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Naidoo KK, Highton AJ, Baiyegunhi OO, Bhengu SP, Dong KL, Bunders MJ, Altfeld M, Ndung’u T. Early Initiation of Antiretroviral Therapy Preserves the Metabolic Function of CD4+ T Cells in Subtype C Human Immunodeficiency Virus 1 Infection. J Infect Dis 2024; 229:753-762. [PMID: 37804102 PMCID: PMC10938216 DOI: 10.1093/infdis/jiad432] [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: 05/11/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Immune dysfunction often persists in people living with human immunodeficiency virus (HIV) who are on antiretroviral therapy (ART), clinically manifesting as HIV-1-associated comorbid conditions. Early ART initiation may reduce incidence of HIV-1-associated immune dysfunction and comorbid conditions. Immunometabolism is a critical determinant of functional immunity. We investigated the effect of HIV-1 infection and timing of ART initiation on CD4+ T cell metabolism and function. METHODS Longitudinal blood samples from people living with HIV who initiated ART during hyperacute HIV-1 infection (HHI; before peak viremia) or chronic HIV-1 infection (CHI) were assessed for the metabolic and immune functions of CD4+ T cells. Metabolite uptake and mitochondrial mass were measured using fluorescent analogues and MitoTracker Green accumulation, respectively, and were correlated with CD4+ T cell effector functions. RESULTS Initiation of ART during HHI prevented dysregulation of glucose uptake by CD4+ T cells, but glucose uptake was reduced before and after ART initiation in CHI. Glucose uptake positively correlated with interleukin-2 and tumor necrosis factor-α production by CD4+ T cells. CHI was associated with elevated mitochondrial mass in effector memory CD4+ T cells that persisted after ART and correlated with PD-1 expression. CONCLUSIONS ART initiation in HHI largely prevented metabolic impairment of CD4+ T cells. ART initiation in CHI was associated with persistently dysregulated immunometabolism of CD4+ T cells, which was associated with impaired cellular functions and exhaustion.
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Affiliation(s)
- Kewreshini K Naidoo
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Andrew J Highton
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Sindiswa P Bhengu
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Madeleine J Bunders
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Altfeld
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- German Center for Infection Disease (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Division of Infection and Immunity, University College London, London, United Kingdom
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2
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Tatoud R, Jones RB, Dong K, Ndung'u T, Deeks S, Tiemessen CT. Advancing HIV cure research in low- and middle-income countries requires empowerment of the next generation of scientists. J Virus Erad 2024; 10:100364. [PMID: 38559321 PMCID: PMC10979089 DOI: 10.1016/j.jve.2024.100364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
While low- and middle-income countries (LMICs), especially in Southern and Eastern Africa, bear the largest burden of the HIV globally, investigators working on the front lines in these regions are leading a limited number of research efforts, particularly related to HIV cure. Conducting HIV cure research in high-burden HIV LIMCs provides an unparalleled opportunity to formulate innovative research strategies, design trials tailored to the local context, evaluate clinical outcomes within key and vulnerable populations, meaningful involvement of stakeholders, and to shape policies in areas where HIV prevention and cure interventions can yield the most significant impact. Further, the high prevalence of infection, with varied HIV strains affecting large diverse populations, creates a unique environment for studies that would not be feasible in any other part of the world. This underscores the critical importance of addressing obstacles to unlock the full potential of research efforts in these regions. In this viewpoint, we identify significant challenges facing early career investigators in LMICs, particularly in Africa, that hinder their full engagement in HIV cure research. Drawing examples from the International AIDS Society's Research-for-Cure Academy, we provide practical recommendations to overcome barriers that include limited access to funding, effective mentors, educational and career development opportunities, coupled with inadequate investment in infrastructure that contribute towards the limited number of investigators from high-burden HIV LIMCs who are spearheading cutting-edge cure research. Addressing these challenges is crucial to empower investigators who possess unique insights and expertise, and who are well positioned to lead HIV cure-related research efforts. We acknowledge and welcome initiatives that promote capacity building and knowledge exchange between early-career investigators in LMICs and their peers and scientific leaders from high-income countries (HICs). Prioritizing investment in global collaboration and partnership will play a pivotal role in empowering the next generation of African scientists and clinicians. To expedite advancements of cure-related strategies that will be effective in high-burden HIV LMICs, we endorse the sustainable expansion of these pivotal initiatives in these regions, to enhance their effectiveness and hasten progress in the pursuit of a global HIV cure.
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Affiliation(s)
| | - R Brad Jones
- Weill Cornell Medicine Graduate School of Medical Sciences, New York, USA
| | - Krista Dong
- Ragon Institute of MGH, Harvard Medical School, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa
| | | | - Caroline T. Tiemessen
- National Institute for Communicable Diseases, University of the Witwatersrand, Johannesburg, South Africa
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3
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Zhu M, Frank MW, Radka CD, Jeanfavre S, Tse MW, Pacheco JA, Pierce K, Deik A, Xu J, Hussain S, Hussain FA, Xulu N, Khan N, Pillay V, Dong KL, Ndung’u T, Clish CB, Rock CO, Blainey PC, Bloom SM, Kwon DS. Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.30.573720. [PMID: 38234804 PMCID: PMC10793477 DOI: 10.1101/2023.12.30.573720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Bacterial vaginosis (BV), a common syndrome characterized by Lactobacillus-deficient vaginal microbiota, is associated with adverse health outcomes. BV often recurs after standard antibiotic therapy in part because antibiotics promote microbiota dominance by Lactobacillus iners instead of Lactobacillus crispatus, which has more beneficial health associations. Strategies to promote L. crispatus and inhibit L. iners are thus needed. We show that oleic acid (OA) and similar long-chain fatty acids simultaneously inhibit L. iners and enhance L. crispatus growth. These phenotypes require OA-inducible genes conserved in L. crispatus and related species, including an oleate hydratase (ohyA) and putative fatty acid efflux pump (farE). FarE mediates OA resistance, while OhyA is robustly active in the human vaginal microbiota and sequesters OA in a derivative form that only ohyA-harboring organisms can exploit. Finally, OA promotes L. crispatus dominance more effectively than antibiotics in an in vitro model of BV, suggesting a novel approach for treatment.
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Affiliation(s)
- Meilin Zhu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Matthew W. Frank
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Christopher D. Radka
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky
| | | | - Megan W. Tse
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Kerry Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jiawu Xu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Salina Hussain
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Fatima Aysha Hussain
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nondumiso Xulu
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Nasreen Khan
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | | | - Krista L. Dong
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Health Systems Trust, Durban, South Africa
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Thumbi Ndung’u
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute (AHRI), Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, UK
| | | | - Charles O. Rock
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- passed away on September 22, 2023
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Seth M. Bloom
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Douglas S. Kwon
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Ndung'u T. The KT Jeang retrovirology prize 2023: Thumbi Ndung'u. Retrovirology 2023; 20:17. [PMID: 37848918 PMCID: PMC10583396 DOI: 10.1186/s12977-023-00632-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Affiliation(s)
- Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa.
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA.
- Division of Infection and Immunity, University College London, London, UK.
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5
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Dubé K, Mthimkhulu D, Ngcobo W, Mindry D, Maphalala L, Pillay V, Tran W, Korolkova A, Ndung’u T, Dong K. 'With this study, we have hope that something is coming': community members' perceptions of HIV cure-related research in Durban, South Africa - a qualitative focus group study. HIV Res Clin Pract 2023; 24:2243046. [PMID: 37555592 PMCID: PMC10433450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
BACKGROUND Developing a cure for HIV remains a global scientific priority. In 2022, the Females Rising through Education, Support and Health (FRESH) cohort launched an HIV cure-related trial involving an analytical treatment interruption (ATI) in Durban, South Africa. OBJECTIVES To explore community perspectives about HIV cure-related research. METHODS Between July-August 2022, we conducted three focus groups with community members. We transcribed audio recordings verbatim and used content analysis to analyze the data. RESULTS Twenty community members (13 women and 7 men) participated in three focus groups (HIV status not included). Participants viewed HIV cure-related research as a way to address the issue of defaulting on (not taking) HIV treatment. Participants expressed hesitancy around ATIs, since these contradict longstanding treatment adherence messages. Participants shared concerns around the risk of side effects from experimental interventions balanced against potential efficacy. They advocated for trial participants to have the right to decide whether to inform their sex partners about their HIV status and ATI participation, rather than research teams making disclosure mandatory. Focus group participants also emphasized the importance of using simple language to explain HIV cure-related research. CONCLUSIONS With HIV cure trials set to launch across Africa in the future, there is a critical need to better understand and respond to local community needs and preferences and to adopt this as standard practice prior to regional trial implementation.
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Affiliation(s)
- Karine Dubé
- University of California San Diego (UCSD) School of Medicine, Division of Infectious Diseases and Global Public Health (IDGPH), La Jolla, CA, USA
- University of North Carolina at Chapel Hill Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Deli Mthimkhulu
- Integration of Tuberculosis in Education and Care for HIV/AIDS (ITEACH), Durban, South Africa
| | - Wiseman Ngcobo
- Integration of Tuberculosis in Education and Care for HIV/AIDS (ITEACH), Durban, South Africa
| | - Deborah Mindry
- Center for Gender and Health Justice, University of California Global Health Institute, Los Angeles, CA, USA
| | - Luyanda Maphalala
- Females Rising through Education, Support and Health (FRESH), Durban, South Africa
| | - Vanessa Pillay
- Females Rising through Education, Support and Health (FRESH), Durban, South Africa
| | - Whitney Tran
- University of California San Diego (UCSD) School of Medicine, Division of Infectious Diseases and Global Public Health (IDGPH), La Jolla, CA, USA
| | - Ana Korolkova
- University of California San Diego (UCSD) School of Medicine, Division of Infectious Diseases and Global Public Health (IDGPH), La Jolla, CA, USA
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa
- Africa Health Research Institute (AHRI), Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Krista Dong
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
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6
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Madlala P, Mkhize Z, Naicker S, Khathi SP, Maikoo S, Gopee K, Dong KL, Ndung'u T. Genetic variation of the HIV-1 subtype C transmitted/founder viruses long terminal repeat elements and the impact on transcription activation potential and clinical disease outcomes. PLoS Pathog 2023; 19:e1011194. [PMID: 37307292 DOI: 10.1371/journal.ppat.1011194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/04/2023] [Indexed: 06/14/2023] Open
Abstract
A genetic bottleneck is a hallmark of HIV-1 transmission such that only very few viral strains, termed transmitted/founder (T/F) variants establish infection in a newly infected host. Phenotypic characteristics of these variants may determine the subsequent course of disease. The HIV-1 5' long terminal repeat (LTR) promoter drives viral gene transcription and is genetically identical to the 3' LTR. We hypothesized that HIV-1 subtype C (HIV-1C) T/F virus LTR genetic variation is a determinant of transcriptional activation potential and clinical disease outcome. The 3'LTR was amplified from plasma samples of 41 study participants acutely infected with HIV-1C (Fiebig stages I and V/VI). Paired longitudinal samples were also available at one year post-infection for 31 of the 41 participants. 3' LTR amplicons were cloned into a pGL3-basic luciferase expression vector, and transfected alone or together with Transactivator of transcription (tat) into Jurkat cells in the absence or presence of cell activators (TNF-α, PMA, Prostratin and SAHA). Inter-patient T/F LTR sequence diversity was 5.7% (Renge: 2-12) with subsequent intrahost viral evolution observed in 48.4% of the participants analyzed at 12 months post-infection. T/F LTR variants exhibited differential basal transcriptional activity, with significantly higher Tat-mediated transcriptional activity compared to basal (p<0.001). Basal and Tat-mediated T/F LTR transcriptional activity showed significant positive correlation with contemporaneous viral loads and negative correlation with CD4 T cell counts (p<0.05) during acute infection respectively. Furthermore, Tat-mediated T/F LTR transcriptional activity significanly correlated positively with viral load set point and viral load; and negatively with CD4 T cell counts at one year post infection (all p<0.05). Lastly, PMA, Prostratin, TNF-α and SAHA cell stimulation resulted in enhanced yet heterologous transcriptional activation of different T/F LTR variants. Our data suggest that T/F LTR variants may influence viral transcriptional activity, disease outcomes and sensitivity to cell activation, with potential implications for therapeutic interventions.
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Affiliation(s)
- Paradise Madlala
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zakithi Mkhize
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shamara Naicker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Samukelisiwe P Khathi
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shreyal Maikoo
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Kasmira Gopee
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Africa Health Research Institute (AHRI), Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
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7
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Subtle Longitudinal Alterations in Env Sequence Potentiate Differences in Sensitivity to Broadly Neutralizing Antibodies following Acute HIV-1 Subtype C Infection. J Virol 2022; 96:e0127022. [PMID: 36453881 PMCID: PMC9769376 DOI: 10.1128/jvi.01270-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) for HIV-1 prevention or cure strategies must inhibit transmitted/founder and reservoir viruses. Establishing sensitivity of circulating viruses to bNAbs and genetic patterns affecting neutralization variability may guide rational bNAbs selection for clinical development. We analyzed 326 single env genomes from nine individuals followed longitudinally following acute HIV-1 infection, with samples collected at ~1 week after the first detection of plasma viremia; 300 to 1,709 days postinfection but prior to initiating antiretroviral therapy (ART) (median = 724 days); and ~1 year post ART initiation. Sequences were assessed for phylogenetic relatedness, potential N- and O-linked glycosylation, and variable loop lengths (V1 to V5). A total of 43 env amplicons (median = 3 per patient per time point) were cloned into an expression vector and the TZM-bl assay was used to assess the neutralization profiles of 15 bNAbs targeting the CD4 binding site, V1/V2 region, V3 supersite, MPER, gp120/gp41 interface, and fusion peptide. At 1 μg/mL, the neutralization breadths were as follows: VRC07-LS and N6.LS (100%), VRC01 (86%), PGT151 (81%), 10-1074 and PGT121 (80%), and less than 70% for 10E8, 3BNC117, CAP256.VRC26, 4E10, PGDM1400, and N123-VRC34.01. Features associated with low sensitivity to V1/V2 and V3 bNAbs were higher potential glycosylation sites and/or relatively longer V1 and V4 domains, including known "signature" mutations. The study shows significant variability in the breadth and potency of bNAbs against circulating HIV-1 subtype C envelopes. VRC07-LS, N6.LS, VRC01, PGT151, 10-1074, and PGT121 display broad activity against subtype C variants, and major determinants of sensitivity to most bNAbs were within the V1/V4 domains. IMPORTANCE Broadly neutralizing antibodies (bNAbs) have potential clinical utility in HIV-1 prevention and cure strategies. However, bNAbs target diverse epitopes on the HIV-1 envelope and the virus may evolve to evade immune responses. It is therefore important to identify antibodies with broad activity in high prevalence settings, as well as the genetic patterns that may lead to neutralization escape. We investigated 15 bNAbs with diverse biophysical properties that target six epitopes of the HIV-1 Env glycoprotein for their ability to inhibit viruses that initiated infection, viruses circulating in plasma at chronic infection before antiretroviral treatment (ART), or viruses that were archived in the reservoir during ART in subtype C infected individuals in South Africa, a high burden country. We identify the antibodies most likely to be effective for clinical use in this setting and describe mutational patterns associated with neutralization escape from these antibodies.
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8
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Gilbertson A, Tucker JD, Dubé K, Dijkstra M, Rennie S. Ethical considerations for HIV remission clinical research involving participants diagnosed during acute HIV infection. BMC Med Ethics 2021; 22:169. [PMID: 34961509 PMCID: PMC8714439 DOI: 10.1186/s12910-021-00716-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
HIV remission clinical researchers are increasingly seeking study participants who are diagnosed and treated during acute HIV infection—the brief period between infection and the point when the body creates detectable HIV antibodies. This earliest stage of infection is often marked by flu-like illness and may be an especially tumultuous period of confusion, guilt, anger, and uncertainty. Such experiences may present added ethical challenges for HIV research recruitment, participation, and retention. The purpose of this paper is to identify potential ethical challenges associated with involving acutely diagnosed people living with HIV in remission research and considerations for how to mitigate them. We identify three domains of potential ethical concern for clinicians, researchers, and ethics committee members to consider: 1) Recruitment and informed consent; (2) Transmission risks and partner protection; and (3) Ancillary and continuing care. We discuss each of these domains with the aim of inspiring further work to advance the ethical conduct of HIV remission research. For example, experiences of confusion and uncertainty regarding illness and diagnosis during acute HIV infection may complicate informed consent procedures in studies that seek to recruit directly after diagnosis. To address this, it may be appropriate to use staged re-consent procedures or comprehension assessment. Responsible conduct of research requires a broad understanding of acute HIV infection that encompasses its biomedical, psychological, social, and behavioral dimensions. We argue that the lived experience of acute HIV infection may introduce ethical concerns that researchers and reviewers should address during study design and ethical approval.
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Affiliation(s)
- Adam Gilbertson
- Pacific Institute for Research and Evaluation, Chapel Hill Center, 101 Conner Drive, Suite 200, Chapel Hill, NC, 27514-7038, USA. .,UNC Center for Bioethics, Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Joseph D Tucker
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WCE1, UK.,UNC Project-China, 2 Lujing Road, Guangzhou, China
| | - Karine Dubé
- Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maartje Dijkstra
- Department of Infectious Diseases, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, The Netherlands
| | - Stuart Rennie
- UNC Center for Bioethics, Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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9
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Miall A, McLellan R, Dong K, Ndung'u T, Saberi P, Sauceda JA, Dubé K. Bringing social context into global biomedical HIV cure-related research: An urgent call to action. J Virus Erad 2021; 8:100062. [PMID: 35169489 PMCID: PMC8829132 DOI: 10.1016/j.jve.2021.100062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/27/2021] [Indexed: 02/04/2023] Open
Abstract
Advances in science have ushered in a wave of new potential curative and control strategies for HIV that could eliminate the current requirement for life-long antiretroviral therapy (ART) for people living with HIV (PLWH). In this article, we argue that it is critical to consider social contexts in the development of HIV cure trial protocols. The biological and behavioral risk factors for HIV acquisition by study participants are inseparable from the social context in which these participants live. The article discusses an example of a cohort established to further HIV cure research that included social context, called the FRESH Acute HIV study, which combines a sociostructural intervention while conducting HIV prevention, treatment and cure-related research in Durban, South Africa. We make an urgent call to action to include sociobehavioral components as instrumental in future HIV cure trials in global context.
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Affiliation(s)
| | | | - Krista Dong
- Harvard Medical School, MA, USA,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA,Massachusetts General Hospital, MA, USA
| | - Thumbi Ndung'u
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA,Africa Health Research Institute (AHRI), Durban, South Africa,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa,Division of Infection and Immunity, University College London, London, UK
| | - Parya Saberi
- Center for AIDS Prevention Studies (CAPS), Division of Prevention Sciences, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - John A. Sauceda
- Center for AIDS Prevention Studies (CAPS), Division of Prevention Sciences, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Karine Dubé
- UNC Gillings School of Global Public Health, Chapel Hill, NC, USA,Corresponding author. UNC Gillings School of Global Public Health, 4108 McGavran-Greenberg Hall, Chapel Hill, NC, USA.
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10
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Bashirova AA, Zheng W, Akdag M, Augusto DG, Vince N, Dong KL, O'hUigin C, Carrington M. Population-specific diversity of the immunoglobulin constant heavy G chain (IGHG) genes. Genes Immun 2021; 22:327-334. [PMID: 34864821 PMCID: PMC8674132 DOI: 10.1038/s41435-021-00156-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 11/22/2021] [Indexed: 12/27/2022]
Abstract
Human immunoglobulin G (IgG) molecules, IgG1, IgG2 and IgG3, exhibit substantial inter-individual variation in their constant heavy chain regions, as discovered by serological methods. This polymorphism is encoded by the IGHG1, IGHG2, and IGHG3 genes and may influence antibody function. We sequenced the coding fragments of these genes in 95 European Americans, 94 African Americans, and 94 Black South Africans. Striking differences were observed between the population groups, including extremely low amino acid sequence variation in IGHG1 among South Africans, and higher IGHG2 and IGHG3 diversity in individuals of African descent compared to individuals of European descent. Molecular definition of the loci illustrates a greater level of allelic polymorphism than previously described, including the presence of common IGHG2 and IGHG3 variants that were indistinguishable serologically. Comparison of our data with the 1000 Genome Project sequences indicates overall agreement between the datasets, although some inaccuracies in the 1000 Genomes Project are likely. These data represent the most comprehensive analysis of IGHG polymorphisms across major populations, which can now be applied to deciphering their functional impact.
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Affiliation(s)
- Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Wanjing Zheng
- The Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Marjan Akdag
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000, Nantes, France
| | - Krista L Dong
- Females Rising through Education, Support, and Health, Durban, KwaZulu-Natal, South Africa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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11
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Naidoo KK, Ndumnego OC, Ismail N, Dong KL, Ndung'u T. Antigen Presenting Cells Contribute to Persistent Immune Activation Despite Antiretroviral Therapy Initiation During Hyperacute HIV-1 Infection. Front Immunol 2021; 12:738743. [PMID: 34630420 PMCID: PMC8498034 DOI: 10.3389/fimmu.2021.738743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022] Open
Abstract
Human immunodeficiency virus (HIV)-induced changes in immune cells during the acute phase of infection can cause irreversible immunological damage and predict the rate of disease progression. Antiretroviral therapy (ART) remains the most effective strategy for successful immune restoration in immunocompromised people living with HIV and the earlier ART is initiated after infection, the better the long-term clinical outcomes. Here we explored the effect of ART on peripheral antigen presenting cell (APC) phenotype and function in women with HIV-1 subtype C infection who initiated ART in the hyperacute phase (before peak viremia) or during chronic infection. Peripheral blood mononuclear cells obtained longitudinally from study participants were used for immunophenotyping and functional analysis of monocytes and dendritic cells (DCs) using multiparametric flow cytometry and matched plasma was used for measurement of inflammatory markers IL-6 and soluble CD14 (sCD14) by enzyme-linked immunosorbent assay. HIV infection was associated with expansion of monocyte and plasmacytoid DC (pDC) frequencies and perturbation of monocyte subsets compared to uninfected persons despite antiretroviral treatment during hyperacute infection. Expression of activation marker CD69 on monocytes and pDCs in early treated HIV was similar to uninfected individuals. However, despite early ART, HIV infection was associated with elevation of plasma IL-6 and sCD14 levels which correlated with monocyte activation. Furthermore, HIV infection with or without early ART was associated with downmodulation of the co-stimulatory molecule CD86. Notably, early ART was associated with preserved toll-like receptor (TLR)-induced IFN-α responses of pDCs. Overall, this data provides evidence of the beneficial impact of ART initiated in hyperacute infection in preservation of APC functional cytokine production activity; but also highlights persistent inflammation facilitated by monocyte activation even after prolonged viral suppression and suggests the need for therapeutic interventions that target residual immune activation.
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Affiliation(s)
- Kewreshini K Naidoo
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Nasreen Ismail
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Krista L Dong
- Females Rising Through Education, Support and Health, Durban, South Africa.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, United States
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute, Durban, South Africa.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, United States.,Max Planck Institute for Infection Biology, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
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12
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Munoz A, Hayward MR, Bloom SM, Rocafort M, Ngcapu S, Mafunda NA, Xu J, Xulu N, Dong M, Dong KL, Ismail N, Ndung’u T, Ghebremichael MS, Kwon DS. Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health. MICROBIOME 2021; 9:163. [PMID: 34311774 PMCID: PMC8314590 DOI: 10.1186/s40168-021-01096-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/18/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cervicovaginal bacterial communities composed of diverse anaerobes with low Lactobacillus abundance are associated with poor reproductive outcomes such as preterm birth, infertility, cervicitis, and risk of sexually transmitted infections (STIs), including human immunodeficiency virus (HIV). Women in sub-Saharan Africa have a higher prevalence of these high-risk bacterial communities when compared to Western populations. However, the transition of cervicovaginal communities between high- and low-risk community states over time is not well described in African populations. RESULTS We profiled the bacterial composition of 316 cervicovaginal swabs collected at 3-month intervals from 88 healthy young Black South African women with a median follow-up of 9 months per participant and developed a Markov-based model of transition dynamics that accurately predicted bacterial composition within a broader cross-sectional cohort. We found that Lactobacillus iners-dominant, but not Lactobacillus crispatus-dominant, communities have a high probability of transitioning to high-risk states. Simulating clinical interventions by manipulating the underlying transition probabilities, our model predicts that the population prevalence of low-risk microbial communities could most effectively be increased by manipulating the movement between L. iners- and L. crispatus-dominant communities. CONCLUSIONS The Markov model we present here indicates that L. iners-dominant communities have a high probability of transitioning to higher-risk states. We additionally identify transitions to target to increase the prevalence of L. crispatus-dominant communities. These findings may help guide future intervention strategies targeted at reducing bacteria-associated adverse reproductive outcomes among women living in sub-Saharan Africa. Video Abstract.
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Affiliation(s)
- Alexander Munoz
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
- Harvard Medical School, Boston, MA 02115 USA
| | - Matthew R. Hayward
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
- Harvard Medical School, Boston, MA 02115 USA
| | - Seth M. Bloom
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
- Harvard Medical School, Boston, MA 02115 USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Muntsa Rocafort
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Nomfuneko A. Mafunda
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
| | - Jiawu Xu
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
| | - Nondumiso Xulu
- HIV Pathogenesis Programme (HPP), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Mary Dong
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
- Females Rising through Education, Support, and Health, Durban, KwaZulu-Natal South Africa
- Massachusetts General Hospital, Boston, MA 02114 USA
| | - Krista L. Dong
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
- Females Rising through Education, Support, and Health, Durban, KwaZulu-Natal South Africa
- Massachusetts General Hospital, Boston, MA 02114 USA
| | - Nasreen Ismail
- HIV Pathogenesis Programme (HPP), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung’u
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
- HIV Pathogenesis Programme (HPP), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute (AHRI), Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Musie S. Ghebremichael
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
| | - Douglas S. Kwon
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139 USA
- Harvard Medical School, Boston, MA 02115 USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
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13
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Abstract
Although the development of effective vaccines has saved countless lives from infectious diseases, the basic workings of the human immune system are complex and have required the development of animal models, such as inbred mice, to define mechanisms of immunity. More recently, new strategies and technologies have been developed to directly explore the human immune system with unprecedented precision. We discuss how these approaches are advancing our mechanistic understanding of human immunology and are facilitating the development of vaccines and therapeutics for infection, autoimmune diseases, and cancer.
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Affiliation(s)
- Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA.
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H: Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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14
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Ndhlovu ZM, Kazer SW, Nkosi T, Ogunshola F, Muema DM, Anmole G, Swann SA, Moodley A, Dong K, Reddy T, Brockman MA, Shalek AK, Ndung'u T, Walker BD. Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection. Sci Transl Med 2020; 11:11/493/eaau0528. [PMID: 31118290 DOI: 10.1126/scitranslmed.aau0528] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/31/2018] [Accepted: 03/28/2019] [Indexed: 12/13/2022]
Abstract
Sustained viremia after acute HIV infection is associated with profound CD4+ T cell loss and exhaustion of HIV-specific CD8+ T cell responses. To determine the impact of combination antiretroviral therapy (cART) on these processes, we examined the evolution of immune responses in acutely infected individuals initiating treatment before peak viremia. Immediate treatment of Fiebig stages I and II infection led to a rapid decline in viral load and diminished magnitude of HIV-specific (tetramer+) CD8+ T cell responses compared to untreated donors. There was a strong positive correlation between cumulative viral antigen exposure before full cART-induced suppression and immune responses measured by MHC class I tetramers, IFN-γ ELISPOT, and CD8+ T cell activation. HIV-specific CD8+ T responses of early treated individuals were characterized by increased CD127 and BCL-2 expression, greater in vitro IFN-γ secretion, and enhanced differentiation into effector memory (Tem) cells. Transcriptional analysis of tetramer+ CD8+ T cells from treated persons revealed reduced expression of genes associated with activation and apoptosis, with concurrent up-regulation of prosurvival genes including BCL-2, AXL, and SRC Early treatment also resulted in robust HIV-specific CD4+ T cell responses compared to untreated HIV-infected individuals. Our data show that limiting acute viremia results in enhanced functionality of HIV-specific CD4+ and CD8+ T cells, preserving key antiviral properties of these cells.
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Affiliation(s)
- Zaza M Ndhlovu
- Africa Health Research Institute, 4036 Durban, South Africa. .,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Samuel W Kazer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA 02139, USA.,Department of Chemistry and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Thandeka Nkosi
- Africa Health Research Institute, 4036 Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Funsho Ogunshola
- Africa Health Research Institute, 4036 Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Daniel M Muema
- Africa Health Research Institute, 4036 Durban, South Africa
| | - Gursev Anmole
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Shayda A Swann
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Amber Moodley
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Krista Dong
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Tarylee Reddy
- South Africa Medical Research Council, 4091 Durban, South Africa
| | - Mark A Brockman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Alex K Shalek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA 02139, USA.,Department of Chemistry and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute, 4036 Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa.,Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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15
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Kazer SW, Aicher TP, Muema DM, Carroll SL, Ordovas-Montanes J, Miao VN, Tu AA, Ziegler CGK, Nyquist SK, Wong EB, Ismail N, Dong M, Moodley A, Berger B, Love JC, Dong KL, Leslie A, Ndhlovu ZM, Ndung'u T, Walker BD, Shalek AK. Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection. Nat Med 2020; 26:511-518. [PMID: 32251406 PMCID: PMC7237067 DOI: 10.1038/s41591-020-0799-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
Cellular immunity is critical for controlling intracellular pathogens, but individual cellular dynamics and cell-cell cooperativity in evolving human immune responses remain poorly understood. Single-cell RNA-sequencing (scRNA-seq) represents a powerful tool for dissecting complex multicellular behaviors in health and disease1,2 and nominating testable therapeutic targets3. Its application to longitudinal samples could afford an opportunity to uncover cellular factors associated with the evolution of disease progression without potentially confounding inter-individual variability4. Here, we present an experimental and computational methodology that uses scRNA-seq to characterize dynamic cellular programs and their molecular drivers, and apply it to HIV infection. By performing scRNA-seq on peripheral blood mononuclear cells from four untreated individuals before and longitudinally during acute infection5, we were powered within each to discover gene response modules that vary by time and cell subset. Beyond previously unappreciated individual- and cell-type-specific interferon-stimulated gene upregulation, we describe temporally aligned gene expression responses obscured in bulk analyses, including those involved in proinflammatory T cell differentiation, prolonged monocyte major histocompatibility complex II upregulation and persistent natural killer (NK) cell cytolytic killing. We further identify response features arising in the first weeks of infection, for example proliferating natural killer cells, which potentially may associate with future viral control. Overall, our approach provides a unified framework for characterizing multiple dynamic cellular responses and their coordination.
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Affiliation(s)
- Samuel W Kazer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toby P Aicher
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel M Muema
- African Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Shaina L Carroll
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jose Ordovas-Montanes
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Vincent N Miao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Ang A Tu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carly G K Ziegler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Sarah K Nyquist
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily B Wong
- African Health Research Institute, Durban, South Africa
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Division of Infection and Immunity, University College London, London, UK
- Harvard Medical School, Boston, MA, USA
| | - Nasreen Ismail
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mary Dong
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Amber Moodley
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J Christopher Love
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Krista L Dong
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Alasdair Leslie
- African Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Zaza M Ndhlovu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- African Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Thumbi Ndung'u
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- African Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Alex K Shalek
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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16
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Single-dose bNAb cocktail or abbreviated ART post-exposure regimens achieve tight SHIV control without adaptive immunity. Nat Commun 2020; 11:70. [PMID: 31911610 PMCID: PMC6946664 DOI: 10.1038/s41467-019-13972-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 12/10/2019] [Indexed: 12/31/2022] Open
Abstract
Vertical transmission accounts for most human immunodeficiency virus (HIV) infection in children, and treatments for newborns are needed to abrogate infection or limit disease progression. We showed previously that short-term broadly neutralizing antibody (bNAb) therapy given 24 h after oral exposure cleared simian-human immunodeficiency virus (SHIV) in a macaque model of perinatal infection. Here, we report that all infants given either a single dose of bNAbs at 30 h, or a 21-day triple-drug ART regimen at 48 h, are aviremic with almost no virus in tissues. In contrast, bNAb treatment beginning at 48 h leads to tight control without adaptive immune responses in half of animals. We conclude that both bNAbs and ART mediate effective post-exposure prophylaxis in infant macaques within 30-48 h of oral SHIV exposure. Our findings suggest that optimizing the treatment regimen may extend the window of opportunity for preventing perinatal HIV infection when treatment is delayed.
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17
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Lee GQ, Reddy K, Einkauf KB, Gounder K, Chevalier JM, Dong KL, Walker BD, Yu XG, Ndung'u T, Lichterfeld M. HIV-1 DNA sequence diversity and evolution during acute subtype C infection. Nat Commun 2019; 10:2737. [PMID: 31227699 PMCID: PMC6588551 DOI: 10.1038/s41467-019-10659-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/24/2019] [Indexed: 01/02/2023] Open
Abstract
Little is known about the genotypic make-up of HIV-1 DNA genomes during the earliest stages of HIV-1 infection. Here, we use near-full-length, single genome next-generation sequencing to longitudinally genotype and quantify subtype C HIV-1 DNA in four women identified during acute HIV-1 infection in Durban, South Africa, through twice-weekly screening of high-risk participants. In contrast to chronically HIV-1-infected patients, we found that at the earliest phases of infection in these four participants, the majority of viral DNA genomes are intact, lack APOBEC-3G/F-associated hypermutations, have limited genome truncations, and over one year show little indication of cytotoxic T cell-driven immune selections. Viral sequence divergence during acute infection is predominantly fueled by single-base substitutions and is limited by treatment initiation during the earliest stages of disease. Our observations provide rare longitudinal insights of HIV-1 DNA sequence profiles during the first year of infection to inform future HIV cure research.
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Affiliation(s)
- Guinevere Q Lee
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Brigham and Women's Hospital, Boston, 02115, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Kavidha Reddy
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Brigham and Women's Hospital, Boston, 02115, MA, USA
| | - Kamini Gounder
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
| | | | - Krista L Dong
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Brigham and Women's Hospital, Boston, 02115, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Brigham and Women's Hospital, Boston, 02115, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Thumbi Ndung'u
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, 4001, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
- Max Planck Institute for Infection Biology, 10117, Berlin, Germany
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
- Brigham and Women's Hospital, Boston, 02115, MA, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Naidoo KK, Ngubane A, Gaza P, Moodley A, Ndung'u T, Thobakgale CF. Neutrophil Effector Functions Are Not Impaired in Duffy Antigen Receptor for Chemokines (DARC)-Null Black South Africans. Front Immunol 2019; 10:551. [PMID: 30972057 PMCID: PMC6443851 DOI: 10.3389/fimmu.2019.00551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/28/2019] [Indexed: 12/23/2022] Open
Abstract
Neutrophils are well-recognized for their pathogen killing mechanisms and disorders of neutrophil count and function are associated with recurrent infections. The Duffy Antigen Receptor for Chemokines (DARC)-null genotype is predominant in sub-Saharan African ancestry populations and is the major genetic determinant of benign ethnic neutropenia which has been associated with increased risk of Human Immunodeficiency Virus (HIV)-1 acquisition and mother-to-child transmission. However, the impact of DARC-null-linked neutropenia on HIV disease progression remains controversial. While the DARC-null genotype is associated with low numbers of circulating neutrophils, the effects of the polymorphism on neutrophil functions is unknown. We investigated the impact of the DARC-null trait and lower absolute neutrophil counts (ANCs) on key neutrophil effector functions [proteolytic activity within the phagosome following Fc receptor-mediated phagocytosis, reactive oxygen species (ROS) production, and neutrophil extracellular trap (NET) formation] in 20 HIV negative and 22 HIV-1 chronically infected black South Africans. Phagosome maturation was measured by flow cytometry following Fc-mediated uptake of IgG opsonized beads; ROS production was measured by chemi-luminescence after activation of neutrophils with phorbol 12-myristate 13-acetate (PMA). Activated neutrophils were also visualized by fluorescent microscopy for NET quantification. Study subjects were genotyped for the DARC trait using TaqMan allelic discrimination assays and ANCs were measured by full blood count. As expected, the DARC-null polymorphism was highly prevalent in our participant cohort (69%) and was strongly associated with lower ANCs in uninfected (p = 0.0007) and HIV-1 infected (p = 0.03) subjects. We observed enhanced proteolytic activity within the phagosome in the absence of DARC at 10 min (p = 0.05 and p = 0.009) and 60 min (p = 0.05 and p = 0.07) in uninfected and HIV-1 infected subjects, respectively. ROS was unaffected by DARC trait irrespective of HIV status. Furthermore, formation of NETs was reduced in neutrophils from DARC-null subjects (p = 0.04) following prolonged in vitro stimulation, but only in HIV-1 infected subjects. The data indicate differential neutrophil function in the absence of DARC that may be moderately modulated by HIV-1 infection but overall, the data suggest that DARC-null trait is not deleterious to neutrophil effector functions in African populations.
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Affiliation(s)
- Kewreshini K Naidoo
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Ayanda Ngubane
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Pedzisai Gaza
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Amber Moodley
- Females Rising through Education, Support and Health (FRESH), Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, United States.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Christina F Thobakgale
- HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,School of Pathology, National Institute for Communicable Diseases, University of the Witwatersrand, Johannesburg, South Africa
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