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Lou Y, Du M, Wang P, Wu Y. An Augmented Approach for Regression Analysis of Case-Cohort Interval-Censored Failure Time Data. Stat Med 2025; 44:e70115. [PMID: 40387064 DOI: 10.1002/sim.70115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 02/20/2025] [Accepted: 04/26/2025] [Indexed: 05/20/2025]
Abstract
The case-cohort design is a valuable two-phase sampling scheme often used in situations with low disease incidence and challenges in obtaining covariate data due to cost constraints, and many methods have been proposed for its analysis. However, most of the existing approaches, particularly for interval-censored data, ignore the presence of non-expensive covariates that are typically observed for the entire cohort and thus can result in the significant loss of efficiency. To address this, under the framework of the semi-parametric transformation hazards model, we propose a supersampling approach that augments the case-cohort samples by introducing an additional sub-cohort, allowing us to incorporate non-expensive covariates. In the proposed method, the multiple imputation procedure is employed based on rejection sampling, and the asymptotic properties of the resulting estimator of regression parameters are established. To evaluate the finite sample performance of the proposed method, a simulation study is conducted, and it demonstrates its effectiveness in practical situations. Finally, the proposed methodology is applied to an HIV vaccine trial that motivated this study.
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Affiliation(s)
- Yichen Lou
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Mingyue Du
- School of Mathematics, Jilin University, Changchun, China
| | - Peijie Wang
- School of Mathematics, Jilin University, Changchun, China
| | - Yuxiang Wu
- Department of Statistics, University of Missouri, Columbia, Missouri, USA
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2
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Zubair A, Sujan A, Ali M, Hussain SM. Current Challenges With Highly Active Antiretroviral Therapy and New Hope and Horizon With CRISPR-CAS9 Technology for HIV Treatment. Chem Biol Drug Des 2025; 105:e70121. [PMID: 40356298 DOI: 10.1111/cbdd.70121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 04/18/2025] [Accepted: 04/28/2025] [Indexed: 05/15/2025]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR/Cas system) is now the predominant approach for genome editing. Compared to conventional genetic editing methods, CRISPR/Cas technology offers several advantages that were previously unavailable. Key benefits include the ability to simultaneously modify multiple locations, reduced costs, enhanced efficiency, and a more user-friendly design. By directing Cas-mediated DNA cleavage to specific genomic targets and utilizing intrinsic DNA repair processes, this system can produce site-specific gene modifications. This goal is achieved through an RNA-guided procedure. As the most effective gene editing method currently available, the CRISPR/Cas system has proven to be highly valuable in genomic research across a wide range of species since its discovery as a component of the adaptive immune system in bacteria. Its applicability extends to various organisms, making it increasingly prevalent in the medical field, where it shows great promise in investigating viral infections, cancer, and genetic disorders. Furthermore, it enhances our understanding of fundamental genetics. This article outlines the current antiretroviral therapy and its adverse effects but also CRISPR/Cas technology. This review article also discusses its mechanism of action and potential applications in the treatment of HIV/AIDS.
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Affiliation(s)
- Akmal Zubair
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Arooba Sujan
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syeda Maryam Hussain
- Department of Livestock Production and Management, Faculty of Veterinary and Animal Sciences PIR Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Punjab, Pakistan
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3
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Fisher LH, Lazarus E, Yu C, Moodie Z, Stieh DJ, Yates N, Zhang L, Sawant S, De Rosa SC, Cohen KW, Morris D, Grant S, Randhawa A, Miner MD, Hendriks J, Wegmann F, Gill KM, Laher F, Bekker LG, Gray GE, Corey L, McElrath MJ, Martin T, Gilbert PB, Tomaras G, Walsh SR, Baden LR, The HVTN 100, HVTN 117/HPX2004 study teams. ALVAC-prime and monomeric gp120 protein boost induces distinct HIV-1 specific humoral and cellular responses compared with adenovirus-prime and trimeric gp140 protein boost. PLOS GLOBAL PUBLIC HEALTH 2025; 5:e0004250. [PMID: 40215224 PMCID: PMC11990749 DOI: 10.1371/journal.pgph.0004250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 02/17/2025] [Indexed: 04/14/2025]
Abstract
Although clade-specific and cross-clade mosaic prime-boost HIV-1 vaccine regimens were advanced to the HVTN 702 and HVTN 705 efficacy trials, neither regimen prevented HIV acquisition. The respective Phase 1/2a studies, HVTN 100 (NCT02404311) and HVTN 117/HPX2004 (NCT02788045), provided rich immunological data, including previously identified correlates of risk, for comparing immune responses elicited by these vaccine regimens over time. We analyzed antibody responses measured by binding antibody multiplex assay, and CD4+ and CD8+ T-cell responses measured by intracellular cytokine staining in per-protocol vaccinees in HVTN 100 (n=186) vs. HVTN 117/HPX2004 (n=99) after the months 6 and 12 vaccinations (months 6.5/7 and 12.5/13), and 6 months after the last vaccination (month 18). At month 12.5/13, both regimens induced similarly high IgG breadth against gp120, gp140, and V1V2 antigens, and similar IgG responses to gp70-BCaseA V1V2. IgG V1V2 responses were more durable in HVTN 117/HPX2004, with the largest difference in the gp70-BCaseA V1V2 IgG response rate at month 18 (17.8% in HVTN 100 vs 61.9% in HVTN 117/HPX2004, p<0.001). IgG3 responses to consensus Env antigens were higher and more durable in HVTN117/HPX2004; for example, IgG3 response rate to the consensus gp140 antigen was 65.9% in HVTN 117/HPX2004 vs 6.3% in HVTN 100 at month 18 (TMLE p<0.0001). At month 18, both regimens induced similar IgG3 responses to gp70-BCaseA V1V2 (3.2% in HVTN 100 vs 1.1% in HVTN 117/HPX2004). Polyfunctional CD4+ Env was significantly higher in HVTN 100, and polyfunctional CD4+ Gag was higher in HVTN 117/HPX2004. CD8+ T-cell responses were not seen in HVTN 100, while CD8+ T-cell response rates in HVTN 117/HPX2004 reached up to 42%. Despite the distinct immune responses induced by the two HIV vaccine regimens, the lack of demonstrated efficacy suggests that broader, higher magnitude, and possibly qualitatively different immune responses are needed for protection against HIV acquisition. Trial registration: ClinicalTrials.gov NCT02404311 and NCT02788045; South African National Clinical Trials Registry (DOH-27-0215-4796).
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Affiliation(s)
- Leigh H. Fisher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Erica Lazarus
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Chenchen Yu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | | | - Nicole Yates
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Lu Zhang
- Duke University, Durham, North Carolina, United States of America
| | - Sheetal Sawant
- Duke University, Durham, North Carolina, United States of America
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Daryl Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Shannon Grant
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - April Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Maurine D. Miner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | | | - Frank Wegmann
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | - Katherine M. Gill
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Fatima Laher
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Soweto, South Africa
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Glenda E. Gray
- South African Medical Research Council, Cape Town, South Africa
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Troy Martin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Georgia Tomaras
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Stephen R. Walsh
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Lindsey R. Baden
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
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Richardson BD, Blette BS, Gilbert PB, Hudgens MG. Addressing confounding and continuous exposure measurement error using corrected score functions. Biometrics 2025; 81:ujaf045. [PMID: 40297938 PMCID: PMC12038274 DOI: 10.1093/biomtc/ujaf045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 02/03/2025] [Accepted: 03/27/2025] [Indexed: 04/30/2025]
Abstract
Confounding and exposure measurement error can introduce bias when drawing inference about the marginal effect of an exposure on an outcome of interest. While there are broad methodologies for addressing each source of bias individually, confounding and exposure measurement error frequently co-occur, and there is a need for methods that address them simultaneously. In this paper, corrected score methods are derived under classical additive measurement error to draw inference about marginal exposure effects using only measured variables. Three estimators are proposed based on g-formula, inverse probability weighting, and doubly-robust estimation techniques. The estimators are shown to be consistent and asymptotically normal, and the doubly-robust estimator is shown to exhibit its namesake property. The methods, which are implemented in the R package mismex, perform well in finite samples under both confounding and measurement error as demonstrated by simulation studies. The proposed doubly-robust estimator is applied to study the effects of two biomarkers on HIV-1 infection using data from the HVTN 505 preventative vaccine trial.
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Affiliation(s)
- Brian D Richardson
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Bryan S Blette
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Peter B Gilbert
- Department of Biostatistics, University of Washington and Fred Hutchinson Cancer Center, Seattle, WA 98109, United States
| | - Michael G Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
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Lin L, Spreng RL, Seaton KE, Dennison SM, Dahora LC, Schuster DJ, Sawant S, Gilbert PB, Fong Y, Kisalu N, Pollard AJ, Tomaras GD, Li J. GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies. PLoS Comput Biol 2024; 20:e1012581. [PMID: 39541411 PMCID: PMC11594404 DOI: 10.1371/journal.pcbi.1012581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 11/26/2024] [Accepted: 10/23/2024] [Indexed: 11/16/2024] Open
Abstract
Despite significant progress in vaccine research, the level of protection provided by vaccination can vary significantly across individuals. As a result, understanding immunologic variation across individuals in response to vaccination is important for developing next-generation efficacious vaccines. Accurate outcome prediction and identification of predictive biomarkers would represent a significant step towards this goal. Moreover, in early phase vaccine clinical trials, small datasets are prevalent, raising the need and challenge of building a robust and explainable prediction model that can reveal heterogeneity in small datasets. We propose a new model named Generative Mixture of Logistic Regression (GeM-LR), which combines characteristics of both a generative and a discriminative model. In addition, we propose a set of model selection strategies to enhance the robustness and interpretability of the model. GeM-LR extends a linear classifier to a non-linear classifier without losing interpretability and empowers the notion of predictive clustering for characterizing data heterogeneity in connection with the outcome variable. We demonstrate the strengths and utility of GeM-LR by applying it to data from several studies. GeM-LR achieves better prediction results than other popular methods while providing interpretations at different levels.
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Affiliation(s)
- Lin Lin
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
| | - Rachel L. Spreng
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Kelly E. Seaton
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - S. Moses Dennison
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Lindsay C. Dahora
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
| | - Daniel J. Schuster
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
| | - Sheetal Sawant
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Neville Kisalu
- Center for Vaccine Innovation and Access, PATH, Washington, DC, United States of America
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Jia Li
- Department of Statistics, The Pennsylvania State University, Pennsylvania, United States of America
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Graciaa DS, Walsh SR, Rouphael N. Human Immunodeficiency Virus Vaccine: Promise and Challenges. Infect Dis Clin North Am 2024; 38:475-485. [PMID: 38876903 PMCID: PMC11305931 DOI: 10.1016/j.idc.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Development of a safe and effective human immunodeficiency virus (HIV) vaccine is a persistent challenge despite decades of research. Previous strategies utilizing protein subunit and viral vector vaccines were safe but not protective. Current strategies seek to induce broadly neutralizing antibodies, with multiple early phase trials in progress seeking to achieve this through sequential vaccination, mRNA, or updated viral-vectored vaccines. A safe and effective vaccine is critical to ending the HIV epidemic.
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Affiliation(s)
- Daniel S Graciaa
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA; Hope Clinic of Emory Vaccine Center, 500 Irvin Court, Suite 200, Decatur, GA 30030, USA.
| | - Stephen R Walsh
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Nadine Rouphael
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA; Hope Clinic of Emory Vaccine Center, 500 Irvin Court, Suite 200, Decatur, GA 30030, USA
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7
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Zubair A, Bibi B, Habib F, Sujan A, Ali M. Clinical trials and recent progress in HIV vaccine development. Funct Integr Genomics 2024; 24:143. [PMID: 39192058 DOI: 10.1007/s10142-024-01425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/08/2024] [Accepted: 08/17/2024] [Indexed: 08/29/2024]
Abstract
The greatest obstacle for scientists is to develop an effective HIV vaccine. An effective vaccine represents the last hope for halting the unstoppable global spread of HIV and its catastrophic clinical consequences. Creating this vaccine has been challenging due to the virus's extensive genetic variability and the unique role of cytotoxic T lymphocytes (CTL) in containing it. Innovative methods to stimulate CTL have demonstrated significant therapeutic advantages in nonhuman primate model systems, unlike traditional vaccination techniques that are not expected to provide safe and efficient protection against HIV. Human clinical trials are currently evaluating these vaccination strategies, which involve plasmid DNA and live recombinant vectors. This review article covers the existing vaccines and ongoing trial vaccines. It also explores the different approaches used in developing HIV vaccines, including their molecular mechanisms, target site effectiveness, and potential side effects.
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Affiliation(s)
- Akmal Zubair
- Department of Biotechnology Quaid-i, Azam University Islamabad Pakistan, Islamabad Capital Territory, Pakistan.
| | - Bushra Bibi
- Department of Biotechnology Quaid-i, Azam University Islamabad Pakistan, Islamabad Capital Territory, Pakistan
| | - Faiza Habib
- Department of Biotechnology Quaid-i, Azam University Islamabad Pakistan, Islamabad Capital Territory, Pakistan
| | - Arooba Sujan
- Department of Biotechnology Quaid-i, Azam University Islamabad Pakistan, Islamabad Capital Territory, Pakistan
| | - Muhammad Ali
- Department of Biotechnology Quaid-i, Azam University Islamabad Pakistan, Islamabad Capital Territory, Pakistan.
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Borgo GM, Rutishauser RL. Generating and measuring effective vaccine-elicited HIV-specific CD8 + T cell responses. Curr Opin HIV AIDS 2023; 18:331-341. [PMID: 37751362 PMCID: PMC10552829 DOI: 10.1097/coh.0000000000000824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
PURPOSE OF REVIEW There is growing consensus that eliciting CD8 + T cells in addition to antibodies may be required for an effective HIV vaccine for both prevention and cure. Here, we review key qualities of vaccine-elicited CD8 + T cells as well as major CD8 + T cell-based delivery platforms used in recent HIV vaccine clinical trials. RECENT FINDINGS Much progress has been made in improving HIV immunogen design and delivery platforms to optimize CD8 + T cell responses. With regards to viral vectors, recent trials have tested newer chimp and human adenovirus vectors as well as a CMV vector. DNA vaccine immunogenicity has been increased by delivering the vaccines by electroporation and together with adjuvants as well as administering them as part of a heterologous regimen. In preclinical models, self-amplifying RNA vaccines can generate durable tissue-based CD8 + T cells. While it may be beneficial for HIV vaccines to recapitulate the functional and phenotypic features of HIV-specific CD8 + T cells isolated from elite controllers, most of these features are not routinely measured in HIV vaccine clinical trials. SUMMARY Identifying a vaccine capable of generating durable T cell responses that target mutationally vulnerable epitopes and that can rapidly intercept infecting or rebounding virus remains a challenge for HIV. Comprehensive assessment of HIV vaccine-elicited CD8 + T cells, as well as comparisons between different vaccine platforms, will be critical to advance our understanding of how to design better CD8 + T cell-based vaccines for HIV.
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Affiliation(s)
- Gina M Borgo
- Department of Medicine, University of California, San Francisco, California, USA
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9
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Williams LD, Shen X, Sawant SS, Akapirat S, Dahora LC, Tay MZ, Stanfield-Oakley S, Wills S, Goodman D, Tenney D, Spreng RL, Zhang L, Yates NL, Montefiori DC, Eller MA, Easterhoff D, Hope TJ, Rerks-Ngarm S, Pittisuttithum P, Nitayaphan S, Excler JL, Kim JH, Michael NL, Robb ML, O’Connell RJ, Karasavvas N, Vasan S, Ferrari G, Tomaras GD, RV305 study team. Viral vector delivered immunogen focuses HIV-1 antibody specificity and increases durability of the circulating antibody recall response. PLoS Pathog 2023; 19:e1011359. [PMID: 37256916 PMCID: PMC10284421 DOI: 10.1371/journal.ppat.1011359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/21/2023] [Accepted: 04/14/2023] [Indexed: 06/02/2023] Open
Abstract
The modestly efficacious HIV-1 vaccine regimen (RV144) conferred 31% vaccine efficacy at 3 years following the four-shot immunization series, coupled with rapid waning of putative immune correlates of decreased infection risk. New strategies to increase magnitude and durability of protective immunity are critically needed. The RV305 HIV-1 clinical trial evaluated the immunological impact of a follow-up boost of HIV-1-uninfected RV144 recipients after 6-8 years with RV144 immunogens (ALVAC-HIV alone, AIDSVAX B/E gp120 alone, or ALVAC-HIV + AIDSVAX B/E gp120). Previous reports demonstrated that this regimen elicited higher binding, antibody Fc function, and cellular responses than the primary RV144 regimen. However, the impact of the canarypox viral vector in driving antibody specificity, breadth, durability and function is unknown. We performed a follow-up analysis of humoral responses elicited in RV305 to determine the impact of the different booster immunogens on HIV-1 epitope specificity, antibody subclass, isotype, and Fc effector functions. Importantly, we observed that the ALVAC vaccine component directly contributed to improved breadth, function, and durability of vaccine-elicited antibody responses. Extended boosts in RV305 increased circulating antibody concentration and coverage of heterologous HIV-1 strains by V1V2-specific antibodies above estimated protective levels observed in RV144. Antibody Fc effector functions, specifically antibody-dependent cellular cytotoxicity and phagocytosis, were boosted to higher levels than was achieved in RV144. V1V2 Env IgG3, a correlate of lower HIV-1 risk, was not increased; plasma Env IgA (specifically IgA1), a correlate of increased HIV-1 risk, was elevated. The quality of the circulating polyclonal antibody response changed with each booster immunization. Remarkably, the ALVAC-HIV booster immunogen induced antibody responses post-second boost, indicating that the viral vector immunogen can be utilized to selectively enhance immune correlates of decreased HIV-1 risk. These results reveal a complex dynamic of HIV-1 immunity post-vaccination that may require careful balancing to achieve protective immunity in the vaccinated population. Trial registration: RV305 clinical trial (ClinicalTrials.gov number, NCT01435135). ClinicalTrials.gov Identifier: NCT00223080.
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Affiliation(s)
- LaTonya D. Williams
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sheetal S. Sawant
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Siriwat Akapirat
- Department of Retrovirology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Lindsay C. Dahora
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Matthew Zirui Tay
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sherry Stanfield-Oakley
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Saintedym Wills
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Derrick Goodman
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - DeAnna Tenney
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Rachel L. Spreng
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Lu Zhang
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Nicole L. Yates
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Michael A. Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - David Easterhoff
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Thomas J. Hope
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | | | - Punnee Pittisuttithum
- Royal Thai Army Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sorachai Nitayaphan
- Royal Thai Army Component, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jean-Louis Excler
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, 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
| | - 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
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Robert J. O’Connell
- Department of Retrovirology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Nicos Karasavvas
- Department of Retrovirology, US Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Guido Ferrari
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
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10
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Haynes BF, Wiehe K, Borrow P, Saunders KO, Korber B, Wagh K, McMichael AJ, Kelsoe G, Hahn BH, Alt F, Shaw GM. Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nat Rev Immunol 2023; 23:142-158. [PMID: 35962033 PMCID: PMC9372928 DOI: 10.1038/s41577-022-00753-w] [Citation(s) in RCA: 180] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
After nearly four decades of research, a safe and effective HIV-1 vaccine remains elusive. There are many reasons why the development of a potent and durable HIV-1 vaccine is challenging, including the extraordinary genetic diversity of HIV-1 and its complex mechanisms of immune evasion. HIV-1 envelope glycoproteins are poorly recognized by the immune system, which means that potent broadly neutralizing antibodies (bnAbs) are only infrequently induced in the setting of HIV-1 infection or through vaccination. Thus, the biology of HIV-1-host interactions necessitates novel strategies for vaccine development to be designed to activate and expand rare bnAb-producing B cell lineages and to select for the acquisition of critical improbable bnAb mutations. Here we discuss strategies for the induction of potent and broad HIV-1 bnAbs and outline the steps that may be necessary for ultimate success.
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Affiliation(s)
- Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Kshitij Wagh
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederick Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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11
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Abstract
Human immunodeficiency virus type 1 (HIV-1) envelope (Env), a heterotrimer of gp120-gp41 subunits, mediates fusion of the viral and host cell membranes after interactions with the host receptor CD4 and a coreceptor. CD4 binding induces rearrangements in Env trimer, resulting in a CD4-induced (CD4i) open Env conformation. Structural studies of antibodies isolated from infected donors have defined antibody-Env interactions, with one class of antibodies specifically recognizing the CD4i open Env conformation. In this study, we characterized a group of monoclonal antibodies isolated from HIV-1 infected donors (V2i MAbs) that displayed characteristics of CD4i antibodies. Binding experiments demonstrated that the V2i MAbs preferentially recognize CD4-bound open Env trimers. Structural characterizations of V2i MAb-Env-CD4 trimer complexes using single-particle cryo-electron microscopy showed recognition by V2i MAbs using different angles of approach to the gp120 V1V2 domain and the β2/β3 strands on a CD4i open conformation Env with no direct interactions of the MAbs with CD4. We also characterized CG10, a CD4i antibody that was raised in mice immunized with a gp120-CD4 complex, bound to an Env trimer plus CD4. CG10 exhibited characteristics similar to those of the V2i antibodies, i.e., recognition of the open Env conformation, but showed direct contacts to both CD4 and gp120. Structural comparisons of these and previously characterized CD4i antibody interactions with Env provide a suggested mechanism for how these antibodies are elicited during HIV-1 infection. IMPORTANCE The RV144 HIV-1 clinical vaccination trial showed modest protection against viral infection. Antibody responses to the V1V2 region of HIV-1 Env gp120 were correlated inversely with the risk of infection, and data from three other clinical vaccine trials suggested a similar signal. In addition, antibodies targeting V1V2 have been correlated with protections from simian immunodeficiency virus (SIV) and simian-human immunodeficiency virus (SHIV) infections in nonhuman primates. We structurally characterized V2i antibodies directed against V1V2 isolated from HIV-1 infected humans in complex with open Env trimers bound to the host receptor CD4. We also characterized a CD4i antibody that interacts with CD4 as well as the gp120 subunit of an open Env trimer. Our study suggests how V2i and CD4i antibodies were elicited during HIV-1 infection.
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12
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Mayer-Blackwell K, Johnson AM, Potchen N, Minot SS, Heptinstall J, Seaton K, Sawant S, Shen X, Tomaras GD, Fiore-Gartland A, Kublin JG. Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines. Front Immunol 2022; 13:983313. [PMID: 36311720 PMCID: PMC9597301 DOI: 10.3389/fimmu.2022.983313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Many participants in HIV-1 vaccine trials, who have not previously been exposed to or vaccinated against HIV-1, display serum immunoglobulin antibodies that bind the gp41 region of HIV-1 envelope prior to vaccination. Previous studies have hypothesized that these pre-existing antibodies may be cross-reactive and may skew future vaccine responses. In 12 large studies conducted by the HIV Vaccine Trial Network (HVTN) (n=1470 individuals), we find wide variation among participants in the pre-vaccine levels of gp41-reactive antibodies as measured by the binding antibody multiplex assay (BAMA). In the absence of exposure to the gp41 immunogen, anti-gp41 IgG levels were temporally stable over 26-52 weeks in repeated measures of placebo recipients. The analysis revealed that the geometric mean of pre-vaccine anti-gp41 IgG response was greater among participants in South Africa compared with participants in the United States. With gene-level metagenomic sequencing of pre-vaccination fecal samples collected from participants in one trial (HVTN 106), we detected positive associations between pre-vaccine anti-gp41 IgG and abundance of genes from multiple taxa in the Eubacteriales order. The genes most strongly associated with higher baseline anti-gp41 IgG mapped to a clade containing Blautia wexlerae and closely related strains. In trials with vaccine products containing the full or partial portion of gp41 immunogen alongside a gp120 immunogen, we did not find evidence that individuals with higher baseline anti-gp41 IgG had different levels of anti-gp120 IgG after vaccination compared to individuals with lower pre-vaccine anti-gp41 levels (pooled estimate of standardized mean difference -0.01 with a 95% CI [-0.37; 0.34]).
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Affiliation(s)
- Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Andrew M. Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Nicole Potchen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Simon S. Minot
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jack Heptinstall
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Kelly Seaton
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Sheetal Sawant
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Xiaoying Shen
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, NC, United States
- Department of Surgery, Duke University, Durham, NC, United States
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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13
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Files JK, Sterrett S, Henostroza S, Fucile C, Maroney K, Fram T, Mallal S, Kalams S, Carlson J, Rosenberg A, Erdmann N, Bansal A, Goepfert PA. HLA-II-Associated HIV-1 Adaptation Decreases CD4 + T-Cell Responses in HIV-1 Vaccine Recipients. J Virol 2022; 96:e0119122. [PMID: 36000845 PMCID: PMC9472760 DOI: 10.1128/jvi.01191-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
Abstract
Epitopes with evidence of HLA-II-associated adaptation induce poorly immunogenic CD4+ T-cell responses in HIV-positive (HIV+) individuals. Many such escaped CD4+ T-cell epitopes are encoded by HIV-1 vaccines being evaluated in clinical trials. Here, we assessed whether this viral adaptation adversely impacts CD4+ T-cell responses following HIV-1 vaccination, thereby representing escaped epitopes. When evaluated in separate peptide pools, vaccine-encoded adapted epitopes (AE) induced CD4+ T-cell responses less frequently than nonadapted epitopes (NAE). We also demonstrated that in a polyvalent vaccine, where both forms of the same epitope were encoded, AE were less immunogenic. NAE-specific CD4+ T cells had increased, albeit low, levels of interferon gamma (IFN-γ) cytokine production. Single-cell transcriptomic analyses showed that NAE-specific CD4+ T cells expressed interferon-related genes, while AE-specific CD4+ T cells resembled a Th2 phenotype. Importantly, the magnitude of NAE-specific CD4+ T-cell responses, but not that of AE-specific responses, was found to positively correlate with Env-specific antibodies in a vaccine efficacy trial. Together, these findings show that HLA-II-associated viral adaptation reduces CD4+ T-cell responses in HIV-1 vaccine recipients and suggest that vaccines encoding a significant number of AE may not provide optimal B-cell help for HIV-specific antibody production. IMPORTANCE Despite decades of research, an effective HIV-1 vaccine remains elusive. Vaccine strategies leading to the generation of broadly neutralizing antibodies are likely needed to provide the best opportunity of generating a protective immune response against HIV-1. Numerous studies have demonstrated that T-cell help is necessary for effective antibody generation. However, immunogen sequences from recent HIV-1 vaccine efficacy trials include CD4+ T-cell epitopes that have evidence of immune escape. Our study shows that these epitopes, termed adapted epitopes, elicit lower frequencies of CD4+ T-cell responses in recipients from multiple HIV-1 vaccine trials. Additionally, the counterparts to these epitopes, termed nonadapted epitopes, elicited CD4+ T-cell responses that correlated with Env-specific antibodies in one efficacy trial. These results suggest that vaccine-encoded adapted epitopes dampen CD4+ T-cell responses, potentially impacting both HIV-specific antibody production and efficacious vaccine efforts.
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Affiliation(s)
- Jacob K. Files
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sarah Sterrett
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sebastian Henostroza
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher Fucile
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kevin Maroney
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tim Fram
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Simon Mallal
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Spyros Kalams
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Alexander Rosenberg
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathan Erdmann
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anju Bansal
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul A. Goepfert
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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14
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Moodie Z, Dintwe O, Sawant S, Grove D, Huang Y, Janes H, Heptinstall J, Omar FL, Cohen K, De Rosa SC, Zhang L, Yates NL, Sarzotti-Kelsoe M, Seaton KE, Laher F, Bekker LG, Malahleha M, Innes C, Kassim S, Naicker N, Govender V, Sebe M, Singh N, Kotze P, Lazarus E, Nchabeleng M, Ward AM, Brumskine W, Dubula T, Randhawa AK, Grunenberg N, Hural J, Kee JJ, Benkeser D, Jin Y, Carpp LN, Allen M, D’Souza P, Tartaglia J, DiazGranados CA, Koutsoukos M, Gilbert PB, Kublin JG, Corey L, Andersen-Nissen E, Gray GE, Tomaras GD, McElrath MJ. Analysis of the HIV Vaccine Trials Network 702 Phase 2b-3 HIV-1 Vaccine Trial in South Africa Assessing RV144 Antibody and T-Cell Correlates of HIV-1 Acquisition Risk. J Infect Dis 2022; 226:246-257. [PMID: 35758878 PMCID: PMC9890908 DOI: 10.1093/infdis/jiac260] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The ALVAC/gp120 + MF59 vaccines in the HIV Vaccine Trials Network (HVTN) 702 efficacy trial did not prevent human immunodeficiency virus-1 (HIV-1) acquisition. Vaccine-matched immunological endpoints that were correlates of HIV-1 acquisition risk in RV144 were measured in HVTN 702 and evaluated as correlates of HIV-1 acquisition. METHODS Among 1893 HVTN 702 female vaccinees, 60 HIV-1-seropositive cases and 60 matched seronegative noncases were sampled. HIV-specific CD4+ T-cell and binding antibody responses were measured 2 weeks after fourth and fifth immunizations. Cox proportional hazards models assessed prespecified responses as predictors of HIV-1 acquisition. RESULTS The HVTN 702 Env-specific CD4+ T-cell response rate was significantly higher than in RV144 (63% vs 40%, P = .03) with significantly lower IgG binding antibody response rate and magnitude to 1086.C V1V2 (67% vs 100%, P < .001; Pmag < .001). Although no significant univariate associations were observed between any T-cell or binding antibody response and HIV-1 acquisition, significant interactions were observed (multiplicity-adjusted P ≤.03). Among vaccinees with high IgG A244 V1V2 binding antibody responses, vaccine-matched CD4+ T-cell endpoints associated with decreased HIV-1 acquisition (estimated hazard ratios = 0.40-0.49 per 1-SD increase in CD4+ T-cell endpoint). CONCLUSIONS HVTN 702 and RV144 had distinct immunogenicity profiles. However, both identified significant correlations (univariate or interaction) for IgG V1V2 and polyfunctional CD4+ T cells with HIV-1 acquisition. Clinical Trials Registration . NCT02968849.
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Affiliation(s)
- Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - One Dintwe
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Sheetal Sawant
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Doug Grove
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Jack Heptinstall
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Faatima Laher Omar
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Kristen Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Lu Zhang
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Nicole L Yates
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Marcella Sarzotti-Kelsoe
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Department of Immunology, Duke University, Durham, North Carolina, USA
| | - Kelly E Seaton
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Fatima Laher
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Linda Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Mookho Malahleha
- Setshaba Research Centre, Soshanguve, South Africa
- Synergy Biomed Research Institute, East London, South Africa
| | - Craig Innes
- The Aurum Institute, Klerksdorp, South Africa
| | - Sheetal Kassim
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Nivashnee Naicker
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | | | | | - Nishanta Singh
- South African Medical Research Council, Durban, South Africa
| | - Philip Kotze
- Qhakaza Mbokodo Research Centre, Ladysmith, South Africa
| | - Erica Lazarus
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maphoshane Nchabeleng
- Mecru Clinical Research Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Amy M Ward
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Thozama Dubula
- Nelson Mandela Academic Clinical Research Unit and Department of Internal Medicine and Pharmacology, Walter Sisulu University, Mthatha, South Africa
| | - April K Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nicole Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jia Jin Kee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David Benkeser
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Yutong Jin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Mary Allen
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Patricia D’Souza
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Erica Andersen-Nissen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Durban, South Africa
| | - Georgia D Tomaras
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Department of Immunology, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
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15
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Du M, Zhao X, Sun J. Variable selection for case-cohort studies with informatively interval-censored outcomes. Comput Stat Data Anal 2022. [DOI: 10.1016/j.csda.2022.107484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Han S, Fong Y, Huang Y. Testing a global null hypothesis using ensemble machine learning methods. Stat Med 2022; 41:2417-2426. [PMID: 35253259 PMCID: PMC9035066 DOI: 10.1002/sim.9362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 12/14/2021] [Accepted: 02/12/2022] [Indexed: 08/27/2024]
Abstract
Testing a global null hypothesis that there are no significant predictors for a binary outcome of interest among a large set of biomarker measurements is an important task in biomedical studies. We seek to improve the power of such testing methods by leveraging ensemble machine learning methods. Ensemble machine learning methods such as random forest, bagging, and adaptive boosting model the relationship between the outcome and the predictor nonparametrically, while stacking combines the strength of multiple learners. We demonstrate the power of the proposed testing methods through Monte Carlo studies and show the use of the methods by applying them to the immunologic biomarkers dataset from the RV144 HIV vaccine efficacy trial.
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Affiliation(s)
- Sunwoo Han
- 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
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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17
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Cable J, Rappuoli R, Klemm EJ, Kang G, Mutreja A, Wright GJ, Pizza M, Castro SA, Hoffmann JP, Alter G, Carfi A, Pollard AJ, Krammer F, Gupta RK, Wagner CE, Machado V, Modjarrad K, Corey L, B Gilbert P, Dougan G, Lurie N, Bjorkman PJ, Chiu C, Nemes E, Gordon SB, Steer AC, Rudel T, Blish CA, Sandberg JT, Brennan K, Klugman KP, Stuart LM, Madhi SA, Karp CL. Innovative vaccine approaches-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1511:59-86. [PMID: 35029310 DOI: 10.1111/nyas.14739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022]
Abstract
The rapid development of COVID-19 vaccines was the result of decades of research to establish flexible vaccine platforms and understand pathogens with pandemic potential, as well as several novel changes to the vaccine discovery and development processes that partnered industry and governments. And while vaccines offer the potential to drastically improve global health, low-and-middle-income countries around the world often experience reduced access to vaccines and reduced vaccine efficacy. Addressing these issues will require novel vaccine approaches and platforms, deeper insight how vaccines mediate protection, and innovative trial designs and models. On June 28-30, 2021, experts in vaccine research, development, manufacturing, and deployment met virtually for the Keystone eSymposium "Innovative Vaccine Approaches" to discuss advances in vaccine research and development.
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Affiliation(s)
| | | | | | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK.,Department of Biology, Hull York Medical School, and York Biomedical Research Institute, University of York, York, UK
| | | | - Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joseph P Hoffmann
- Departments of Pediatrics and Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts.,Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Florian Krammer
- The Tisch Cancer Institute and Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK.,Africa Health Research Institute, Durban, South Africa
| | - Caroline E Wagner
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Viviane Machado
- Measles and Respiratory Viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Lawrence Corey
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Lurie
- Coalition for Epidemic Preparedness Innovations, Oslo, Norway.,Harvard Medical School, Boston, Massachusetts
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Elisa Nemes
- Division of Immunology, Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Andrew C Steer
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Department of General Medicine, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Thomas Rudel
- Microbiology Biocenter, University of Würzburg, Würzburg, Germany
| | - Catherine A Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford Immunology Program, Stanford University School of Medicine, Stanford, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - John Tyler Sandberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kiva Brennan
- National Children's Research Centre, Crumlin and School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Lynda M Stuart
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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18
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Fong Y, Xu J. Forward Stepwise Deep Autoencoder-based Monotone Nonlinear Dimensionality Reduction Methods. J Comput Graph Stat 2021; 30:519-529. [PMID: 34924737 DOI: 10.1080/10618600.2020.1856119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Dimensionality reduction is an unsupervised learning task aimed at creating a low-dimensional summary and/or extracting the most salient features of a dataset. Principal components analysis (PCA) is a linear dimensionality reduction method in the sense that each principal component is a linear combination of the input variables. To allow features that are nonlinear functions of the input variables, many nonlinear dimensionality reduction methods have been proposed. In this paper we propose novel nonlinear dimensionality reduction methods based on bottleneck deep autoencoders (Kramer, 1991). Our contributions are two-fold: (1) We introduce a monotonicity constraint into bottleneck deep autoencoders for estimating a single nonlinear component and propose two methods for fitting the model. (2) We propose a new, forward stepwise (FS) deep learning architecture for estimating multiple nonlinear components. The former helps extract interpretable, monotone components when the assumption of monotonicity holds, and the latter helps evaluate reconstruction errors in the original data space for a range of components. We conduct numerical studies to compare different model fitting methods and use two real data examples from the studies of human immune responses to HIV to illustrate the proposed methods.
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Affiliation(s)
- Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Jun Xu
- Cincinnati, United States
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19
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Hejazi NS, van der Laan MJ, Janes HE, Gilbert PB, Benkeser DC. Efficient nonparametric inference on the effects of stochastic interventions under two-phase sampling, with applications to vaccine efficacy trials. Biometrics 2021; 77:1241-1253. [PMID: 32949147 PMCID: PMC8016405 DOI: 10.1111/biom.13375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/02/2020] [Accepted: 09/01/2020] [Indexed: 12/17/2022]
Abstract
The advent and subsequent widespread availability of preventive vaccines has altered the course of public health over the past century. Despite this success, effective vaccines to prevent many high-burden diseases, including human immunodeficiency virus (HIV), have been slow to develop. Vaccine development can be aided by the identification of immune response markers that serve as effective surrogates for clinically significant infection or disease endpoints. However, measuring immune response marker activity is often costly, which has motivated the usage of two-phase sampling for immune response evaluation in clinical trials of preventive vaccines. In such trials, the measurement of immunological markers is performed on a subset of trial participants, where enrollment in this second phase is potentially contingent on the observed study outcome and other participant-level information. We propose nonparametric methodology for efficiently estimating a counterfactual parameter that quantifies the impact of a given immune response marker on the subsequent probability of infection. Along the way, we fill in theoretical gaps pertaining to the asymptotic behavior of nonparametric efficient estimators in the context of two-phase sampling, including a multiple robustness property enjoyed by our estimators. Techniques for constructing confidence intervals and hypothesis tests are presented, and an open source software implementation of the methodology, the txshift R package, is introduced. We illustrate the proposed techniques using data from a recent preventive HIV vaccine efficacy trial.
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Affiliation(s)
- Nima S Hejazi
- Graduate Group in Biostatistics, University of California, Berkeley, California
- Center for Computational Biology, University of California, Berkeley, California
| | - Mark J van der Laan
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, California
- Department of Statistics, University of California, Berkeley, California
| | - Holly E Janes
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Peter B Gilbert
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - David C Benkeser
- Department of Biostatistics & Computational Biology, Rollins School of Public Health, Emory University, Atlanta, Georgia
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20
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Han S, Williamson BD, Fong Y. Improving random forest predictions in small datasets from two-phase sampling designs. BMC Med Inform Decis Mak 2021; 21:322. [PMID: 34809631 PMCID: PMC8607560 DOI: 10.1186/s12911-021-01688-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While random forests are one of the most successful machine learning methods, it is necessary to optimize their performance for use with datasets resulting from a two-phase sampling design with a small number of cases-a common situation in biomedical studies, which often have rare outcomes and covariates whose measurement is resource-intensive. METHODS Using an immunologic marker dataset from a phase III HIV vaccine efficacy trial, we seek to optimize random forest prediction performance using combinations of variable screening, class balancing, weighting, and hyperparameter tuning. RESULTS Our experiments show that while class balancing helps improve random forest prediction performance when variable screening is not applied, class balancing has a negative impact on performance in the presence of variable screening. The impact of the weighting similarly depends on whether variable screening is applied. Hyperparameter tuning is ineffective in situations with small sample sizes. We further show that random forests under-perform generalized linear models for some subsets of markers, and prediction performance on this dataset can be improved by stacking random forests and generalized linear models trained on different subsets of predictors, and that the extent of improvement depends critically on the dissimilarities between candidate learner predictions. CONCLUSION In small datasets from two-phase sampling design, variable screening and inverse sampling probability weighting are important for achieving good prediction performance of random forests. In addition, stacking random forests and simple linear models can offer improvements over random forests.
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Affiliation(s)
- Sunwoo Han
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Brian D. Williamson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
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21
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Shangguan S, Ehrenberg PK, Geretz A, Yum L, Kundu G, May K, Fourati S, Nganou-Makamdop K, Williams LD, Sawant S, Lewitus E, Pitisuttithum P, Nitayaphan S, Chariyalertsak S, Rerks-Ngarm S, Rolland M, Douek DC, Gilbert P, Tomaras GD, Michael NL, Vasan S, Thomas R. Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1. eLife 2021; 10:69577. [PMID: 34533134 PMCID: PMC8514236 DOI: 10.7554/elife.69577] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
A gene signature was previously found to be correlated with mosaic adenovirus 26 vaccine protection in simian immunodeficiency virus and simian-human immunodeficiency virus challenge models in non-human primates. In this report, we investigated the presence of this signature as a correlate of reduced risk in human clinical trials and potential mechanisms of protection. The absence of this gene signature in the DNA/rAd5 human vaccine trial, which did not show efficacy, strengthens our hypothesis that this signature is only enriched in studies that demonstrated protection. This gene signature was enriched in the partially effective RV144 human trial that administered the ALVAC/protein vaccine, and we find that the signature associates with both decreased risk of HIV-1 acquisition and increased vaccine efficacy (VE). Total RNA-seq in a clinical trial that used the same vaccine regimen as the RV144 HIV vaccine implicated antibody-dependent cellular phagocytosis (ADCP) as a potential mechanism of vaccine protection. CITE-seq profiling of 53 surface markers and transcriptomes of 53,777 single cells from the same trial showed that genes in this signature were primarily expressed in cells belonging to the myeloid lineage, including monocytes, which are major effector cells for ADCP. The consistent association of this transcriptome signature with VE represents a tool both to identify potential mechanisms, as with ADCP here, and to screen novel approaches to accelerate the development of new vaccine candidates.
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Affiliation(s)
- Shida Shangguan
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Philip K Ehrenberg
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States
| | - Aviva Geretz
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Lauren Yum
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Gautam Kundu
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Kelly May
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Slim Fourati
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, United States
| | | | - LaTonya D Williams
- Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
| | - Sheetal Sawant
- Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
| | - Eric Lewitus
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Punnee Pitisuttithum
- Vaccine Trial Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Suwat Chariyalertsak
- Research Institute for Health Sciences and Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | | | - Morgane Rolland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | | | - Peter Gilbert
- Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Georgia D Tomaras
- Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, United States
| | - Nelson L Michael
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States
| | - Sandhya Vasan
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Rasmi Thomas
- US Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, United States
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22
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Eslamizar L, Petrovas C, Leggat DJ, Furr K, Lifton ML, Levine G, Ma S, Fletez-Brant C, Hoyland W, Prabhakaran M, Narpala S, Boswell K, Yamamoto T, Liao HX, Pickup D, Ramsburg E, Sutherland L, McDermott A, Roederer M, Montefiori D, Koup RA, Haynes BF, Letvin NL, Santra S. Recombinant MVA-prime elicits neutralizing antibody responses by inducing antigen-specific B cells in the germinal center. NPJ Vaccines 2021; 6:15. [PMID: 33495459 PMCID: PMC7835239 DOI: 10.1038/s41541-020-00277-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/07/2020] [Indexed: 01/23/2023] Open
Abstract
The RV144 HIV-1 vaccine trial has been the only clinical trial to date that has shown any degree of efficacy and associated with the presence of vaccine-elicited HIV-1 envelope-specific binding antibody and CD4+ T-cell responses. This trial also showed that a vector-prime protein boost combined vaccine strategy was better than when used alone. Here we have studied three different priming vectors-plasmid DNA, recombinant MVA, and recombinant VSV, all encoding clade C transmitted/founder Env 1086 C gp140, for priming three groups of six non-human primates each, followed by a protein boost with adjuvanted 1086 C gp120 protein. Our data showed that MVA-priming favors the development of higher antibody binding titers and neutralizing activity compared with other vectors. Analyses of the draining lymph nodes revealed that MVA-prime induced increased germinal center reactivity characterized by higher frequencies of germinal center (PNAhi) B cells, higher frequencies of antigen-specific B-cell responses as well as an increased frequency of the highly differentiated (ICOShiCD150lo) Tfh-cell subset.
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Affiliation(s)
- Leila Eslamizar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Integrative Toxicology, Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals, Inc., 175 Briar Ridge Road, Ridgefield, CT, 06877, USA
| | - Constantinos Petrovas
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland.
| | | | - Kathryn Furr
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Michelle L Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gail Levine
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Steven Ma
- Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | | | | | | | | | | | | | - Hua-Xin Liao
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | - Norman L Letvin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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23
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Affiliation(s)
- Cesar J. Lopez Angel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Duke Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Georgia D. Tomaras
- Duke Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
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24
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Palli R, Seaton KE, Piepenbrink MS, Hural J, Goepfert PA, Laher F, Buchbinder SP, Churchyard G, Gray GE, Robinson HL, Huang Y, Janes H, Kobie JJ, Keefer MC, Tomaras GD, Thakar J. Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature. Sci Rep 2020; 10:13031. [PMID: 32747654 PMCID: PMC7398916 DOI: 10.1038/s41598-020-69007-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Efficacious HIV-1 vaccination requires elicitation of long-lived antibody responses. However, our understanding of how different vaccine types elicit durable antibody responses is lacking. To assess the impact of vaccine type on antibody responses, we measured IgG isotypes against four consensus HIV antigens from 2 weeks to 10 years post HIV-1 vaccination and used mixed effects models to estimate half-life of responses in four human clinical trials. Compared to protein-boosted regimens, half-lives of gp120-specific antibodies were longer but peak magnitudes were lower in Modified Vaccinia Ankara (MVA)-boosted regimens. Furthermore, gp120-specific B cell transcriptomics from MVA-boosted and protein-boosted vaccines revealed a distinct signature at a peak (2 weeks after last vaccination) including CD19, CD40, and FCRL2-5 activation along with increased B cell receptor signaling. Additional analysis revealed contributions of RIG-I-like receptor pathway and genes such as SMAD5 and IL-32 to antibody durability. Thus, this study provides novel insights into vaccine induced antibody durability and B-cell receptor signaling.
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Affiliation(s)
- Rohith Palli
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kelly E Seaton
- Duke Human Vaccine Institute and Departments of Surgery, Immunology, and Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Michael S Piepenbrink
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul A Goepfert
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fatima Laher
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan P Buchbinder
- Bridge HIV, San Francisco Department of Public Health and Departments of Medicine, Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Cape Town, South Africa
| | | | - Yunda Huang
- 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, USA
| | - James J Kobie
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael C Keefer
- Department of Medicine, Infectious Diseases Division, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute and Departments of Surgery, Immunology, and Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14620, USA.
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, 14620, USA.
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25
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Systems serology for decoding infection and vaccine-induced antibody responses to HIV-1. Curr Opin HIV AIDS 2020; 14:253-264. [PMID: 31033729 DOI: 10.1097/coh.0000000000000558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW Experimental and analytical advances have enabled systematic, high-resolution studies of humoral immune responses, and are beginning to define mechanisms of immunity to HIV. RECENT FINDINGS High-throughput, information-rich experimental and analytical methods, whether genomic, proteomic, or transcriptomic, have firmly established their value across a diversity of fields. Consideration of these tools as trawlers in 'fishing expeditions' has faded as 'data-driven discovery' has come to be valued as an irreplaceable means to develop fundamental understanding of biological systems. Collectively, studies of HIV-1 infection and vaccination including functional, biophysical, and biochemical humoral profiling approaches have provided insights into the phenotypic characteristics of individual and pools of antibodies. Relating these measures to clinical status, protection/efficacy outcomes, and cellular profiling data using machine learning has offered the possibility of identifying unanticipated mechanisms of action and gaining insights into fundamental immunological processes that might otherwise be difficult to decipher. SUMMARY Recent evidence establishes that systematic data collection and application of machine learning approaches can identify humoral immune correlates that are generalizable across distinct HIV-1 immunogens and vaccine regimens and translatable between model organisms and the clinic. These outcomes provide a strong rationale supporting the utility and further expansion of these approaches both in support of vaccine development and more broadly in defining mechanisms of immunity.
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26
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Abstract
Development of improved approaches for HIV-1 prevention will likely be required for a durable end to the global AIDS pandemic. Recent advances in preclinical studies and early phase clinical trials offer renewed promise for immunologic strategies for blocking acquisition of HIV-1 infection. Clinical trials are currently underway to evaluate the efficacy of two vaccine candidates and a broadly neutralizing antibody (bNAb) to prevent HIV-1 infection in humans. However, the vast diversity of HIV-1 is a major challenge for both active and passive immunization. Here we review current immunologic strategies for HIV-1 prevention, with a focus on current and next-generation vaccines and bNAbs.
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Affiliation(s)
- Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA;
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- New Mexico Consortium, Los Alamos, New Mexico 87545, USA
| | - Bette Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- New Mexico Consortium, Los Alamos, New Mexico 87545, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA;
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
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27
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Du M, Zhou Q, Zhao S, Sun J. Regression Analysis of Case-cohort Studies in the Presence of Dependent Interval Censoring. J Appl Stat 2020; 48:846-865. [PMID: 33767519 PMCID: PMC7986575 DOI: 10.1080/02664763.2020.1752633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
Abstract
The case-cohort design is widely used as a means of reducing the cost in large cohort studies, especially when the disease rate is low and covariate measurements may be expensive, and has been discussed by many authors. In this paper, we discuss regression analysis of case-cohort studies that produce interval-censored failure time with dependent censoring, a situation for which there does not seem to exist an established approach. For inference, a sieve inverse probability weighting estimation procedure is developed with the use of Bernstein polynomials to approximate the unknown baseline cumulative hazard functions. The proposed estimators are shown to be consistent and the asymptotic normality of the resulting regression parameter estimators are established. A simulation study is conducted to assess the finite sample properties of the proposed approach and indicates that it works well in practical situations. The proposed method is applied to an HIV/AIDS case-cohort study that motivated this investigation.
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Affiliation(s)
- Mingyue Du
- Center for Applied Statistical Research and College of Mathematics, Jilin University, Changchun, People's Republic of China
| | - Qingning Zhou
- Department of Mathematics and Statistics, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Shishun Zhao
- Center for Applied Statistical Research and College of Mathematics, Jilin University, Changchun, People's Republic of China
| | - Jianguo Sun
- Department of Statistics, University of Missouri, Columbia, MO, USA
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28
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Korber B, Fischer W. T cell-based strategies for HIV-1 vaccines. Hum Vaccin Immunother 2020; 16:713-722. [PMID: 31584318 PMCID: PMC7227724 DOI: 10.1080/21645515.2019.1666957] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/19/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Despite 30 years of effort, we do not have an effective HIV-1 vaccine. Over the past decade, the HIV-1 vaccine field has shifted emphasis toward antibody-based vaccine strategies, following a lack of efficacy in CD8+ T-cell-based vaccine trials. Several lines of evidence, however, suggest that improved CD8+ T-cell-directed strategies could benefit an HIV-1 vaccine. First, T-cell responses often correlate with good outcomes in non-human primate (NHP) challenge models. Second, subgroup studies of two no-efficacy human clinical vaccine trials found associations between CD8+ T-cell responses and protective effects. Finally, improved strategies can increase the breadth and potency of CD8+ T-cell responses, direct them toward preferred epitopes (that are highly conserved and/or associated with viral control), or both. Optimized CD8+ T-cell vaccine strategies are promising in both prophylactic and therapeutic settings. This commentary briefly outlines some encouraging findings from T-cell vaccine studies, and then directly compares key features of some T-cell vaccine candidates currently in the clinical pipeline.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Will Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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29
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Zhao H, Wu Q, Gilbert PB, Chen YQ, Sun J. A regularized estimation approach for case-cohort periodic follow-up studies with an application to HIV vaccine trials. Biom J 2020; 62:1176-1191. [PMID: 32080888 DOI: 10.1002/bimj.201900180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/21/2019] [Accepted: 11/27/2019] [Indexed: 11/05/2022]
Abstract
This paper discusses regression analysis of the failure time data arising from case-cohort periodic follow-up studies, and one feature of such data, which makes their analysis much more difficult, is that they are usually interval-censored rather than right-censored. Although some methods have been developed for general failure time data, there does not seem to exist an established procedure for the situation considered here. To address the problem, we present a semiparametric regularized procedure and develop a simple algorithm for the implementation of the proposed method. In addition, unlike some existing procedures for similar situations, the proposed procedure is shown to have the oracle property, and an extensive simulation is conducted and it suggests that the presented approach seems to work well for practical situations. The method is applied to an HIV vaccine trial that motivated this study.
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Affiliation(s)
- Hui Zhao
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Wuhan, P. R. China
| | - Qiwei Wu
- Department of Statistics, University of Missouri, Columbia, MO, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center & Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ying Q Chen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center & Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jianguo Sun
- Department of Statistics, University of Missouri, Columbia, MO, USA
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30
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Valliyott L, Dungdung R, Pilankatta R. Semi-quantification of antibody-dependent enhancement (ADE) in the uptake of Adenovirus serotype 5 into THP-1 cells. Anal Biochem 2020; 591:113568. [PMID: 31881180 DOI: 10.1016/j.ab.2019.113568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022]
Abstract
Replication defective recombinant Ad5 vectors (rAdV5) are extensively explored for its applications in gene therapy and vaccine delivery. Ad5 enter into monocytes and macrophages through CAR independent route as an immune complex termed as antibody-dependent enhancement (ADE). We developed an effective method for estimating the ADE of rAdV5 encoding GFP (rAdV5-GFP) into THP-1 cells, using fluorimetric semi-quantification of GFP. Initially, twenty numbers of human sera samples were screened in HeLa cells for anti-Ad5 antibody titer using neutralization assay. Uptake of rAdV5-GFP in THP-1 cells was observed only after pre-incubation with the serially diluted human sera which are attributed to ADE. The optimal dilution which showed the maximum GFP expression as per the fluorescence microscopic analysis in THP-1 cells was used for further analysis. Fluorimetric analysis of the THP-1 cell lysate showed a maximum GFP intensity of 17058 RFU, which was equivalent to the 0.397 pmoles of Alexa Fluor 488 under the same experimental condition. Similarly, immunoblot analysis of GFP in THP-1 cell lysate and HeLa cell lysate confirmed the entry of rAdV5-GFP into the cells. The assay can serve as a platform for understanding the molecular events involved in ADE for the uptake of viruses into immune cells.
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Affiliation(s)
- Lathika Valliyott
- Department of Biochemistry and Molecular Biology, School of Biological Sciences, Krishna Block, Central University of Kerala, Periya, Kasargod, Kerala, 671316, India
| | - Ranjeet Dungdung
- Department of Biochemistry and Molecular Biology, School of Biological Sciences, Krishna Block, Central University of Kerala, Periya, Kasargod, Kerala, 671316, India
| | - Rajendra Pilankatta
- Department of Biochemistry and Molecular Biology, School of Biological Sciences, Krishna Block, Central University of Kerala, Periya, Kasargod, Kerala, 671316, India.
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31
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Li SS, Gilbert PB, Carpp LN, Pyo CW, Janes H, Fong Y, Shen X, Neidich SD, Goodman D, deCamp A, Cohen KW, Ferrari G, Hammer SM, Sobieszczyk ME, Mulligan MJ, Buchbinder SP, Keefer MC, DeJesus E, Novak RM, Frank I, McElrath MJ, Tomaras GD, Geraghty DE, Peng X. Fc Gamma Receptor Polymorphisms Modulated the Vaccine Effect on HIV-1 Risk in the HVTN 505 HIV Vaccine Trial. J Virol 2019; 93:e02041-18. [PMID: 31434737 PMCID: PMC6803257 DOI: 10.1128/jvi.02041-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 08/14/2019] [Indexed: 12/19/2022] Open
Abstract
HIV Vaccine Trials Network (HVTN) 505 was a phase 2b efficacy trial of a DNA/recombinant adenovirus 5 (rAd5) HIV vaccine regimen. Although the trial was stopped early for lack of overall efficacy, later correlates of risk and sieve analyses generated the hypothesis that the DNA/rAd5 vaccine regimen protected some vaccinees from HIV infection yet enhanced HIV infection risk for others. Here, we assessed whether and how host Fc gamma receptor (FcγR) genetic variations influenced the DNA/rAd5 vaccine regimen's effect on HIV infection risk. We found that vaccine receipt significantly increased HIV acquisition compared with placebo receipt among participants carrying the FCGR2C-TATA haplotype (comprising minor alleles of four FCGR2C single-nucleotide polymorphism [SNP] sites) (hazard ratio [HR] = 9.79, P = 0.035) but not among participants without the haplotype (HR = 0.86, P = 0.67); the interaction of vaccine and haplotype effect was significant (P = 0.034). Similarly, vaccine receipt increased HIV acquisition compared with placebo receipt among participants carrying the FCGR3B-AGA haplotype (comprising minor alleles of the 3 FCGR3B SNPs) (HR = 2.78, P = 0.058) but not among participants without the haplotype (HR = 0.73, P = 0.44); again, the interaction of vaccine and haplotype was significant (P = 0.047). The FCGR3B-AGA haplotype also influenced whether a combined Env-specific CD8+ T-cell polyfunctionality score and IgG response correlated significantly with HIV risk; an FCGR2A SNP and two FCGR2B SNPs influenced whether anti-gp140 antibody-dependent cellular phagocytosis correlated significantly with HIV risk. These results provide further evidence that Fc gamma receptor genetic variations may modulate HIV vaccine effects and immune function after HIV vaccination.IMPORTANCE By analyzing data from the HVTN 505 efficacy trial of a DNA/recombinant adenovirus 5 (rAd5) vaccine regimen, we found that host genetics, specifically Fc gamma receptor genetic variations, influenced whether receiving the DNA/rAd5 regimen was beneficial, neutral, or detrimental to an individual with respect to HIV-1 acquisition risk. Moreover, Fc gamma receptor genetic variations influenced immune responses to the DNA/rAd5 vaccine regimen. Thus, Fc gamma receptor genetic variations should be considered in the analysis of future HIV vaccine trials and the development of HIV vaccines.
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Affiliation(s)
- Shuying S Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - 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
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chul-Woo Pyo
- Clinical Research 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
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Scott D Neidich
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Derrick Goodman
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Allan deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Scott M Hammer
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Magdalena E Sobieszczyk
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Mark J Mulligan
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Susan P Buchbinder
- Department of Medicine, University of California, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Michael C Keefer
- Division of Infectious Diseases, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | | | | | - Ian Frank
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
- Department of Immunology, Duke University, Durham, North Carolina, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Neidich SD, Fong Y, Li SS, Geraghty DE, Williamson BD, Young WC, Goodman D, Seaton KE, Shen X, Sawant S, Zhang L, deCamp AC, Blette BS, Shao M, Yates NL, Feely F, Pyo CW, Ferrari G, HVTN 505 Team, Frank I, Karuna ST, Swann EM, Mascola JR, Graham BS, Hammer SM, Sobieszczyk ME, Corey L, Janes HE, McElrath MJ, Gottardo R, Gilbert PB, Tomaras GD. Antibody Fc effector functions and IgG3 associate with decreased HIV-1 risk. J Clin Invest 2019; 129:4838-4849. [PMID: 31589165 PMCID: PMC6819135 DOI: 10.1172/jci126391] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 08/07/2019] [Indexed: 12/30/2022] Open
Abstract
HVTN 505 is a preventative vaccine efficacy trial testing DNA followed by recombinant adenovirus serotype 5 (rAd5) in circumcised, Ad5-seronegative men and transgendered persons who have sex with men in the United States. Identified immune correlates of lower HIV-1 risk and a virus sieve analysis revealed that, despite lacking overall efficacy, vaccine-elicited responses exerted pressure on infecting HIV-1 viruses. To interrogate the mechanism of the antibody correlate of HIV-1 risk, we examined antigen-specific antibody recruitment of Fcγ receptors (FcγRs), antibody-dependent cellular phagocytosis (ADCP), and the role of anti-envelope (anti-Env) IgG3. In a prespecified immune correlates analysis, antibody-dependent monocyte phagocytosis and antibody binding to FcγRIIa correlated with decreased HIV-1 risk. Follow-up analyses revealed that anti-Env IgG3 breadth correlated with reduced HIV-1 risk, anti-Env IgA negatively modified infection risk by Fc effector functions, and that vaccine recipients with a specific FcγRIIa single-nucleotide polymorphism locus had a stronger correlation with decreased HIV-1 risk when ADCP, Env-FcγRIIa, and IgG3 binding were high. Additionally, FcγRIIa engagement correlated with decreased viral load setpoint in vaccine recipients who acquired HIV-1. These data support a role for vaccine-elicited anti-HIV-1 Env IgG3, antibody engagement of FcRs, and phagocytosis as potential mechanisms for HIV-1 prevention.
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Affiliation(s)
- Scott D. Neidich
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Youyi Fong
- Statistical Center for HIV/AIDS Research and Prevention
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Shuying S. Li
- Statistical Center for HIV/AIDS Research and Prevention
- 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
| | - Brian D. Williamson
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | | | - Derrick Goodman
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Kelly E. Seaton
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Sheetal Sawant
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Lu Zhang
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | | | - Bryan S. Blette
- Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Mengshu Shao
- Statistical Center for HIV/AIDS Research and Prevention
| | - Nicole L. Yates
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Frederick Feely
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Chul-Woo Pyo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Surgery and
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - HVTN 505 Team
- The HVTN 505 Team is detailed in the Supplemental Acknowledgments
| | - Ian Frank
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia Pennsylvania, USA
| | - Shelly T. Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Scott M. Hammer
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, USA
| | - Magdalena E. Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Holly E. Janes
- Statistical Center for HIV/AIDS Research and Prevention
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Raphael Gottardo
- Statistical Center for HIV/AIDS Research and Prevention
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Peter B. Gilbert
- Statistical Center for HIV/AIDS Research and Prevention
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Surgery and
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
- Department of Immunology, Duke University, Durham, North Carolina, USA
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33
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Hanke T. Aiming for protective T-cell responses: a focus on the first generation conserved-region HIVconsv vaccines in preventive and therapeutic clinical trials. Expert Rev Vaccines 2019; 18:1029-1041. [PMID: 31613649 DOI: 10.1080/14760584.2019.1675518] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: Despite life-saving antiretroviral drugs, an effective HIV-1 vaccine is the best solution and likely a necessary component of any strategy for halting the AIDS epidemic. The currently prevailing aim is to pursue antibody-mediated vaccine protection. With ample evidence for the ability of T cells to control HIV-1 replication, their protective potential should be also harnessed by vaccination. The challenge is to elicit not just any, but protective T cells.Areas covered: This article reviews the clinical experience with the first-generation conserved-region immunogen HIVconsv delivered by combinations of plasmid DNA, simian adenovirus, and poxvirus MVA. The aim of our strategy is to induce strong and broad T cells targeting functionally important parts of HIV-1 proteins common to global variants. These vaccines were tested in eight phase 1/2 preventive and therapeutic clinical trials in Europe and Africa, and induced high frequencies of broadly specific CD8+ T cells capable of in vitro inhibition of four major HIV-1 clades A, B, C and D, and in combination with latency-reactivating agent provided a signal of drug-free virological control in early treated patients.Expert opinion: A number of critical T-cell traits have to come together at the same time to achieve control over HIV-1.
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Affiliation(s)
- Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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34
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Incomplete Downregulation of CD4 Expression Affects HIV-1 Env Conformation and Antibody-Dependent Cellular Cytotoxicity Responses. J Virol 2018; 92:JVI.00484-18. [PMID: 29669829 PMCID: PMC6002730 DOI: 10.1128/jvi.00484-18] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022] Open
Abstract
HIV-1-infected cells expressing envelope glycoproteins (Env) in the CD4-bound conformation on their surfaces are targeted by antibody-dependent cellular cytotoxicity (ADCC) mediated by CD4-induced (CD4i) antibodies and sera from HIV-1-infected individuals (HIV+ sera). By downregulating the surface expression of CD4, Nef prevents Env-CD4 interaction, thus protecting HIV-1-infected cells from ADCC. HIV-1 infectious molecular clones (IMCs) are widely used to measure ADCC. In order to facilitate the identification of infected cells and high-throughput ADCC analysis, reporter genes (e.g., the Renilla luciferase [LucR] gene) are often introduced into IMC constructs. We evaluated the susceptibility of HIV-1-infected CD4+ T lymphocytes to ADCC using a panel of parental IMCs and derivatives that expressed the LucR reporter gene, utilizing different molecular strategies, including one specifically designed to retain Nef expression. We found that in some of these constructs, Nef expression in CD4+ T cells was suboptimal, and consequently, CD4 downregulation was incomplete. CD4 molecules remaining on the cell surface resulted in the exposure of ADCC-mediating CD4i epitopes on Env and a dramatic increase in the susceptibility of the infected cells to ADCC. Strikingly, protection from ADCC was observed when cells were infected with the parental IMC, which exhibited strong CD4 downregulation. This discrepancy between the parental and Nef-impaired viruses was independent of the strains of Env expressed, but rather, it was correlated with the levels of CD4 surface expression. Overall, our results indicate that caution should be taken when selecting IMCs for ADCC measurements and that CD4 downregulation needs to be carefully monitored when drawing conclusions about the nature and magnitude of ADCC. IMPORTANCE In-depth understanding of the susceptibility of HIV-1-infected cells to ADCC might help establish correlates of vaccine protection and guide the development of HIV-1 vaccine strategies. Different ADCC assays have been developed, including those using infectious molecular clones (IMCs) carrying a LucR reporter gene that greatly facilitates large-scale quantitative analysis. We previously reported different molecular strategies for introducing LucR while maintaining Nef expression and function and, consequently, CD4 surface downregulation. Here, we demonstrate that utilizing IMCs that exhibit impaired Nef expression can have undesirable consequences due to incomplete CD4 downregulation. CD4 molecules remaining on the cell surface resulted in the exposure of ADCC-mediating CD4i epitopes on Env and a dramatic increase in the susceptibility of the infected cells to ADCC. Overall, our results indicate that CD4 downregulation needs to be carefully monitored when drawing conclusions about the nature and magnitude of ADCC.
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