch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Linda-Gail Bekker
- Desmond Tutu HIV Foundation, University of Cape Town, Cape Town, South Africa
| | | | | | - Koleka Mlisana
- Centre for AIDS Programme for Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Fatima Laher
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Surita Roux
- Desmond Tutu HIV Foundation, University of Cape Town, Cape Town, South Africa
| | - Kathryn Mngadi
- Centre for AIDS Programme for Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Craig Innes
- Aurum Institute for Health Research, Johannesburg, South Africa
| | - Matsontso Mathebula
- MEDUNSA HIV Clinical Research Unit, University of Limpopo, Mankweng-E, South Africa
| | - Mary Allen
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - M Julie McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Robertson
- Infectious Diseases and Vaccines Clinical Research, Merck and Company, North Wales, PA, USA
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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191
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Zolla-Pazner S, deCamp A, Gilbert PB, Williams C, Yates NL, Williams WT, Howington R, Fong Y, Morris DE, Soderberg KA, Irene C, Reichman C, Pinter A, Parks R, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Nitayaphan S, Andrews C, O’Connell RJ, Yang ZY, Nabel GJ, Kim JH, Michael NL, Montefiori DC, Liao HX, Haynes BF, Tomaras GD. Vaccine-induced IgG antibodies to V1V2 regions of multiple HIV-1 subtypes correlate with decreased risk of HIV-1 infection. PLoS One 2014; 9:e87572. [PMID: 24504509 PMCID: PMC3913641 DOI: 10.1371/journal.pone.0087572] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [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: 09/12/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022] Open
Abstract
UNLABELLED In the RV144 HIV-1 vaccine efficacy trial, IgG antibody (Ab) binding levels to variable regions 1 and 2 (V1V2) of the HIV-1 envelope glycoprotein gp120 were an inverse correlate of risk of HIV-1 infection. To determine if V1V2-specific Abs cross-react with V1V2 from different HIV-1 subtypes, if the nature of the V1V2 antigen used to asses cross-reactivity influenced infection risk, and to identify immune assays for upcoming HIV-1 vaccine efficacy trials, new V1V2-scaffold antigens were designed and tested. Protein scaffold antigens carrying the V1V2 regions from HIV-1 subtypes A, B, C, D or CRF01_AE were assayed in pilot studies, and six were selected to assess cross-reactive Abs in the plasma from the original RV144 case-control cohort (41 infected vaccinees, 205 frequency-matched uninfected vaccinees, and 40 placebo recipients) using ELISA and a binding Ab multiplex assay. IgG levels to these antigens were assessed as correlates of risk in vaccine recipients using weighted logistic regression models. Levels of Abs reactive with subtype A, B, C and CRF01_AE V1V2-scaffold antigens were all significant inverse correlates of risk (p-values of 0.0008-0.05; estimated odds ratios of 0.53-0.68 per 1 standard deviation increase). Thus, levels of vaccine-induced IgG Abs recognizing V1V2 regions from multiple HIV-1 subtypes, and presented on different scaffolds, constitute inverse correlates of risk for HIV-1 infection in the RV144 vaccine trial. The V1V2 antigens provide a link between RV144 and upcoming HIV-1 vaccine trials, and identify reagents and methods for evaluating V1V2 Abs as possible correlates of protection against HIV-1 infection. TRIAL REGISTRATION ClinicalTrials.gov NCT00223080.
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Affiliation(s)
- Susan Zolla-Pazner
- Department of Veterans Affairs New York Harbor Healthcare System, New York, New York, United States of America
- New York University School of Medicine, New York, New York, United States of America
- * E-mail:
| | - Allan deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Constance Williams
- New York University School of Medicine, New York, New York, United States of America
| | - Nicole L. Yates
- Duke University, Durham, North Carolina, United States of America
| | | | - Robert Howington
- Duke University, Durham, North Carolina, United States of America
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Daryl E. Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | - Carmela Irene
- Public Health Research Institute, University of Medicine and Dentistry, Newark, New Jersey, United States of America
| | - Charles Reichman
- Public Health Research Institute, University of Medicine and Dentistry, Newark, New Jersey, United States of America
| | - Abraham Pinter
- Public Health Research Institute, University of Medicine and Dentistry, Newark, New Jersey, United States of America
| | - Robert Parks
- Duke University, Durham, North Carolina, United States of America
| | | | | | | | | | - Charla Andrews
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Robert J. O’Connell
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Zhi-yong Yang
- Virology Laboratory, Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gary J. Nabel
- Virology Laboratory, Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jerome H. Kim
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | | | - Hua-Xin Liao
- Duke University, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke University, Durham, North Carolina, United States of America
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192
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Abstract
Principal surrogate (PS) endpoints are relatively inexpensive and easy to measure study outcomes that can be used to reliably predict treatment effects on clinical endpoints of interest. Few statistical methods for assessing the validity of potential PSs utilize time-to-event clinical endpoint information and to our knowledge none allow for the characterization of time-varying treatment effects. We introduce the time-dependent and surrogate-dependent treatment efficacy curve, ${\mathrm {TE}}(t|s)$, and a new augmented trial design for assessing the quality of a biomarker as a PS. We propose a novel Weibull model and an estimated maximum likelihood method for estimation of the ${\mathrm {TE}}(t|s)$ curve. We describe the operating characteristics of our methods via simulations. We analyze data from the Diabetes Control and Complications Trial, in which we find evidence of a biomarker with value as a PS.
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Affiliation(s)
- Erin E Gabriel
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
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193
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Hammer SM, Sobieszczyk ME, Janes H, Karuna ST, Mulligan MJ, Grove D, Koblin BA, Buchbinder SP, Keefer MC, Tomaras GD, Frahm N, Hural J, Anude C, Graham BS, Enama ME, Adams E, DeJesus E, Novak RM, Frank I, Bentley C, Ramirez S, Fu R, Koup RA, Mascola JR, Nabel GJ, Montefiori DC, Kublin J, McElrath MJ, Corey L, Gilbert PB. Efficacy trial of a DNA/rAd5 HIV-1 preventive vaccine. N Engl J Med 2013; 369:2083-92. [PMID: 24099601 PMCID: PMC4030634 DOI: 10.1056/nejmoa1310566] [Citation(s) in RCA: 440] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND A safe and effective vaccine for the prevention of human immunodeficiency virus type 1 (HIV-1) infection is a global priority. We tested the efficacy of a DNA prime-recombinant adenovirus type 5 boost (DNA/rAd5) vaccine regimen in persons at increased risk for HIV-1 infection in the United States. METHODS At 21 sites, we randomly assigned 2504 men or transgender women who have sex with men to receive the DNA/rAd5 vaccine (1253 participants) or placebo (1251 participants). We assessed HIV-1 acquisition from week 28 through month 24 (termed week 28+ infection), viral-load set point (mean plasma HIV-1 RNA level 10 to 20 weeks after diagnosis), and safety. The 6-plasmid DNA vaccine (expressing clade B Gag, Pol, and Nef and Env proteins from clades A, B, and C) was administered at weeks 0, 4, and 8. The rAd5 vector boost (expressing clade B Gag-Pol fusion protein and Env glycoproteins from clades A, B, and C) was administered at week 24. RESULTS In April 2013, the data and safety monitoring board recommended halting vaccinations for lack of efficacy. The primary analysis showed that week 28+ infection had been diagnosed in 27 participants in the vaccine group and 21 in the placebo group (vaccine efficacy, -25.0%; 95% confidence interval, -121.2 to 29.3; P=0.44), with mean viral-load set points of 4.46 and 4.47 HIV-1 RNA log10 copies per milliliter, respectively. Analysis of all infections during the study period (41 in the vaccine group and 31 in the placebo group) also showed lack of vaccine efficacy (P=0.28). The vaccine regimen had an acceptable side-effect profile. CONCLUSIONS The DNA/rAd5 vaccine regimen did not reduce either the rate of HIV-1 acquisition or the viral-load set point in the population studied. (Funded by the National Institute of Allergy and Infectious Diseases; ClinicalTrials.gov number, NCT00865566.).
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194
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Gilbert PB, Yu X, Rotnitzky A. Optimal auxiliary-covariate-based two-phase sampling design for semiparametric efficient estimation of a mean or mean difference, with application to clinical trials. Stat Med 2013; 33:901-17. [PMID: 24123289 DOI: 10.1002/sim.6006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 02/22/2012] [Revised: 08/14/2013] [Accepted: 09/19/2013] [Indexed: 11/10/2022]
Abstract
To address the objective in a clinical trial to estimate the mean or mean difference of an expensive endpoint Y, one approach employs a two-phase sampling design, wherein inexpensive auxiliary variables W predictive of Y are measured in everyone, Y is measured in a random sample, and the semiparametric efficient estimator is applied. This approach is made efficient by specifying the phase two selection probabilities as optimal functions of the auxiliary variables and measurement costs. While this approach is familiar to survey samplers, it apparently has seldom been used in clinical trials, and several novel results practicable for clinical trials are developed. We perform simulations to identify settings where the optimal approach significantly improves efficiency compared to approaches in current practice. We provide proofs and R code. The optimality results are developed to design an HIV vaccine trial, with objective to compare the mean 'importance-weighted' breadth (Y) of the T-cell response between randomized vaccine groups. The trial collects an auxiliary response (W) highly predictive of Y and measures Y in the optimal subset. We show that the optimal design-estimation approach can confer anywhere between absent and large efficiency gain (up to 24 % in the examples) compared to the approach with the same efficient estimator but simple random sampling, where greater variability in the cost-standardized conditional variance of Y given W yields greater efficiency gains. Accurate estimation of E[Y | W] is important for realizing the efficiency gain, which is aided by an ample phase two sample and by using a robust fitting method.
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Affiliation(s)
- Peter B Gilbert
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A.; Department of Biostatistics, University of Washington, Seattle, WA 98105, U.S.A
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Abstract
Assessing per-protocol treatment effcacy on a time-to-event endpoint is a common objective of randomized clinical trials. The typical analysis uses the same method employed for the intention-to-treat analysis (e.g., standard survival analysis) applied to the subgroup meeting protocol adherence criteria. However, due to potential post-randomization selection bias, this analysis may mislead about treatment efficacy. Moreover, while there is extensive literature on methods for assessing causal treatment effects in compliers, these methods do not apply to a common class of trials where a) the primary objective compares survival curves, b) it is inconceivable to assign participants to be adherent and event-free before adherence is measured, and c) the exclusion restriction assumption fails to hold. HIV vaccine efficacy trials including the recent RV144 trial exemplify this class, because many primary endpoints (e.g., HIV infections) occur before adherence is measured, and nonadherent subjects who receive some of the planned immunizations may be partially protected. Therefore, we develop methods for assessing per-protocol treatment efficacy for this problem class, considering three causal estimands of interest. Because these estimands are not identifiable from the observable data, we develop nonparametric bounds and semiparametric sensitivity analysis methods that yield estimated ignorance and uncertainty intervals. The methods are applied to RV144.
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Affiliation(s)
- Peter B Gilbert
- Department of Biostatistics, University of Washington and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, U.S.A
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Janes H, Friedrich DP, Krambrink A, Smith RJ, Kallas EG, Horton H, Casimiro DR, Carrington M, Geraghty DE, Gilbert PB, McElrath MJ, Frahm N. Vaccine-induced gag-specific T cells are associated with reduced viremia after HIV-1 infection. J Infect Dis 2013; 208:1231-9. [PMID: 23878319 DOI: 10.1093/infdis/jit322] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [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] [Indexed: 11/12/2022] Open
Abstract
The contribution of host T-cell immunity and HLA class I alleles to the control of human immunodeficiency virus (HIV-1) replication in natural infection is widely recognized. We assessed whether vaccine-induced T-cell immunity, or expression of certain HLA alleles, impacted HIV-1 control after infection in the Step MRKAd5/HIV-1 gag/pol/nef study. Vaccine-induced T cells were associated with reduced plasma viremia, with subjects targeting ≥3 gag peptides presenting with half-log lower mean viral loads than subjects without Gag responses. This effect was stronger in participants infected proximal to vaccination and was independent of our observed association of HLA-B*27, -B*57 and -B*58:01 alleles with lower HIV-1 viremia. These findings support the ability of vaccine-induced T-cell responses to influence postinfection outcome and provide a rationale for the generation of T-cell responses by vaccination to reduce viremia if protection from acquisition is not achieved. Clinical trials identifier: NCT00095576.
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Affiliation(s)
- Holly Janes
- Vaccine and Infectious Disease Division and the HIV Vaccine Trials Network, Fred Hutchinson Cancer Research Center
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197
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Dai JY, Li SS, Gilbert PB. Case-only method for cause-specific hazards models with application to assessing differential vaccine efficacy by viral and host genetics. Biostatistics 2013; 15:196-203. [PMID: 23813283 DOI: 10.1093/biostatistics/kxt018] [Citation(s) in RCA: 11] [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: 11/13/2022] Open
Abstract
Cause-specific proportional hazards models are commonly used for analyzing competing risks data in clinical studies. Motivated by the objective to assess differential vaccine protection against distinct pathogen types in randomized preventive vaccine efficacy trials, we present an alternative case-only method to standard maximum partial likelihood estimation that applies to a rare failure event, e.g. acquisition of HIV infection. A logistic regression model is fit to the counts of cause-specific events (infecting pathogen type) within study arms, with an offset adjusting for the randomization ratio. This formulation of cause-specific hazard ratio estimation permits immediate incorporation of host-genetic factors to be assessed as effect modifiers, an important area of vaccine research for identifying immune correlates of protection, thus inheriting the estimation efficiency, and cost benefits of the case-only estimator commonly used for assessing gene-treatment interactions. The method is used to reassess HIV genotype-specific vaccine efficacy in the RV144 trial, providing nearly identical results to standard Cox methods, and to assess if and how this vaccine efficacy depends on Fc-γ receptor genes.
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Affiliation(s)
- James Y Dai
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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198
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Juraska M, Gilbert PB. Mark-specific hazard ratio model with multivariate continuous marks: an application to vaccine efficacy. Biometrics 2013; 69:328-37. [PMID: 23421613 DOI: 10.1111/biom.12016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 10/01/2012] [Accepted: 12/01/2012] [Indexed: 11/28/2022]
Abstract
In randomized placebo-controlled preventive HIV vaccine efficacy trials, an objective is to evaluate the relationship between vaccine efficacy to prevent infection and genetic distances of the exposing HIV strains to the multiple HIV sequences included in the vaccine construct, where the set of genetic distances is considered as the continuous multivariate "mark" observed in infected subjects only. This research develops a multivariate mark-specific hazard ratio model in the competing risks failure time analysis framework for the assessment of mark-specific vaccine efficacy. It allows improved efficiency of estimation by employing the semiparametric method of maximum profile likelihood estimation in the vaccine-to-placebo mark density ratio model. The model also enables the use of a more efficient estimation method for the overall log hazard ratio in the Cox model. In addition, we propose testing procedures to evaluate two relevant hypotheses concerning mark-specific vaccine efficacy. The asymptotic properties and finite-sample performance of the inferential procedures are investigated. Finally, we apply the proposed methods to data collected in the Thai RV144 HIV vaccine efficacy trial.
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Affiliation(s)
- M Juraska
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
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199
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Huang Y, Gilbert PB, Wolfson J. Design and estimation for evaluating principal surrogate markers in vaccine trials. Biometrics 2013; 69:301-9. [PMID: 23409839 DOI: 10.1111/biom.12014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 11/01/2012] [Accepted: 11/01/2012] [Indexed: 11/26/2022]
Abstract
In vaccine research, immune biomarkers that can reliably predict a vaccine's effect on the clinical endpoint (i.e., surrogate markers) are important tools for guiding vaccine development. This article addresses issues on optimizing two-phase sampling study design for evaluating surrogate markers in a principal surrogate framework, motivated by the design of a future HIV vaccine trial. To address the problem of missing potential outcomes in a standard trial design, novel trial designs have been proposed that utilize baseline predictors of the immune response biomarker(s) and/or augment the trial by vaccinating uninfected placebo recipients at the end of the trial and measuring their immune biomarkers. However, inefficient use of the augmented information can lead to counter-intuitive results on the precision of estimation. To remedy this problem, we propose a pseudo-score type estimator suitable for the augmented design and characterize its asymptotic properties. This estimator has superior performance compared with existing estimators and allows calculation of analytical variances useful for guiding study design. Based on the new estimator we investigate in detail the problem of optimizing the sampling scheme of a biomarker in a vaccine efficacy trial for efficiently estimating its surrogate effect, as characterized by the vaccine efficacy curve (a causal effect predictiveness curve) and by the predicted overall vaccine efficacy using the biomarker.
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Affiliation(s)
- Ying Huang
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Dai JY, Gilbert PB, Hughes JP, Brown ER. Estimating the efficacy of preexposure prophylaxis for HIV prevention among participants with a threshold level of drug concentration. Am J Epidemiol 2013; 177:256-63. [PMID: 23302152 DOI: 10.1093/aje/kws324] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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] [Indexed: 11/12/2022] Open
Abstract
Assays for detecting levels of antiretroviral drugs in study participants are increasingly popular in preexposure prophylaxis (PrEP) trials, since they provide an objective measure of adherence. Current correlation analyses of drug concentration data are prone to bias. In this article, we formulate the causal estimand of prevention efficacy among drug compliers, those who would have had a threshold level of drug concentration had they been assigned to the drug arm of the trial. The identifiability of the causal estimand is facilitated by exploiting the exclusion restriction; that is, drug noncompliers do not acquire any prevention benefit. In addition, we develop an approach to sensitivity analysis that relaxes the exclusion restriction. Applications to published data from 2 PrEP trials, namely the Preexposure Prophylaxis Initiative (iPrEx) trial and the Centre for the AIDS Programme of Research in South Africa (CAPRISA) 004 trial, suggest high efficacy estimates among drug compliers (in the iPrEx trial, odds ratio = 0.097 (95% confidence interval: 0.027, 0.352); in the CAPRISA 004 trial, odds ratio = 0.104 (95% confidence interval: 0.024, 0.447)). In summary, the proposed inferential method provides an unbiased assessment of PrEP efficacy among drug compliers, thus adding to the primary intention-to-treat analysis and correlation analyses of drug concentration data.
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Affiliation(s)
- James Y Dai
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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