1
|
Scott TM, Arnold LM, Powers JA, McCann DA, Christensen DE, Zhou W, Torrez RM, Iwasa JH, Kranzusch PJ, Sundquist WI, Johnson JS. Cell-free assays reveal the HIV-1 capsid protects reverse transcripts from cGAS. bioRxiv 2024:2024.04.22.590513. [PMID: 38712059 PMCID: PMC11071359 DOI: 10.1101/2024.04.22.590513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Retroviruses can be detected by the innate immune sensor cyclic GMP-AMP synthase (cGAS), which recognizes reverse-transcribed DNA and activates an antiviral response. However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. We found that wild-type HIV-1 capsids protect their genomes from cGAS even after completion of reverse transcription. Viral DNA could be "deprotected" by thermal stress, capsid mutations, or reduced concentrations of inositol hexakisphosphate (IP6) that destabilize the capsid. Strikingly, capsid inhibitors also disrupted viral cores and dramatically potentiated cGAS activity, both in vitro and in cellular infections. Our results provide biochemical evidence that the HIV-1 capsid lattice conceals the genome from cGAS and that chemical or physical disruption of the viral core can expose HIV-1 DNA and activate innate immune signaling.
Collapse
|
2
|
Zhou S, Long N, Swanstrom R. Evolution Driven By A Varying Host Environment Selects For Distinct HIV-1 Entry Phenotypes and Other Informative Variants. Front Virol 2023; 3:1291996. [PMID: 38239974 PMCID: PMC10795538 DOI: 10.3389/fviro.2023.1291996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
HIV-1 generates remarkable intra- and inter-host viral diversity during infection. In response to dynamic selective pressures of the host environment, HIV-1 will evolve distinct phenotypes - biological features that provide fitness advantages. The transmitted form of HIV-1 has been shown to require a high density of CD4 on the target cell surface (as found on CD4+ T cells) and typically uses CCR5 as a co-receptor during entry. This phenotype is referred to as R5 T cell-tropic (or R5 T-tropic); however, HIV-1 can switch to a secondary co-receptor, CXCR4, resulting in a X4 T cell-tropic phenotype. Macrophage-tropic (or M-tropic) HIV-1 can evolve to efficiently enter cells expressing low densities of CD4 on their surface (such as macrophages/microglia). So far only CCR5-using M-tropic viruses have been found. M-tropic HIV-1 is most frequently found within the central nervous system, and infection of the CNS has been associated with neurological impairment. It has been shown that interferon resistance phenotypes have a selective advantage during transmission, but the underlying mechanism of this is still unclear. During untreated infection, HIV-1 evolves under selective pressure from both the humoral/antibody response and CD8+ T cell killing. Sufficiently potent antiviral therapy will suppress viral replication, but if the antiviral drugs are not sufficiently potent to stop replication then the replicating virus will evolve drug resistance. HIV-1 phenotypes are highly relevant to treatment efforts, clinical outcomes, vaccine studies, and cure strategies. Therefore, it is critical to understand the dynamics of the host environment that drive these phenotypes and how they affect HIV-1 pathogenesis. This review will provide a comprehensive discussion of HIV-1 entry, transmission, and drug resistance phenotypes. Finally, we will assess the methods used in previous and current research to characterize these phenotypes.
Collapse
Affiliation(s)
- Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nathan Long
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
3
|
Jackson PEH, Holsey J, Turse L, Hammarskjold ML, Rekosh D. Rev-Rev Response Element Activity Selection Bias at the Human Immunodeficiency Virus Transmission Bottleneck. Open Forum Infect Dis 2023; 10:ofad486. [PMID: 37854107 PMCID: PMC10580148 DOI: 10.1093/ofid/ofad486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
Background Sexual transmission of human immunodeficiency virus (HIV) is inefficient and results in selection of viral variants based on incompletely understood factors. Functional variation in the Rev-Rev response element (RRE) regulatory axis of HIV affect replication kinetics and relative expression of viral proteins. We explored whether differences in this axis among viral isolates affect transmission fitness. Methods HIV sequences were identified from nine female-to-male transmission pairs. Using a rapid flow cytometric assay, we analyzed Rev-RRE functional activity of primary isolates. Results Rev-RRE activity was significantly lower in recipient viruses compared with corresponding donor viruses. In most transmission events, recipient virus Rev-RRE activity clustered at the extreme low end of the range of donor virus activity. Conclusions These data indicate selection pressure on the Rev-RRE axis during female-to-male sexual transmission. Variation in Rev-RRE activity may permit viral adaptation to different fitness landscapes and could play an important role in HIV pathogenesis.
Collapse
Affiliation(s)
- Patrick E H Jackson
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Jordan Holsey
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Lauren Turse
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
4
|
Herbert NG, Goulder PJR. Impact of early antiretroviral therapy, early life immunity and immune sex differences on HIV disease and posttreatment control in children. Curr Opin HIV AIDS 2023; 18:229-236. [PMID: 37421384 PMCID: PMC10399946 DOI: 10.1097/coh.0000000000000807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
PURPOSE OF REVIEW To review recent insights into the factors affecting HIV disease progression in children living with HIV, contrasting outcomes: following early ART initiation with those in natural, antiretroviral therapy (ART)-naive infection; in children versus adults; and in female individuals versus male individuals. RECENT FINDINGS Early life immune polarization and several factors associated with mother-to-child transmission of HIV result in an ineffective HIV-specific CD8+ T-cell response and rapid disease progression in most children living with HIV. However, the same factors result in low immune activation and antiviral efficacy mediated mainly through natural killer cell responses in children and are central features of posttreatment control. By contrast, rapid activation of the immune system and generation of a broad HIV-specific CD8+ T-cell response in adults, especially in the context of 'protective' HLA class I molecules, are associated with superior disease outcomes in ART-naive infection but not with posttreatment control. The higher levels of immune activation in female individuals versus male individuals from intrauterine life onwards increase HIV infection susceptibility in females in utero and may favour ART-naive disease outcomes rather than posttreatment control. SUMMARY Early-life immunity and factors associated with mother-to-child transmission typically result in rapid HIV disease progression in ART-naive infection but favour posttreatment control in children following early ART initiation.
Collapse
Affiliation(s)
- Nicholas G Herbert
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
5
|
Geretz A, Ehrenberg PK, Clifford RJ, Laliberté A, Prelli Bozzo C, Eiser D, Kundu G, Yum LK, Apps R, Creegan M, Gunady M, Shangguan S, Sanders-Buell E, Sacdalan C, Phanuphak N, Tovanabutra S, Russell RM, Bibollet-Ruche F, Robb ML, Michael NL, Ake JA, Vasan S, Hsu DC, Hahn BH, Kirchhoff F, Thomas R. Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo. Sci Transl Med 2023; 15:eadg0873. [PMID: 37531416 DOI: 10.1126/scitranslmed.adg0873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Host restriction factors play key roles in innate antiviral defense, but it remains poorly understood which of them restricts HIV-1 in vivo. Here, we used single-cell transcriptomic analysis to identify host factors associated with HIV-1 control during acute infection by correlating host gene expression with viral RNA abundance within individual cells. Wide sequencing of cells from one participant with the highest plasma viral load revealed that intracellular viral RNA transcription correlates inversely with expression of the gene PTMA, which encodes prothymosin α. This association was genome-wide significant (Padjusted < 0.05) and was validated in 28 additional participants from Thailand and the Americas with HIV-1 CRF01_AE and subtype B infections, respectively. Overexpression of prothymosin α in vitro confirmed that this cellular factor inhibits HIV-1 transcription and infectious virus production. Our results identify prothymosin α as a host factor that restricts HIV-1 infection in vivo, which has implications for viral transmission and cure strategies.
Collapse
Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Daina Eiser
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauren K Yum
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Mohamed Gunady
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| |
Collapse
|
6
|
Luthuli B, Gounder K, Deymier MJ, Dong KL, Balazs AB, Mann JK, Ndung'u T. Generation and characterization of infectious molecular clones of transmitted/founder HIV-1 subtype C viruses. Virology 2023; 583:14-26. [PMID: 37084644 DOI: 10.1016/j.virol.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
The genetic diversity of HIV impedes vaccine development. Identifying the viral properties of transmitted/founder (T/F) variants may provide a common vaccine target. To study the biological nature of T/F viruses, we constructed full-length clones from women detected during Fiebig stage I acute HIV-1 infection (AHI) from heterosexual male-to-female (MTF) transmission; and clones after one year of infection using In-Fusion-based cloning. Eighteen full-length T/F clones were generated from 9 women and six chronic infection clones were from 2 individuals. All clones but one were non-recombinant subtype C. Three of the 5 T/F clones and 3 chronic clones tested replicated efficiently in PBMCs and utilised CCR5 coreceptor for cell entry. Transmitted/founder and chronic infection clones displayed heterogenous in vitro replicative capacity and resistance to type I interferon. T/F viruses had shorter Env glycoproteins and fewer N-linked glycosylation sites in Env. Our findings suggest MTF transmission may select viruses with compact envelopes.
Collapse
Affiliation(s)
| | - Kamini Gounder
- Africa Health Research Institute, Durban, South Africa; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Martin J Deymier
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Krista L Dong
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Alejandro B Balazs
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - 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; The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA; Division of Infection and Immunity, University College London, London, UK.
| |
Collapse
|
7
|
Jackson PEH, Holsey J, Turse L, Marie-Louise H, Rekosh D. Rev-Rev Response Element Activity Selection Bias at the HIV Transmission Bottleneck. bioRxiv 2023:2023.04.05.535732. [PMID: 37066242 PMCID: PMC10104022 DOI: 10.1101/2023.04.05.535732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
HIV is not efficiently transmitted between hosts, and selection of viral variants occurs during the process of sexual transmission. The factors that confer selective advantage at the transmission bottleneck remain incompletely understood. We explored whether differences in the Rev-Rev Response Element (RRE) regulatory axis of HIV affect transmission fitness, since functional variation in the Rev-RRE axis in different viral isolates has been shown to affect replication kinetics and relative expression of many HIV proteins. Single genome HIV sequences were identified from nine linked subject pairs near the time of female-to-male transmission. Using a rapid flow-cytometric assay, we found that the functional Rev-RRE activity varied significantly between isolates. Moreover, it was generally lower in recipients' viruses compared to the corresponding donor viruses. In six of nine transmission events, recipient virus Rev-RRE activity clustered at the extreme low end of the range of donor virus activity. Rev-RRE pair activity was an unpredictable product of component Rev and RRE activity variation. These data indicate selection pressure on the Rev-RRE axis during female-to-male sexual transmission. Variation in the activity of the Rev-RRE axis may permit viral adaptation to different fitness landscapes and could play an important role in HIV pathogenesis.
Collapse
Affiliation(s)
- Patrick E. H. Jackson
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Jordan Holsey
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Lauren Turse
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Hammarskjold Marie-Louise
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
8
|
Baxter J, Langhorne S, Shi T, Tully DC, Villabona-Arenas CJ, Hué S, Albert J, Leigh Brown A, Atkins KE. Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis. Lancet Microbe 2023; 4:e102-e112. [PMID: 36642083 DOI: 10.1016/s2666-5247(22)00327-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND HIV-1 infections initiated by multiple founder variants are characterised by a higher viral load and a worse clinical prognosis than those initiated with single founder variants, yet little is known about the routes of exposure through which transmission of multiple founder variants is most probable. Here we used individual patient data to calculate the probability of multiple founders stratified by route of HIV exposure and study methodology. METHODS We conducted a systematic review and meta-analysis of studies that estimated founder variant multiplicity in HIV-1 infection, searching MEDLINE, Embase, and Global Health databases for papers published between Jan 1, 1990, and Sept 14, 2020. Eligible studies must have reported original estimates of founder variant multiplicity in people with acute or early HIV-1 infections, have clearly detailed the methods used, and reported the route of exposure. Studies were excluded if they reported data concerning people living with HIV-1 who had known or suspected superinfection, who were documented as having received pre-exposure prophylaxis, or if the transmitting partner was known to be receiving antiretroviral treatment. Individual patient data were collated from all studies, with authors contacted if these data were not publicly available. We applied logistic meta-regression to these data to estimate the probability that an HIV infection is initiated by multiple founder variants. We calculated a pooled estimate using a random effects model, subsequently stratifying this estimate across exposure routes in a univariable analysis. We then extended our model to adjust for different study methods in a multivariable analysis, recalculating estimates across the exposure routes. This study is registered with PROSPERO, CRD42020202672. FINDINGS We included 70 publications in our analysis, comprising 1657 individual patients. Our pooled estimate of the probability that an infection is initiated by multiple founder variants was 0·25 (95% CI 0·21-0·29), with moderate heterogeneity (Q=132·3, p<0·0001, I2=64·2%). Our multivariable analysis uncovered differences in the probability of multiple variant infection by exposure route. Relative to a baseline of male-to-female transmission, the predicted probability for female-to-male multiple variant transmission was significantly lower at 0·13 (95% CI 0·08-0·20), and the probabilities were significantly higher for transmissions in people who inject drugs (0·37 [0·24-0·53]) and men who have sex with men (0·30 [0·33-0·40]). There was no significant difference in the probability of multiple variant transmission between male-to-female transmission (0·21 [0·14-0·31]), post-partum transmission (0·18 [0·03-0·57]), pre-partum transmission (0·17 [0·08-0·33]), and intra-partum transmission (0·27 [0·14-0·45]). INTERPRETATION We identified that transmissions in people who inject drugs and men who have sex with men are significantly more likely to result in an infection initiated by multiple founder variants, and female-to-male infections are significantly less probable. Quantifying how the routes of HIV infection affect the transmission of multiple variants allows us to better understand how the evolution and epidemiology of HIV-1 determine clinical outcomes. FUNDING Medical Research Council Precision Medicine Doctoral Training Programme and a European Research Council Starting Grant.
Collapse
Affiliation(s)
- James Baxter
- Usher Institute, The University of Edinburgh, Edinburgh, UK.
| | - Sarah Langhorne
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Ting Shi
- Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Damien C Tully
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ch Julián Villabona-Arenas
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Stéphane Hué
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew Leigh Brown
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - Katherine E Atkins
- Usher Institute, The University of Edinburgh, Edinburgh, UK; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| |
Collapse
|
9
|
Sazonov I, Grebennikov D, Savinkov R, Soboleva A, Pavlishin K, Meyerhans A, Bocharov G. Stochastic Modelling of HIV-1 Replication in a CD4 T Cell with an IFN Response. Viruses 2023; 15:v15020296. [PMID: 36851511 PMCID: PMC9966781 DOI: 10.3390/v15020296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
A mathematical model of the human immunodeficiency virus Type 1 (HIV-1) life cycle in CD4 T cells was constructed and calibrated. It describes the activation of the intracellular Type I interferon (IFN-I) response and the IFN-induced suppression of viral replication. The model includes viral replication inhibition by interferon-induced antiviral factors and their inactivation by the viral proteins Vpu and Vif. Both deterministic and stochastic model formulations are presented. The stochastic model was used to predict efficiency of IFN-I-induced suppression of viral replication in different initial conditions for autocrine and paracrine effects. The probability of virion excretion for various MOIs and various amounts of IFN-I was evaluated and the statistical properties of the heterogeneity of HIV-1 and IFN-I production characterised.
Collapse
Affiliation(s)
- Igor Sazonov
- Faculty of Science and Engineering, Swansea University, Bay Campus, Fabian Way SA1 8EN, UK
- Correspondence:
| | - Dmitry Grebennikov
- Marchuk Institute of Numerical Mathematics of the RAS, 119333 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics at INM RAS, 119333 Moscow, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Rostislav Savinkov
- Marchuk Institute of Numerical Mathematics of the RAS, 119333 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics at INM RAS, 119333 Moscow, Russia
- Institute for Computer Science and Mathematical Modelling, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Arina Soboleva
- Department of Control and Applied Mathematics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Kirill Pavlishin
- Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andreas Meyerhans
- I CREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
- Infection Biology Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gennady Bocharov
- Marchuk Institute of Numerical Mathematics of the RAS, 119333 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics at INM RAS, 119333 Moscow, Russia
- Institute for Computer Science and Mathematical Modelling, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| |
Collapse
|
10
|
Altfeld M, Scully EP. Sex Differences in HIV Infection. Curr Top Microbiol Immunol 2023; 441:61-73. [PMID: 37695425 DOI: 10.1007/978-3-031-35139-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Biological sex has wide-ranging impacts on HIV infection spanning differences in acquisition risk, the pathogenesis of untreated infection, impact of chronic treated disease and prospects for HIV eradication or functional cure. This chapter summarizes the scope of these differences and discusses several features of the immune response thought to contribute to the clinical outcomes.
Collapse
Affiliation(s)
- Marcus Altfeld
- Department Virus Immunology, Leibniz Institute for Virology, Hamburg, Germany
| | - Eileen P Scully
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
11
|
Warger J, Gaudieri S. On the Evolutionary Trajectory of SARS-CoV-2: Host Immunity as a Driver of Adaptation in RNA Viruses. Viruses 2022; 15:70. [PMID: 36680110 PMCID: PMC9866609 DOI: 10.3390/v15010070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Host immunity can exert a complex array of selective pressures on a pathogen, which can drive highly mutable RNA viruses towards viral escape. The plasticity of a virus depends on its rate of mutation, as well as the balance of fitness cost and benefit of mutations, including viral adaptations to the host's immune response. Since its emergence, SARS-CoV-2 has diversified into genetically distinct variants, which are characterised often by clusters of mutations that bolster its capacity to escape human innate and adaptive immunity. Such viral escape is well documented in the context of other pandemic RNA viruses such as the human immunodeficiency virus (HIV) and influenza virus. This review describes the selection pressures the host's antiviral immunity exerts on SARS-CoV-2 and other RNA viruses, resulting in divergence of viral strains into more adapted forms. As RNA viruses obscure themselves from host immunity, they uncover weak points in their own armoury that can inform more comprehensive, long-lasting, and potentially cross-protective vaccine coverage.
Collapse
Affiliation(s)
- Jacob Warger
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA 6009, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Mandurah, WA 6150, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| |
Collapse
|
12
|
Aristotelous AC, Chen A, Forest MG. A hybrid discrete-continuum model of immune responses to SARS-CoV-2 infection in the lung alveolar region, with a focus on interferon induced innate response. J Theor Biol 2022; 555:111293. [PMID: 36208668 PMCID: PMC9533651 DOI: 10.1016/j.jtbi.2022.111293] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 01/14/2023]
Abstract
We develop a lattice-based, hybrid discrete-continuum modeling framework for SARS-CoV-2 exposure and infection in the human lung alveolar region, or parenchyma, the massive surface area for gas exchange. COVID-19 pneumonia is alveolar infection by the SARS-CoV-2 virus significant enough to compromise gas exchange. The modeling framework orchestrates the onset and progression of alveolar infection, spatially and temporally, beginning with a pre-immunity baseline, upon which we superimpose multiple mechanisms of immune protection conveyed by interferons and antibodies. The modeling framework is tunable to individual profiles, focusing here on degrees of innate immunity, and to the evolving infection-replication properties of SARS-CoV-2 variant strains. The model employs partial differential equations for virion, interferon, and antibody concentrations governed by diffusion in the thin fluid coating of alveolar cells, species and lattice interactions corresponding to sources and sinks for each species, and multiple immune protections signaled by interferons. The spatial domain is a two-dimensional, rectangular lattice of alveolar type I (non-infectable) and type II (infectable) cells with a stochastic, species-concentration-governed, switching dynamics of type II lattice sites from healthy to infected. Once infected, type II cells evolve through three phases: an eclipse phase during which RNA copies (virions) are assembled; a shedding phase during which virions and interferons are released; and then cell death. Model simulations yield the dynamic spread of, and immune protection against, alveolar infection and viral load from initial sites of exposure. We focus in this paper on model illustrations of the diversity of outcomes possible from alveolar infection, first absent of immune protection, and then with varying degrees of four known mechanisms of interferon-induced innate immune protection. We defer model illustrations of antibody protection to future studies. Results presented reinforce previous recognition that interferons produced solely by infected cells are insufficient to maintain a high efficacy level of immune protection, compelling additional mechanisms to clear alveolar infection, such as interferon production by immune cells and adaptive immunity (e.g., T cells). This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
Collapse
Affiliation(s)
- Andreas C. Aristotelous
- Department of Mathematics, The University of Akron, Akron, OH 44325-4002, United States of America,Corresponding author
| | - Alex Chen
- Department of Mathematics, California State University, Dominguez Hills, CA 90747, United States of America
| | - M. Gregory Forest
- Departments of Mathematics, Applied Physical Sciences, and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3250, United States of America
| |
Collapse
|
13
|
Zuliani-Alvarez L, Govasli ML, Rasaiyaah J, Monit C, Perry SO, Sumner RP, McAlpine-Scott S, Dickson C, Rifat Faysal KM, Hilditch L, Miles RJ, Bibollet-Ruche F, Hahn BH, Boecking T, Pinotsis N, James LC, Jacques DA, Towers GJ. Evasion of cGAS and TRIM5 defines pandemic HIV. Nat Microbiol 2022; 7:1762-76. [PMID: 36289397 DOI: 10.1038/s41564-022-01247-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022]
Abstract
Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
Collapse
|
14
|
Guo K, Barrett BS, Morrison JH, Mickens KL, Vladar EK, Hasenkrug KJ, Poeschla EM, Santiago ML. Interferon resistance of emerging SARS-CoV-2 variants. Proc Natl Acad Sci U S A 2022; 119:e2203760119. [PMID: 35867811 PMCID: PMC9371743 DOI: 10.1073/pnas.2203760119] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/26/2022] [Indexed: 01/08/2023] Open
Abstract
The emergence of SARS-CoV-2 variants with enhanced transmissibility, pathogenesis, and resistance to vaccines presents urgent challenges for curbing the COVID-19 pandemic. While Spike mutations that enhance virus infectivity or neutralizing antibody evasion may drive the emergence of these novel variants, studies documenting a critical role for interferon responses in the early control of SARS-CoV-2 infection, combined with the presence of viral genes that limit these responses, suggest that interferons may also influence SARS-CoV-2 evolution. Here, we compared the potency of 17 different human interferons against multiple viral lineages sampled during the course of the global outbreak, including ancestral and five major variants of concern that include the B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma), B.1.617.2 (delta), and B.1.1.529 (omicron) lineages. Our data reveal that relative to ancestral isolates, SARS-CoV-2 variants of concern exhibited increased interferon resistance, suggesting that evasion of innate immunity may be a significant, ongoing driving force for SARS-CoV-2 evolution. These findings have implications for the increased transmissibility and/or lethality of emerging variants and highlight the interferon subtypes that may be most successful in the treatment of early infections.
Collapse
Affiliation(s)
- Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Bradley S. Barrett
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - James H. Morrison
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Kaylee L. Mickens
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Eszter K. Vladar
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Eric M. Poeschla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| |
Collapse
|
15
|
Abstract
Combination antiretroviral therapy (ART) can block multiple stages of the HIV-1 life cycle to prevent progression to AIDS in people living with HIV-1. However, owing to the persistence of a reservoir of latently infected CD4+ T cells, life-long ART is necessary to prevent viral rebound. One strategy currently under consideration for curing HIV-1 infection is known as 'shock and kill'. This strategy uses latency-reversing agents to induce expression of HIV-1 genes, allowing for infected cells to be cleared by cytolytic immune cells. The role of innate immunity in HIV-1 pathogenesis is best understood in the context of acute infection. Here, we suggest that innate immunity can also be used to improve the efficacy of HIV-1 cure strategies, with a particular focus on dendritic cells (DCs) and natural killer cells. We discuss novel latency-reversing agents targeting DCs as well as DC-based strategies to enhance the clearance of infected cells by CD8+ T cells and strategies to improve the killing activity of natural killer cells.
Collapse
Affiliation(s)
- Nathan L Board
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Milica Moskovljevic
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, USA.
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
16
|
Olson RM, Gornalusse G, Whitmore LS, Newhouse D, Tisoncik-Go J, Smith E, Ochsenbauer C, Hladik F, Gale M. Innate immune regulation in HIV latency models. Retrovirology 2022; 19:15. [PMID: 35804422 PMCID: PMC9270781 DOI: 10.1186/s12977-022-00599-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/25/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Innate immunity and type 1 interferon (IFN) defenses are critical for early control of HIV infection within CD4 + T cells. Despite these defenses, some acutely infected cells silence viral transcription to become latently infected and form the HIV reservoir in vivo. Latently infected cells persist through antiretroviral therapy (ART) and are a major barrier to HIV cure. Here, we evaluated innate immunity and IFN responses in multiple T cell models of HIV latency, including established latent cell lines, Jurkat cells latently infected with a reporter virus, and a primary CD4 + T cell model of virologic suppression. RESULTS We found that while latently infected T cell lines have functional RNA sensing and IFN signaling pathways, they fail to induce specific interferon-stimulated genes (ISGs) in response to innate immune activation or type 1 IFN treatment. Jurkat cells latently infected with a fluorescent reporter HIV similarly demonstrate attenuated responses to type 1 IFN. Using bulk and single-cell RNA sequencing we applied a functional genomics approach and define ISG expression dynamics in latent HIV infection, including HIV-infected ART-suppressed primary CD4 + T cells. CONCLUSIONS Our observations indicate that HIV latency and viral suppression each link with cell-intrinsic defects in specific ISG induction. We identify a set of ISGs for consideration as latency restriction factors whose expression and function could possibly mitigate establishing latent HIV infection.
Collapse
Affiliation(s)
- Rebecca M. Olson
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Germán Gornalusse
- grid.270240.30000 0001 2180 1622Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Obstetrics & Gynecology, University of Washington, Seattle, WA USA
| | - Leanne S. Whitmore
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Dan Newhouse
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Jennifer Tisoncik-Go
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Elise Smith
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Christina Ochsenbauer
- grid.270240.30000 0001 2180 1622Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Florian Hladik
- grid.270240.30000 0001 2180 1622Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Obstetrics & Gynecology, University of Washington, Seattle, WA USA ,grid.34477.330000000122986657Department of Medicine, University of Washington, Seattle, WA USA
| | - Michael Gale
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| |
Collapse
|
17
|
Vieira VA, Herbert N, Cromhout G, Adland E, Goulder P. Role of Early Life Cytotoxic T Lymphocyte and Natural Killer Cell Immunity in Paediatric HIV Cure/Remission in the Anti-Retroviral Therapy Era. Front Immunol 2022; 13:886562. [PMID: 35634290 PMCID: PMC9130627 DOI: 10.3389/fimmu.2022.886562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Only three well-characterised cases of functional cure have been described in paediatric HIV infection over the past decade. This underlines the fact that early initiation of combination antiretroviral therapy (cART), whilst minimising the size of the viral reservoir, is insufficient to achieve cure, unless other factors contribute. In this review, we consider these additional factors that may facilitate functional cure in paediatric infection. Among the early life immune activity, these include HIV-specific cytotoxic T-lymphocyte (CTL) and natural killer (NK) cell responses. The former have less potent antiviral efficacy in paediatric compared with adult infection, and indeed, in early life, NK responses have greater impact in suppressing viral replication than CTL. This fact may contribute to a greater potential for functional cure to be achieved in paediatric versus adult infection, since post-treatment control in adults is associated less with highly potent CTL activity, and more with effective antiviral NK cell responses. Nonetheless, antiviral CTL responses can play an increasingly effective role through childhood, especially in individuals expressing then 'protective' HLA-I molecules HLA-B*27/57/58:01/8101. The role of the innate system on preventing infection, in shaping the particular viruses transmitted, and influencing outcome is discussed. The susceptibility of female fetuses to in utero mother-to-child transmission, especially in the setting of recent maternal infection, is a curiosity that also provides clues to mechanisms by which cure may be achieved, since initial findings are that viral rebound is less frequent among males who interrupt cART. The potential of broadly neutralising antibody therapy to facilitate cure in children who have received early cART is discussed. Finally, we draw attention to the impact of the changing face of the paediatric HIV epidemic on cure potential. The effect of cART is not limited to preventing AIDS and reducing the risk of transmission. cART also affects which mothers transmit. No longer are mothers who transmit those who carry genes associated with poor immune control of HIV. In the cART era, a high proportion (>70% in our South African study) of transmitting mothers are those who seroconvert in pregnancy or who for social reasons are diagnosed late in pregnancy. As a result, now, genes associated with poor immune control of HIV are not enriched in mothers who transmit HIV to their child. These changes will likely influence the effectiveness of HLA-associated immune responses and therefore cure potential among children.
Collapse
Affiliation(s)
- Vinicius A. Vieira
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicholas Herbert
- Africa Health Research Institute (AHRI), Nelson R Mandela School of Medicine, Durban, South Africa
| | - Gabriela Cromhout
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Emily Adland
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, United Kingdom,Africa Health Research Institute (AHRI), Nelson R Mandela School of Medicine, Durban, South Africa,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa,*Correspondence: Philip Goulder,
| |
Collapse
|
18
|
Balinda SN, Kapaata A, Xu R, Salazar MG, Mezzell AT, Qin Q, Herard K, Dilernia D, Kamali A, Ruzagira E, Kibengo FM, Song H, Ochsenbauer C, Salazar-Gonzalez JF, Gilmour J, Hunter E, Yue L, Kaleebu P. Characterization of Near Full-Length Transmitted/Founder HIV-1 Subtype D and A/D Recombinant Genomes in a Heterosexual Ugandan Population (2006–2011). Viruses 2022; 14:v14020334. [PMID: 35215928 PMCID: PMC8874453 DOI: 10.3390/v14020334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 12/04/2022] Open
Abstract
Detailed characterization of transmitted HIV-1 variants in Uganda is fundamentally important to inform vaccine design, yet studies on the transmitted full-length strains of subtype D viruses are limited. Here, we amplified single genomes and characterized viruses, some of which were previously classified as subtype D by sub-genomic pol sequencing that were transmitted in Uganda between December 2006 to June 2011. Analysis of 5′ and 3′ half genome sequences showed 73% (19/26) of infections involved single virus transmissions, whereas 27% (7/26) of infections involved multiple variant transmissions based on predictions of a model of random virus evolution. Subtype analysis of inferred transmitted/founder viruses showed a high transmission rate of inter-subtype recombinants (69%, 20/29) involving mainly A1/D, while pure subtype D variants accounted for one-third of infections (31%, 9/29). Recombination patterns included a predominance of subtype D in the gag/pol region and a highly recombinogenic envelope gene. The signal peptide-C1 region and gp41 transmembrane domain (Tat2/Rev2 flanking region) were hotspots for A1/D recombination events. Analysis of a panel of 14 transmitted/founder molecular clones showed no difference in replication capacity between subtype D viruses (n = 3) and inter-subtype mosaic recombinants (n = 11). However, individuals infected with high replication capacity viruses had a faster CD4 T cell loss. The high transmission rate of unique inter-subtype recombinants is striking and emphasizes the extraordinary challenge for vaccine design and, in particular, for the highly variable and recombinogenic envelope gene, which is targeted by rational designs aimed to elicit broadly neutralizing antibodies.
Collapse
Affiliation(s)
- Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
- Correspondence: ; Tel.: +25-675-466-0098
| | - Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Allison T. Mezzell
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 3230, Eden Ave, Cincinnati, OH 45267, USA;
| | - Qianhong Qin
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Kimberly Herard
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Anatoli Kamali
- International AIDS Vaccine Initiative (IAVI), Nairobi 00202, Kenya;
| | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Freddie M. Kibengo
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Heeyah Song
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London SW10 9NH, UK;
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329, USA
| | - Ling Yue
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| |
Collapse
|
19
|
Zacharopoulou P, Marchi E, Ogbe A, Robinson N, Brown H, Jones M, Parolini L, Pace M, Grayson N, Kaleebu P, Rees H, Fidler S, Goulder P, Klenerman P, Frater J. Expression of type I interferon-associated genes at antiretroviral therapy interruption predicts HIV virological rebound. Sci Rep 2022; 12:462. [PMID: 35013427 PMCID: PMC8748440 DOI: 10.1038/s41598-021-04212-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/08/2021] [Indexed: 12/25/2022] Open
Abstract
Although certain individuals with HIV infection can stop antiretroviral therapy (ART) without viral load rebound, the mechanisms under-pinning 'post-treatment control' remain unclear. Using RNA-Seq we explored CD4 T cell gene expression to identify evidence of a mechanism that might underpin virological rebound and lead to discovery of associated biomarkers. Fourteen female participants who received 12 months of ART starting from primary HIV infection were sampled at the time of stopping therapy. Two analysis methods (Differential Gene Expression with Gene Set Enrichment Analysis, and Weighted Gene Co-expression Network Analysis) were employed to interrogate CD4+ T cell gene expression data and study pathways enriched in post-treatment controllers versus early rebounders. Using independent analysis tools, expression of genes associated with type I interferon responses were associated with a delayed time to viral rebound following treatment interruption (TI). Expression of four genes identified by Cox-Lasso (ISG15, XAF1, TRIM25 and USP18) was converted to a Risk Score, which associated with rebound (p < 0.01). These data link transcriptomic signatures associated with innate immunity with control following stopping ART. The results from this small sample need to be confirmed in larger trials, but could help define strategies for new therapies and identify new biomarkers for remission.
Collapse
Affiliation(s)
- P Zacharopoulou
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - E Marchi
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - A Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - N Robinson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Jones
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - L Parolini
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Pace
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - N Grayson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - P Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Entebbe, Uganda
| | - H Rees
- Wits Reproductive Health and HIV Institute of the University of the Witwatersrand in Johannesburg, Johannesburg, South Africa
| | - S Fidler
- Division of Medicine, Wright Fleming Institute, Imperial College, London, UK
- Imperial College NIHR Biomedical Research Centre, London, UK
| | - P Goulder
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - P Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Biomedical Research Centre, Oxford, UK
| | - J Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- National Institute of Health Research Biomedical Research Centre, Oxford, UK.
| |
Collapse
|
20
|
Guo K, Barrett BS, Mickens KL, Vladar EK, Morrison JH, Hasenkrug KJ, Poeschla EM, Santiago ML. Interferon Resistance of Emerging SARS-CoV-2 Variants. bioRxiv 2021:2021.03.20.436257. [PMID: 33758840 PMCID: PMC7986999 DOI: 10.1101/2021.03.20.436257] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The emergence of SARS-CoV-2 variants with enhanced transmissibility, pathogenesis and resistance to vaccines presents urgent challenges for curbing the COVID-19 pandemic. While Spike mutations that enhance virus infectivity or neutralizing antibody evasion may drive the emergence of these novel variants, studies documenting a critical role for interferon responses in the early control of SARS-CoV-2 infection, combined with the presence of viral genes that limit these responses, suggest that interferons may also influence SARS-CoV-2 evolution. Here, we compared the potency of 17 different human interferons against multiple viral lineages sampled during the course of the global outbreak, including ancestral and four major variants of concern. Our data reveal increased interferon resistance in emerging SARS-CoV-2 variants, suggesting that evasion of innate immunity may be a significant, ongoing driving force for SARS-CoV-2 evolution. These findings have implications for the increased lethality of emerging variants and highlight the interferon subtypes that may be most successful in the treatment of early infections.
Collapse
Affiliation(s)
- Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Bradley S. Barrett
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kaylee L. Mickens
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Ezster K. Vladar
- Division of Pulmonary Sciences and Critical Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - James H. Morrison
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Eric M. Poeschla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| |
Collapse
|
21
|
Abstract
Although antiretroviral therapy (ART) can reduce viremia to below the limit of detection and allow persons living with HIV-1 (PLWH) to lead relatively normal lives, viremia rebounds when treatment is interrupted. Rebound reflects viral persistence in a stable latent reservoir in resting CD4+ T cells. This reservoir is now recognized as the major barrier to cure and is the focus of intense international research efforts. Strategies to cure HIV-1 infection include interventions to eliminate this reservoir, to prevent viral rebound from the reservoir, or to enhance immune responses such that viral replication is effectively controlled. Here we consider recent developments in understanding the composition of the reservoir and how it can be measured in clinical studies. We also discuss exciting new insights into the in vivo dynamics of the reservoir and the reasons for its remarkable stability. Finally we discuss recent discoveries on the complex processes that govern viral rebound. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; .,Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA
| |
Collapse
|
22
|
Bosso M, Stürzel CM, Kmiec D, Badarinarayan SS, Braun E, Ito J, Sato K, Hahn BH, Sparrer KMJ, Sauter D, Kirchhoff F. An additional NF-κB site allows HIV-1 subtype C to evade restriction by nuclear PYHIN proteins. Cell Rep 2021; 36:109735. [PMID: 34551301 PMCID: PMC8505707 DOI: 10.1016/j.celrep.2021.109735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/23/2021] [Accepted: 08/26/2021] [Indexed: 10/28/2022] Open
Abstract
Subtype C is the most prevalent clade of human immunodeficiency virus type 1 (HIV-1) worldwide. The reasons for this are poorly understood. Here, we demonstrate that a characteristic additional third nuclear factor κB (NF-κB) binding site in the long terminal repeat (LTR) promoter allows subtype C HIV-1 strains to evade restriction by nuclear PYHIN proteins, which sequester the transcription factor Sp1. Further, other LTR alterations are responsible for rare PYHIN resistance of subtype B viruses. Resistance-conferring mutations generally reduce the dependency of HIV-1 on Sp1 for virus production and render LTR transcription highly responsive to stimulation by NF-κB/p65. A third NF-κB binding site increases infectious virus yield in primary CD4+ T cells in an γ-interferon-inducible protein 16 (IFI16)-dependent manner. Comprehensive sequence analyses suggest that the frequency of circulating PYHIN-resistant HIV-1 strains is increasing. Our finding that an additional NF-κB binding site in the LTR confers resistance to nuclear PYHIN proteins helps to explain the dominance of clade C HIV-1 strains.
Collapse
Affiliation(s)
- Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE5 9RS, UK
| | - Smitha Srinivasachar Badarinarayan
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Elisabeth Braun
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | | | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
| |
Collapse
|
23
|
Rojas M, Luz-Crawford P, Soto-Rifo R, Reyes-Cerpa S, Toro-Ascuy D. The Landscape of IFN/ISG Signaling in HIV-1-Infected Macrophages and Its Possible Role in the HIV-1 Latency. Cells 2021; 10:2378. [PMID: 34572027 PMCID: PMC8467246 DOI: 10.3390/cells10092378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
A key characteristic of Human immunodeficiency virus type 1 (HIV-1) infection is the generation of latent viral reservoirs, which have been associated with chronic immune activation and sustained inflammation. Macrophages play a protagonist role in this context since they are persistently infected while being a major effector of the innate immune response through the generation of type-I interferons (type I IFN) and IFN-stimulated genes (ISGs). The balance in the IFN signaling and the ISG induction is critical to promote a successful HIV-1 infection. Classically, the IFNs response is fine-tuned by opposing promotive and suppressive signals. In this context, it was described that HIV-1-infected macrophages can also synthesize some antiviral effector ISGs and, positive and negative regulators of the IFN/ISG signaling. Recently, epitranscriptomic regulatory mechanisms were described, being the N6-methylation (m6A) modification on mRNAs one of the most relevant. The epitranscriptomic regulation can affect not only IFN/ISG signaling, but also type I IFN expression, and viral fitness through modifications to HIV-1 RNA. Thus, the establishment of replication-competent latent HIV-1 infected macrophages may be due to non-classical mechanisms of type I IFN that modulate the activation of the IFN/ISG signaling network.
Collapse
Affiliation(s)
- Masyelly Rojas
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile;
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile;
| | - Patricia Luz-Crawford
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile;
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Faculty of Medicine, Institute of Biomedical Sciences, Universidad of Chile, Santiago 8389100, Chile;
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Daniela Toro-Ascuy
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile;
| |
Collapse
|
24
|
Hassan AS, Hare J, Gounder K, Nazziwa J, Karlson S, Olsson L, Streatfield C, Kamali A, Karita E, Kilembe W, Price MA, Borrow P, Björkman P, Kaleebu P, Allen S, Hunter E, Ndung'u T, Gilmour J, Rowland-Jones S, Esbjörnsson J, Sanders EJ. A Stronger Innate Immune Response During Hyperacute Human Immunodeficiency Virus Type 1 (HIV-1) Infection Is Associated With Acute Retroviral Syndrome. Clin Infect Dis 2021; 73:832-841. [PMID: 33588436 PMCID: PMC8423478 DOI: 10.1093/cid/ciab139] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Acute retroviral syndrome (ARS) is associated with human immunodeficiency virus type 1 (HIV-1) subtype and disease progression, but the underlying immunopathological pathways are poorly understood. We aimed to elucidate associations between innate immune responses during hyperacute HIV-1 infection (hAHI) and ARS. METHODS Plasma samples obtained from volunteers (≥18.0 years) before and during hAHI, defined as HIV-1 antibody negative and RNA or p24 antigen positive, from Kenya, Rwanda, Uganda, Zambia, and Sweden were analyzed. Forty soluble innate immune markers were measured using multiplexed assays. Immune responses were differentiated into volunteers with stronger and comparatively weaker responses using principal component analysis. Presence or absence of ARS was defined based on 11 symptoms using latent class analysis. Logistic regression was used to determine associations between immune responses and ARS. RESULTS Of 55 volunteers, 31 (56%) had ARS. Volunteers with stronger immune responses (n = 36 [65%]) had increased odds of ARS which was independent of HIV-1 subtype, age, and risk group (adjusted odds ratio, 7.1 [95% confidence interval {CI}: 1.7-28.8], P = .003). Interferon gamma-induced protein (IP)-10 was 14-fold higher during hAHI, elevated in 7 of the 11 symptoms and independently associated with ARS. IP-10 threshold >466.0 pg/mL differentiated stronger immune responses with a sensitivity of 84.2% (95% CI: 60.4-96.6) and specificity of 100.0% (95% CI]: 90.3-100.0). CONCLUSIONS A stronger innate immune response during hAHI was associated with ARS. Plasma IP-10 may be a candidate biomarker of stronger innate immunity. Our findings provide further insights on innate immune responses in regulating ARS and may inform the design of vaccine candidates harnessing innate immunity.
Collapse
Affiliation(s)
- Amin S Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Translational Medicine, Lund University, Sweden
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom.,IAVI, New York, New York, USA, and Nairobi, Kenya
| | - Kamini Gounder
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, Sweden
| | - Sara Karlson
- Department of Translational Medicine, Lund University, Sweden
| | - Linnéa Olsson
- Department of Internal Medicine, Helsingborg Hospital, Helsingborg, Sweden
| | | | | | - Etienne Karita
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - William Kilembe
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - Matt A Price
- IAVI, New York, New York, USA, and Nairobi, Kenya.,UCSF Department of Epidemiology and Biostatistics, San Francisco,California, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Per Björkman
- Department of Translational Medicine, Lund University, Sweden
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Uganda, and London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susan Allen
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia.,Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia.,Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - 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.,Max Planck Institute for Infection Biology, Berlin, Germany.,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
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Sarah Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Sweden.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
25
|
Abstract
The latent reservoir for human immunodeficiency virus type 1 (HIV-1) in resting CD4+ T cells is a major barrier to cure. The dimensions of the reservoir problem can be defined with 2 assays. A definitive minimal estimate of the frequency of latently infected cells is provided by the quantitative viral outgrowth assay (QVOA), which detects cells that can be induced by T-cell activation to release infectious virus. In contrast, the intact proviral DNA assay (IPDA) detects all genetically intact proviruses and provides a more accurate upper limit on reservoir size than standard single-amplicon polymerase chain reaction assays which mainly detect defective proviruses. The frequency of cells capable of initiating viral rebound on interruption of antiretroviral therapy lies between the values produced by the QVOA and the IPDA. We argue here that the 1-2-log difference between QVOA and IPDA values in part reflects that the fact that many replication-competent proviruses are not readily induced by T-cell activation. Findings of earlier studies suggest that latently infected cells can be activated to proliferate in vivo without expressing viral genes. The proliferating cells nevertheless retain the ability to produce virus on subsequent stimulation. The low inducibility of latent proviruses is a major problem for the shock-and-kill strategy for curing HIV-1 infection, which uses latency-reversing agents to induce viral gene expression and render infected cells susceptible to immune clearance. The latency-reversing agents developed to date are much less effective at reversing latency than T-cell activation. Taken together, these results indicate that HIV-1 eradication will require the discovery of much more effective ways to induce viral gene expression.
Collapse
Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| |
Collapse
|
26
|
Bauer AM, Bar KJ. Advances in simian--human immunodeficiency viruses for nonhuman primate studies of HIV prevention and cure. Curr Opin HIV AIDS 2020; 15:275-81. [PMID: 32769631 DOI: 10.1097/COH.0000000000000645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Simian--human immunodeficiency viruses (SHIVs), chimeric viruses that encode HIV-1 Env within an SIV backbone, are key reagents for nonhuman primate studies of antibody-based vaccines, broadly neutralizing antibodies (bnAbs), and other Env-targeting reagents. Here, we discuss the provenance and characteristics of currently relevant SHIVs, novel technical advances, recent discoveries enabled by SHIV challenge studies, and the continued development of SHIVs for persistence and cure experiments. RECENT FINDINGS SHIV SF162P3, SHIV AD8EO, and transmitter/founder SHIVs with Env375 mutations are now common reagents in nonhuman primate studies, with increased use and validation establishing their properties and potential applications. Genetic barcoding of SIV and SHIV, which allows tracing of individual lineages and elucidation of viral kinetics from transmission through latency has expanded the experimental capacity of SHIV models. SHIV challenge studies have determined the neutralizing antibody titers that correlate with protection for passive and active immunization and enabled complementary human and nonhuman primate studies of vaccine development. SHIV models of latency continue to evolve, aided by descriptions of SHIV persistence on ART and the proviral landscape. SUMMARY Recent advances and more thorough characterization of SHIVs allow for expanded applications and greater confidence in experimental results.
Collapse
|
27
|
Abstract
Dendritic cell (DC) subsets are abundantly present in genital and intestinal mucosal tissue and are among the first innate immune cells that encounter human immunodeficiency virus type 1 (HIV-1) after sexual contact. Although DCs have specific characteristics that greatly enhance HIV-1 transmission, it is becoming evident that most DC subsets also have virus restriction mechanisms that exert selective pressure on the viruses during sexual transmission. In this review we discuss the current concepts of the immediate events following viral exposure at genital mucosal sites that lead to selection of specific HIV-1 variants called transmitted founder (TF) viruses. We highlight the importance of the TF HIV-1 phenotype and the role of different DC subsets in establishing infection. Understanding the biology of HIV-1 transmission will contribute to the design of novel treatment strategies preventing HIV-1 dissemination.
Collapse
Affiliation(s)
- Bernadien M Nijmeijer
- Department of Experimental Immunology, Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Catharina J M Langedijk
- Department of Experimental Immunology, Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| |
Collapse
|
28
|
Tauzin A, Espinosa Ortiz A, Blake O, Soundaramourty C, Joly-Beauparlant C, Nicolas A, Droit A, Dutrieux J, Estaquier J, Mammano F. Differential Inhibition of HIV Replication by the 12 Interferon Alpha Subtypes. J Virol 2021; 95:e0231120. [PMID: 33980591 DOI: 10.1128/JVI.02311-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Type I interferons (IFNs) are a family of cytokines that represent a first line of defense against virus infections. The 12 different IFN-α subtypes share a receptor on target cells and trigger similar signaling cascades. Several studies have collectively shown that this apparent redundancy conceals qualitatively different responses induced by individual subtypes, which display different efficacies of inhibition of HIV replication. Some studies, however, provided evidence that the disparities are quantitative rather than qualitative. Since RNA expression analyses show a large but incomplete overlap of the genes induced, they may support both models. To explore if the IFN-α subtypes induce functionally relevant different anti-HIV activities, we have compared the efficacies of inhibition of all 12 subtypes on HIV spread and on specific steps of the viral replication cycle, including viral entry, reverse transcription, protein synthesis, and virus release. Finding different hierarchies of inhibition would validate the induction of qualitatively different responses. We found that while most subtypes similarly inhibit virus entry, they display distinctive potencies on other early steps of HIV replication. In addition, only some subtypes were able to target effectively the late steps. The extent of induction of known anti-HIV factors helps to explain some, but not all differences observed, confirming the participation of additional IFN-induced anti-HIV effectors. Our findings support the notion that different IFN-α subtypes can induce the expression of qualitatively different antiviral activities. IMPORTANCE The initial response against viruses relies in large part on type I interferons, which include 12 subtypes of IFN-α. These cytokines bind to a common receptor on the cell surface and trigger the expression of incompletely overlapping sets of genes. Whether the anti-HIV responses induced by IFN-α subtypes differ in the extent of expression or in the nature of the genes involved remains debated. Also, RNA expression profiles led to opposite conclusions, depending on the importance attributed to the induction of common or distinctive genes. To explore if relevant anti-HIV activities can be differently induced by the IFN-α subtypes, we compared their relative efficacies on specific steps of the replication cycle. We show that the hierarchy of IFN potencies depends on the step analyzed, supporting qualitatively different responses. This work will also prompt the search for novel IFN-induced anti-HIV factors acting on specific steps of the replication cycle.
Collapse
|
29
|
Abstract
Emerging or re-emerging viruses are still major threats to public health. Prophylactic vaccines represent the most effective way to prevent virus infection; however, antivirals are more promising for those viruses against which vaccines are not effective enough or contemporarily unavailable. Because of the slow pace of novel antiviral discovery, the high disuse rates, and the substantial cost, repurposing of the well-characterized therapeutics, either approved or under investigation, is becoming an attractive strategy to identify the new directions to treat virus infections. In this review, we described recent progress in identifying broad-spectrum antivirals through drug repurposing. We defined the two major categories of the repurposed antivirals, direct-acting repurposed antivirals (DARA) and host-targeting repurposed antivirals (HTRA). Under each category, we summarized repurposed antivirals with potential broad-spectrum activity against a variety of viruses and discussed the possible mechanisms of action. Finally, we proposed the potential investigative directions of drug repurposing.
Collapse
Affiliation(s)
- Xinlei Li
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, College of Basic Medicine, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, College of Basic Medicine, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
30
|
Jeremiah SS, Miyakawa K, Matsunaga S, Nishi M, Kudoh A, Takaoka A, Sawasaki T, Ryo A. Cleavage of TANK-Binding Kinase 1 by HIV-1 Protease Triggers Viral Innate Immune Evasion. Front Microbiol 2021; 12:643407. [PMID: 33986734 PMCID: PMC8110901 DOI: 10.3389/fmicb.2021.643407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/01/2021] [Indexed: 11/22/2022] Open
Abstract
Type-I interferons (IFN-I) are the innate immune system’s principal defense against viral infections. Human immunodeficiency virus-1 (HIV-1) has evolved several ways to suppress or evade the host’s innate immunity in order to survive and replicate to sustain infection. Suppression of IFN-I is one among the multiple escape strategies used by HIV-1 to prevent its clearance. HIV-1 protease which helps in viral maturation has also been observed to cleave host cellular protein kinases. In this study we performed a comprehensive screening of a human kinase library using AlphaScreen assay and identified that TANK binding kinase-1 (TBK1) was cleaved by HIV-1 protease (PR). We demonstrate that PR cleaved TBK1 fails to phosphorylate IFN regulatory factor 3 (IRF3), thereby reducing the IFN-I promoter activity and further reveal that the PR mediated suppression of IFN-I could be counteracted by protease inhibitors (PI) in vitro. We have also revealed that mutations of HIV-1 PR that confer drug resistance to PIs reduce the enzyme’s ability to cleave TBK1. The findings of this study unearth a direct link between HIV-1 PR activity and evasion of innate immunity by the virus, the possible physiological relevance of which warrants to be determined.
Collapse
Affiliation(s)
| | - Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Satoko Matsunaga
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Mayuko Nishi
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Ayumi Kudoh
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Akinori Takaoka
- Division of Signaling in Cancer and Immunology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| |
Collapse
|
31
|
Hendricks CM, Cordeiro T, Gomes AP, Stevenson M. The Interplay of HIV-1 and Macrophages in Viral Persistence. Front Microbiol 2021; 12:646447. [PMID: 33897659 PMCID: PMC8058371 DOI: 10.3389/fmicb.2021.646447] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/11/2021] [Indexed: 12/18/2022] Open
Abstract
HIV-1 has evolved mechanisms to evade host cell immune responses and persist for lifelong infection. Latent cellular reservoirs are responsible for this persistence of HIV-1 despite the powerful effects of highly active antiretroviral therapies (HAART) to control circulating viral load. While cellular reservoirs have been extensively studied, much of these studies have focused on peripheral blood and resting memory CD4+ T cells containing latent HIV-1 provirus; however, efforts to eradicate cellular reservoirs have been stunted by reservoirs found in tissues compartments that are not easily accessible. These tissues contain resting memory CD4+ T cells and tissue resident macrophages, another latent cellular reservoir to HIV-1. Tissue resident macrophages have been associated with HIV-1 infection since the 1980s, and evidence has continued to grow regarding their role in HIV-1 persistence. Specific biological characteristics play a vital role as to why macrophages are latent cellular reservoirs for HIV-1, and in vitro and in vivo studies exhibit how macrophages contribute to viral persistence in individuals and animals on antiretroviral therapies. In this review, we characterize the role and evolutionary advantages of macrophage reservoirs to HIV-1 and their contribution to HIV-1 persistence. In acknowledging the interplay of HIV-1 and macrophages in the host, we identify reasons why current strategies are incapable of eliminating HIV-1 reservoirs and why efforts must focus on eradicating reservoirs to find a future functional cure.
Collapse
Affiliation(s)
- Chynna M Hendricks
- Department of Microbiology & Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Thaissa Cordeiro
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Ana Paula Gomes
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Mario Stevenson
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States
| |
Collapse
|
32
|
Rindler AE, Kuster H, Neumann K, Leemann C, Braun DL, Metzner KJ, Günthard HF. A Novel High Throughput, Parallel Infection Assay for Determining the Replication Capacities of 346 Primary HIV-1 Isolates of the Zurich Primary HIV-1 Infection Study in Primary Cells. Viruses 2021; 13:404. [PMID: 33806576 PMCID: PMC8000554 DOI: 10.3390/v13030404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 replication capacity is an important characteristic to understand the replication competence of single variants or virus populations. It can further aid in the understanding of HIV-1 pathogenicity, disease progression, and drug resistance mutations. To effectively study RC, many assays have been established. However, there is still demand for a high throughput replication capacity assay using primary cells which is robust and reproducible. In this study, we established such an assay and validated it using 346 primary HIV-1 isolates from patients enrolled in the Zurich Primary HIV Infection study (ZPHI) and two control viruses, HIV-1 JR-CSFWT and HIV-1 JR-CSFK65R_M184V. Replication capacity was determined by measuring the viral growth on PBMCs over 10 days by longitudinally transferring cell culture supernatant to TZM-bl reporter cells. By utilizing the TZM-bl luciferase reporter assay, we determined replication capacity by measuring viral infectivity. The simplicity of the experimental setup allowed for all 346 primary HIV-1 isolates to be replicated at one time. Although the infectious input dose for each virus was normalized, a broad range of replication capacity values over 4 logs was observed. The approach was confirmed by two repeated experiments and we demonstrated that the reproducibility of the replication capacity values is statistically comparable between the two separate experiments. In summary, these results endorse our high throughput replication capacity assay as reproducible and robust and can be utilized for large scale HIV-1 replication capacity experiments in primary cells.
Collapse
Affiliation(s)
- Audrey E. Rindler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
- Life Sciences Graduate School, University of Zürich, 8057 Zürich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Dominique L. Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| |
Collapse
|
33
|
Saygili E, Yildiz-Ozturk E, Green MJ, Ghaemmaghami AM, Yesil-Celiktas O. Human lung-on-chips: Advanced systems for respiratory virus models and assessment of immune response. Biomicrofluidics 2021; 15:021501. [PMID: 33791050 PMCID: PMC7990507 DOI: 10.1063/5.0038924] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/15/2021] [Indexed: 05/06/2023]
Abstract
Respiratory viral infections are leading causes of death worldwide. A number of human respiratory viruses circulate in all age groups and adapt to person-to-person transmission. It is vital to understand how these viruses infect the host and how the host responds to prevent infection and onset of disease. Although animal models have been widely used to study disease states, incisive arguments related to poor prediction of patient responses have led to the development of microfluidic organ-on-chip models, which aim to recapitulate organ-level physiology. Over the past decade, human lung chips have been shown to mimic many aspects of the lung function and its complex microenvironment. In this review, we address immunological responses to viral infections and elaborate on human lung airway and alveolus chips reported to model respiratory viral infections and therapeutic interventions. Advances in the field will expedite the development of therapeutics and vaccines for human welfare.
Collapse
Affiliation(s)
- Ecem Saygili
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Izmir, Turkey
| | - Ece Yildiz-Ozturk
- Translational Pulmonary Research Center, Ege University, 35100 Izmir, Turkey
| | | | | | | |
Collapse
|
34
|
Michael Lavigne G, Russell H, Sherry B, Ke R. Autocrine and paracrine interferon signalling as 'ring vaccination' and 'contact tracing' strategies to suppress virus infection in a host. Proc Biol Sci 2021; 288:20203002. [PMID: 33622135 PMCID: PMC7935137 DOI: 10.1098/rspb.2020.3002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The innate immune response, particularly the interferon response, represents a first line of defence against viral infections. The interferon molecules produced from infected cells act through autocrine and paracrine signalling to turn host cells into an antiviral state. Although the molecular mechanisms of IFN signalling have been well characterized, how the interferon response collectively contribute to the regulation of host cells to stop or suppress viral infection during early infection remain unclear. Here, we use mathematical models to delineate the roles of the autocrine and the paracrine signalling, and show that their impacts on viral spread are dependent on how infection proceeds. In particular, we found that when infection is well-mixed, the paracrine signalling is not as effective; by contrast, when infection spreads in a spatial manner, a likely scenario during initial infection in tissue, the paracrine signalling can impede the spread of infection by decreasing the number of susceptible cells close to the site of infection. Furthermore, we argue that the interferon response can be seen as a parallel to population-level epidemic prevention strategies such as ‘contact tracing’ or ‘ring vaccination’. Thus, our results here may have implications for the outbreak control at the population scale more broadly.
Collapse
Affiliation(s)
- G Michael Lavigne
- Department of Mathematics, North Carolina State University, Raleigh, NC 27606, USA
| | - Hayley Russell
- Department of Mathematics, North Carolina State University, Raleigh, NC 27606, USA
| | - Barbara Sherry
- School of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
| | - Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, NC 27606, USA.,T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| |
Collapse
|
35
|
Rajak P, Ganguly A, Sarkar S, Mandi M, Dutta M, Podder S, Khatun S, Roy S. Immunotoxic role of organophosphates: An unseen risk escalating SARS-CoV-2 pathogenicity. Food Chem Toxicol 2021; 149:112007. [PMID: 33493637 PMCID: PMC7825955 DOI: 10.1016/j.fct.2021.112007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Consistent gathering of immunotoxic substances on earth is a serious global issue affecting people under pathogenic stress. Organophosphates are among such hazardous compounds that are ubiquitous in nature. They fuel oxidative stress to impair antiviral immune response in living entities. Aside, organophosphates promote cytokine burst and pyroptosis in broncho-alveolar chambers leading to severe respiratory ailments. At present, we witness COVID-19 outbreak caused by SARS-CoV-2. Infection triggers cytokine storm coupled with inflammatory manifestations and pulmonary disorders in patients. Since organophosphate-exposure promotes necroinflammation and respiratory troubles hence during current pandemic situation, additional exposure to such chemicals can exacerbate inflammatory outcome and pulmonary maladies in patients, or pre-exposure to organophosphates might turn-out to be a risk factor for compromised immunity. Fortunately, antioxidants alleviate organophosphate-induced immunosuppression and hence under co-exposure circumstances, dietary intake of antioxidants would be beneficial to boost immunity against SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Prem Rajak
- Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India.
| | - Abhratanu Ganguly
- Post Graduate Department of Zoology, A.B.N. Seal College, Cooch Behar, West Bengal, India.
| | - Saurabh Sarkar
- Department of Zoology, Gushkara Mahavidyalaya, Gushkara, Purba Bardhaman, West Bengal, India.
| | - Moutushi Mandi
- Toxicology Research Unit, Department of Zoology, The University of Burdwan, Purba Bardhaman, West Bengal, India.
| | - Moumita Dutta
- Departments of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA.
| | - Sayanti Podder
- Post Graduate Department of Zoology, Modern College of Arts, Science and Commerce, Ganeshkhind, Pune, Maharashtra, India.
| | - Salma Khatun
- Department of Zoology, Krishna Chandra College, Hetampur, West Bengal, India.
| | - Sumedha Roy
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Belgium.
| |
Collapse
|
36
|
Bruxelle JF, Trattnig N, Mureithi MW, Landais E, Pantophlet R. HIV-1 Entry and Prospects for Protecting against Infection. Microorganisms 2021; 9:microorganisms9020228. [PMID: 33499233 PMCID: PMC7911371 DOI: 10.3390/microorganisms9020228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
Human Immunodeficiency Virus type-1 (HIV-1) establishes a latent viral reservoir soon after infection, which poses a major challenge for drug treatment and curative strategies. Many efforts are therefore focused on blocking infection. To this end, both viral and host factors relevant to the onset of infection need to be considered. Given that HIV-1 is most often transmitted mucosally, strategies designed to protect against infection need to be effective at mucosal portals of entry. These strategies need to contend also with cell-free and cell-associated transmitted/founder (T/F) virus forms; both can initiate and establish infection. This review will discuss how insight from the current model of HIV-1 mucosal transmission and cell entry has highlighted challenges in developing effective strategies to prevent infection. First, we examine key viral and host factors that play a role in transmission and infection. We then discuss preventive strategies based on antibody-mediated protection, with emphasis on targeting T/F viruses and mucosal immunity. Lastly, we review treatment strategies targeting viral entry, with focus on the most clinically advanced entry inhibitors.
Collapse
Affiliation(s)
- Jean-François Bruxelle
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Correspondence: (J.-F.B.); (R.P.)
| | - Nino Trattnig
- Chemical Biology and Drug Discovery, Utrecht University, 3584 CG Utrecht, The Netherlands;
| | - Marianne W. Mureithi
- KAVI—Institute of Clinical Research, College of Health Sciences, University of Nairobi, P.O. Box, Nairobi 19676–00202, Kenya;
| | - Elise Landais
- IAVI Neutralizing Antibody Center, La Jolla, CA 92037, USA;
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Correspondence: (J.-F.B.); (R.P.)
| |
Collapse
|
37
|
Gondim MVP, Sherrill-Mix S, Bibollet-Ruche F, Russell RM, Trimboli S, Smith AG, Li Y, Liu W, Avitto AN, DeVoto JC, Connell J, Fenton-May AE, Pellegrino P, Williams I, Papasavvas E, Lorenzi JCC, Salantes DB, Mampe F, Monroy MA, Cohen YZ, Heath S, Saag MS, Montaner LJ, Collman RG, Siliciano JM, Siliciano RF, Plenderleith LJ, Sharp PM, Caskey M, Nussenzweig MC, Shaw GM, Borrow P, Bar KJ, Hahn BH. Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption. Sci Transl Med 2021; 13:eabd8179. [PMID: 33441429 PMCID: PMC7923595 DOI: 10.1126/scitranslmed.abd8179] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/04/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Type 1 interferons (IFN-I) are potent innate antiviral effectors that constrain HIV-1 transmission. However, harnessing these cytokines for HIV-1 cure strategies has been hampered by an incomplete understanding of their antiviral activities at later stages of infection. Here, we characterized the IFN-I sensitivity of 500 clonally derived HIV-1 isolates from the plasma and CD4+ T cells of 26 individuals sampled longitudinally after transmission or after antiretroviral therapy (ART) and analytical treatment interruption. We determined the concentration of IFNα2 and IFNβ that reduced viral replication in vitro by 50% (IC50) and found consistent changes in the sensitivity of HIV-1 to IFN-I inhibition both across individuals and over time. Resistance of HIV-1 isolates to IFN-I was uniformly high during acute infection, decreased in all individuals in the first year after infection, was reacquired concomitant with CD4+ T cell loss, and remained elevated in individuals with accelerated disease. HIV-1 isolates obtained by viral outgrowth during suppressive ART were relatively IFN-I sensitive, resembling viruses circulating just before ART initiation. However, viruses that rebounded after treatment interruption displayed the highest degree of IFNα2 and IFNβ resistance observed at any time during the infection course. These findings indicate a dynamic interplay between host innate responses and the evolving HIV-1 quasispecies, with the relative contribution of IFN-I to HIV-1 control affected by both ART and analytical treatment interruption. Although elevated at transmission, host innate pressures are the highest during viral rebound, limiting the viruses that successfully become reactivated from latency to those that are IFN-I resistant.
Collapse
Affiliation(s)
- Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronnie M Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexa N Avitto
- Gene Therapy Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julia C DeVoto
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jesse Connell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Pierre Pellegrino
- Centre for Clinical Research in Infection and Sexual Health, Institute for Global Health, University College London, London WC1E 6JB, UK
| | - Ian Williams
- Centre for Clinical Research in Infection and Sexual Health, Institute for Global Health, University College London, London WC1E 6JB, UK
| | | | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | | | - Felicity Mampe
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Alexandra Monroy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Sonya Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael S Saag
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Luis J Montaner
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Marina Caskey
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Katharine J Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
38
|
Khan H, Sumner RP, Rasaiyaah J, Tan CP, Rodriguez-Plata MT, Van Tulleken C, Fink D, Zuliani-Alvarez L, Thorne L, Stirling D, Milne RSB, Towers GJ. HIV-1 Vpr antagonizes innate immune activation by targeting karyopherin-mediated NF-κB/IRF3 nuclear transport. eLife 2020; 9:e60821. [PMID: 33300875 PMCID: PMC7759385 DOI: 10.7554/elife.60821] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 must replicate in cells that are equipped to defend themselves from infection through intracellular innate immune systems. HIV-1 evades innate immune sensing through encapsidated DNA synthesis and encodes accessory genes that antagonize specific antiviral effectors. Here, we show that both particle associated, and expressed HIV-1 Vpr, antagonize the stimulatory effect of a variety of pathogen associated molecular patterns by inhibiting IRF3 and NF-κB nuclear transport. Phosphorylation of IRF3 at S396, but not S386, was also inhibited. We propose that, rather than promoting HIV-1 nuclear import, Vpr interacts with karyopherins to disturb their import of IRF3 and NF-κB to promote replication in macrophages. Concordantly, we demonstrate Vpr-dependent rescue of HIV-1 replication in human macrophages from inhibition by cGAMP, the product of activated cGAS. We propose a model that unifies Vpr manipulation of nuclear import and inhibition of innate immune activation to promote HIV-1 replication and transmission.
Collapse
Affiliation(s)
- Hataf Khan
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rebecca P Sumner
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Jane Rasaiyaah
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Choon Ping Tan
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Chris Van Tulleken
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Douglas Fink
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Lucy Thorne
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - David Stirling
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Richard SB Milne
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Greg J Towers
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| |
Collapse
|
39
|
Bouvin-Pley M, Leoz M, Roch E, Moreau A, Migraine J, Bellini N, Blake O, Mammano F, Braibant M, Plantier JC, Brand D. Differential utilization of CD4+ by transmitted/founder and chronic envelope glycoproteins in a MSM HIV-1 subtype B transmission cluster. AIDS 2020; 34:2187-200. [PMID: 32932339 DOI: 10.1097/QAD.0000000000002690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE HIV-1 transmission leads to a genetic bottleneck, with one or a few variants of the donor quasispecies establishing an infection in the new host. We aimed to characterize this bottleneck in more detail, by comparing the properties of HIV envelope glycoproteins from acute and chronic infections within the particular context of a male-to-male transmission cluster. DESIGN We compared the genotypic and phenotypic properties of envelope glycoproteins from viral variants derived from five study participants from the same transmission cluster. METHODS We used single-genome amplification to generate a collection of full-length env sequences. We then constructed pseudotyped viruses expressing selected Env variants from the quasispecies infecting each study participant and compared their infectivities and sensitivities to various entry inhibitors. RESULTS The genotypic analyses confirmed the genetic bottleneck expected after HIV transmission, with a limited number of variants identified in four study participants during acute infection. However, the transmitted sequences harbored no evident common signature and belonged to various genetic lineages. The phenotypic analyses revealed no difference in infectivity, susceptibility to the CCR5 antagonist maraviroc, the fusion inhibitor enfurvitide or type-I interferon between viruses from participants with acute and chronic infections. The key property distinguishing transmitted viruses was a higher resistance to soluble CD4, correlated with greater sensitivity to occupation of the CD4 receptor by the anti-CD4 antibodies LM52 and SK3. CONCLUSION These results suggest that envelope glycoproteins from transmitted/founder viruses bind CD4 less efficiently than those of viruses from chronic infections.
Collapse
|
40
|
Bertagnolli LN, Varriale J, Sweet S, Brockhurst J, Simonetti FR, White J, Beg S, Lynn K, Mounzer K, Frank I, Tebas P, Bar KJ, Montaner LJ, Siliciano RF, Siliciano JD. Autologous IgG antibodies block outgrowth of a substantial but variable fraction of viruses in the latent reservoir for HIV-1. Proc Natl Acad Sci U S A 2020; 117:32066-77. [PMID: 33239444 DOI: 10.1073/pnas.2020617117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In untreated HIV-1 infection, rapid viral evolution allows escape from immune responses. Viral replication can be blocked by antiretroviral therapy. However, HIV-1 persists in a latent reservoir in resting CD4+ T cells, and rebound viremia occurs following treatment interruption. The reservoir, which is maintained in part by clonal expansion, can be measured using quantitative viral outgrowth assays (QVOAs) in which latency is reversed with T cell activation to allow viral outgrowth. Recent studies have shown that viruses detected in QVOAs prior to treatment interruption often differ from rebound viruses. We hypothesized that autologous neutralizing antibodies directed at the HIV-1 envelope (Env) protein might block outgrowth of some reservoir viruses. We modified the QVOA to reflect pressure from low concentrations of autologous antibodies and showed that outgrowth of a substantial but variable fraction of reservoir viruses is blocked by autologous contemporaneous immunoglobulin G (IgG). A reduction in outgrowth of >80% was seen in 6 of 15 individuals. This effect was due to direct neutralization. We established a phylogenetic relationship between rebound viruses and viruses growing out in vitro in the presence of autologous antibodies. Some large infected cell clones detected by QVOA carried neutralization-sensitive viruses, providing a cogent explanation for differences between rebound virus and viruses detected in standard QVOAs. Measurement of the frequency of reservoir viruses capable of outgrowth in the presence of autologous IgG might allow more accurate prediction of time to viral rebound. Ultimately, therapeutic immunization targeting the subset of variants resistant to autologous IgG might contribute to a functional cure.
Collapse
|
41
|
Dickinson M, Kliszczak AE, Giannoulatou E, Peppa D, Pellegrino P, Williams I, Drakesmith H, Borrow P. Dynamics of Transforming Growth Factor (TGF)-β Superfamily Cytokine Induction During HIV-1 Infection Are Distinct From Other Innate Cytokines. Front Immunol 2020; 11:596841. [PMID: 33329587 PMCID: PMC7732468 DOI: 10.3389/fimmu.2020.596841] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection triggers rapid induction of multiple innate cytokines including type I interferons, which play important roles in viral control and disease pathogenesis. The transforming growth factor (TGF)-β superfamily is a pleiotropic innate cytokine family, some members of which (activins and bone morphogenetic proteins (BMPs)) were recently demonstrated to exert antiviral activity against Zika and hepatitis B and C viruses but are poorly studied in HIV-1 infection. Here, we show that TGF-β1 is systemically induced with very rapid kinetics (as early as 1-4 days after viremic spread begins) in acute HIV-1 infection, likely due to release from platelets, and remains upregulated throughout infection. Contrastingly, no substantial systemic upregulation of activins A and B or BMP-2 was observed during acute infection, although plasma activin levels trended to be elevated during chronic infection. HIV-1 triggered production of type I interferons but not TGF-β superfamily cytokines from plasmacytoid dendritic cells (DCs) in vitro, putatively explaining their differing in vivo induction; whilst lipopolysaccharide (but not HIV-1) elicited activin A production from myeloid DCs. These findings underscore the need for better definition of the protective and pathogenic capacity of TGF-β superfamily cytokines, to enable appropriate modulation for therapeutic purposes.
Collapse
Affiliation(s)
- Matthew Dickinson
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Anna E Kliszczak
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Eleni Giannoulatou
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Dimitra Peppa
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,Mortimer Market Centre, Department of HIV, CNWL NHS Trust, London, United Kingdom
| | - Pierre Pellegrino
- Centre for Sexual Health and HIV Research, University College London, London, United Kingdom
| | - Ian Williams
- Centre for Sexual Health and HIV Research, University College London, London, United Kingdom
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
42
|
Smith SA, Murray PM, Amancha PK, Ackerley CG, Hu YJ, Amara RR, Kelley CF. Ex vivo rectal explant model reveals potential opposing roles of Natural Killer cells and Marginal Zone-like B cells in HIV-1 infection. Sci Rep 2020; 10:20154. [PMID: 33214610 DOI: 10.1038/s41598-020-76976-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
Our understanding of innate immune responses in human rectal mucosal tissues (RM) and their contributions to promoting or restricting HIV transmission is limited. We defined the RM composition of innate and innate-like cell subsets, including plasmacytoid dendritic cells; CD1c + myeloid DCs; neutrophils; macrophages; natural killer cells (NK); Marginal Zone-like B cells (MZB); γδ T cells; and mucosal-associated invariant T cells in RM from 69 HIV-negative men by flow cytometry. Associations between these cell subsets and HIV-1 replication in ex vivo RM explant challenge experiments revealed an inverse correlation between RM-NK and p24 production, in contrast to a positive association between RM-MZB and HIV replication. Comparison of RM and blood-derived MZB and NK illustrated qualitative and quantitative differences between tissue compartments. Additionally, 22 soluble molecules were measured in a subset of explant cultures (n = 26). Higher production of IL-17A, IFN-γ, IL-10, IP-10, GM-CSF, sFasL, Granzyme A, Granzyme B, Granulysin, and Perforin following infection positively correlated with HIV replication. These data show novel associations between MZB and NK cells and p24 production in RM and underscore the importance of inflammatory cytokines in mucosal HIV infection, demonstrating the likely critical role these innate immune responses play in early mucosal HIV replication in humans.
Collapse
|
43
|
Guo K, Shen G, Kibbie J, Gonzalez T, Dillon SM, Smith HA, Cooper EH, Lavender K, Hasenkrug KJ, Sutter K, Dittmer U, Kroehl M, Kechris K, Wilson CC, Santiago ML. Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis. PLoS Pathog 2020; 16:e1008986. [PMID: 33064743 PMCID: PMC7592919 DOI: 10.1371/journal.ppat.1008986] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 10/28/2020] [Accepted: 09/16/2020] [Indexed: 12/27/2022] Open
Abstract
The Type I Interferons (IFN-Is) are innate antiviral cytokines that include 12 different IFNα subtypes and IFNβ that signal through the IFN-I receptor (IFNAR), inducing hundreds of IFN-stimulated genes (ISGs) that comprise the 'interferome'. Quantitative differences in IFNAR binding correlate with antiviral activity, but whether IFN-Is exhibit qualitative differences remains controversial. Moreover, the IFN-I response is protective during acute HIV-1 infection, but likely pathogenic during the chronic stages. To gain a deeper understanding of the IFN-I response, we compared the interferomes of IFNα subtypes dominantly-expressed in HIV-1-exposed plasmacytoid dendritic cells (1, 2, 5, 8 and 14) and IFNβ in the earliest cellular targets of HIV-1 infection. Primary gut CD4 T cells from 3 donors were treated for 18 hours ex vivo with individual IFN-Is normalized for IFNAR signaling strength. Of 1,969 IFN-regulated genes, 246 'core ISGs' were induced by all IFN-Is tested. However, many IFN-regulated genes were not shared between the IFNα subtypes despite similar induction of canonical antiviral ISGs such as ISG15, RSAD2 and MX1, formally demonstrating qualitative differences between the IFNα subtypes. Notably, IFNβ induced a broader interferome than the individual IFNα subtypes. Since IFNβ, and not IFNα, is upregulated during chronic HIV-1 infection in the gut, we compared core ISGs and IFNβ-specific ISGs from colon pinch biopsies of HIV-1-uninfected (n = 13) versus age- and gender-matched, antiretroviral-therapy naïve persons with HIV-1 (PWH; n = 19). Core ISGs linked to inflammation, T cell activation and immune exhaustion were elevated in PWH, positively correlated with plasma lipopolysaccharide (LPS) levels and gut IFNβ levels, and negatively correlated with gut CD4 T cell frequencies. In sharp contrast, IFNβ-specific ISGs linked to protein translation and anti-inflammatory responses were significantly downregulated in PWH, negatively correlated with gut IFNβ and LPS, and positively correlated with plasma IL6 and gut CD4 T cell frequencies. Our findings reveal qualitative differences in interferome induction by diverse IFN-Is and suggest potential mechanisms for how IFNβ may drive HIV-1 pathogenesis in the gut.
Collapse
Affiliation(s)
- Kejun Guo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Guannan Shen
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Jon Kibbie
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Tania Gonzalez
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Stephanie M. Dillon
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Harry A. Smith
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Emily H. Cooper
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Kerry Lavender
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Canada
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, Hamilton, MT, United States of America
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University of Duisberg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisberg-Essen, Essen, Germany
| | - Miranda Kroehl
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Katerina Kechris
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Cara C. Wilson
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Mario L. Santiago
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| |
Collapse
|
44
|
Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE. Number of HIV-1 founder variants is determined by the recency of the source partner infection. Science 2020; 369:103-108. [PMID: 32631894 DOI: 10.1126/science.aba5443] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/11/2020] [Indexed: 01/10/2023]
Abstract
During sexual transmission, the high genetic diversity of HIV-1 within an individual is frequently reduced to one founder variant that initiates infection. Understanding the drivers of this bottleneck is crucial to developing effective infection control strategies. Little is known about the importance of the source partner during this bottleneck. To test the hypothesis that the source partner affects the number of HIV founder variants, we developed a phylodynamic model calibrated using genetic and epidemiological data on all existing transmission pairs for whom the direction of transmission and the infection stage of the source partner are known. Our results suggest that acquiring infection from someone in the acute (early) stage of infection increases the risk of multiple-founder variant transmission compared with acquiring infection from someone in the chronic (later) stage of infection. This study provides the first direct test of source partner characteristics to explain the low frequency of multiple-founder strain infections.
Collapse
Affiliation(s)
- Ch Julián Villabona-Arenas
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen G Gaffney
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Roland R Regoes
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Stéphane Hué
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Katherine E Atkins
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK. .,Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Centre for Global Health, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
45
|
Zhuang X, Pedroza-Pacheco I, Nawroth I, Kliszczak AE, Magri A, Paes W, Rubio CO, Yang H, Ashcroft M, Mole D, Balfe P, Borrow P, McKeating JA. Hypoxic microenvironment shapes HIV-1 replication and latency. Commun Biol 2020; 3:376. [PMID: 32665623 PMCID: PMC7360605 DOI: 10.1038/s42003-020-1103-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 06/17/2020] [Indexed: 12/14/2022] Open
Abstract
Viral replication is defined by the cellular microenvironment and one key factor is local oxygen tension, where hypoxia inducible factors (HIFs) regulate the cellular response to oxygen. Human immunodeficiency virus (HIV) infected cells within secondary lymphoid tissues exist in a low-oxygen or hypoxic environment in vivo. However, the majority of studies on HIV replication and latency are performed under laboratory conditions where HIFs are inactive. We show a role for HIF-2α in restricting HIV transcription via direct binding to the viral promoter. Hypoxia reduced tumor necrosis factor or histone deacetylase inhibitor, Romidepsin, mediated reactivation of HIV and inhibiting HIF signaling-pathways reversed this phenotype. Our data support a model where the low-oxygen environment of the lymph node may suppress HIV replication and promote latency. We identify a mechanism that may contribute to the limited efficacy of latency reversing agents in reactivating HIV and suggest new strategies to control latent HIV-1.
Collapse
Affiliation(s)
- Xiaodong Zhuang
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | | | - Isabel Nawroth
- Institute of Immunity and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Anna E Kliszczak
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andrea Magri
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | | | - Hongbing Yang
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Margaret Ashcroft
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH, UK
| | - David Mole
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Peter Balfe
- Institute of Immunity and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Jane A McKeating
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| |
Collapse
|
46
|
Ivanov S, Lagunin A, Filimonov D, Tarasova O. Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction. Front Microbiol 2020; 11:1314. [PMID: 32625189 PMCID: PMC7311653 DOI: 10.3389/fmicb.2020.01314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV–host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV–host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV–human protein–protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies represent a basis for developing new anti-HIV therapeutic strategies such as new drugs preventing infection of CD4+ cells and viral replication, effective vaccines, “shock and kill” and “block and lock” approaches to cure latent infection.
Collapse
Affiliation(s)
- Sergey Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| |
Collapse
|
47
|
Thippeshappa R, Kimata JT, Kaushal D. Toward a Macaque Model of HIV-1 Infection: Roadblocks, Progress, and Future Strategies. Front Microbiol 2020; 11:882. [PMID: 32477302 PMCID: PMC7237640 DOI: 10.3389/fmicb.2020.00882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/16/2020] [Indexed: 12/15/2022] Open
Abstract
The human-specific tropism of Human Immunodeficiency Virus Type 1 (HIV-1) has complicated the development of a macaque model of HIV-1 infection/AIDS that is suitable for preclinical evaluation of vaccines and novel treatment strategies. Several innate retroviral restriction factors, such as APOBEC3 family of proteins, TRIM5α, BST2, and SAMHD1, that prevent HIV-1 replication have been identified in macaque cells. Accessory proteins expressed by Simian Immunodeficiency virus (SIV) such as viral infectivity factor (Vif), viral protein X (Vpx), viral protein R (Vpr), and negative factor (Nef) have been shown to play key roles in overcoming these restriction factors in macaque cells. Thus, substituting HIV-1 accessory genes with those from SIV may enable HIV-1 replication in macaques. We and others have constructed macaque-tropic HIV-1 derivatives [also called simian-tropic HIV-1 (stHIV-1) or Human-Simian Immunodeficiency Virus (HSIV)] carrying SIV vif to overcome APOBEC3 family proteins. Additional modifications to HIV-1 gag in some of the macaque-tropic HIV-1 have also been done to overcome TRIM5α restriction in rhesus and cynomolgus macaques. Although these viruses replicate persistently in macaque species, they do not result in CD4 depletion. Thus, these studies suggest that additional blocks to HIV-1 replication exist in macaques that prevent high-level viral replication. Furthermore, serial animal-to-animal passaging of macaque-tropic HIV-1 in vivo has not resulted in pathogenic variants that cause AIDS in immunocompetent macaques. In this review, we discuss recent developments made toward developing macaque model of HIV-1 infection.
Collapse
Affiliation(s)
- Rajesh Thippeshappa
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Jason T Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| |
Collapse
|
48
|
Gobillot TA, Humes D, Sharma A, Kikawa C, Overbaugh J. The Robust Restriction of Zika Virus by Type-I Interferon in A549 Cells Varies by Viral Lineage and Is Not Determined by IFITM3. Viruses 2020; 12:v12050503. [PMID: 32370187 PMCID: PMC7290589 DOI: 10.3390/v12050503] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Type-I interferon (IFN-I) is a major antiviral host response but its impact on Zika virus (ZIKV) replication is not well defined, particularly as it relates to different circulating strains. Interferon stimulated genes (ISGs) that inhibit ZIKV, such as IFITM3, have been identified largely using overexpression studies. Here, we tested whether diverse ZIKV strains differed in their susceptibility to IFN-I-mediated restriction and the contribution of IFITM3 to this restriction. We identified a robust IFN-I-mediated antiviral effect on ZIKV replication (>100-fold reduction) in A549 cells, a commonly used cell line to study ZIKV replication. The extent of inhibition depended on the IFN-I type and the virus strain tested. Viruses from the American pathogenic outbreak were more sensitive to IFNα (p = 0.049) and IFNβ (p = 0.09) than African-lineage strains, which have not been linked to severe pathogenesis. Knocking out IFITM3 expression did not dampen the IFN-I antiviral effect and only high overexpression of IFITM3 led to ZIKV inhibition. Moreover, IFITM3 expression levels in different cells were not associated with IFN-mediated ZIKV inhibition. Taken together, our findings indicate that there is a robust IFN-I-mediated antiviral effect on ZIKV infection, particularly for American viruses, that is not due to IFITM3. A549 cells, which are a commonly used cell line to study ZIKV replication, present an opportunity for the discovery of novel antiviral ISGs against ZIKV.
Collapse
Affiliation(s)
- Theodore A. Gobillot
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (T.A.G.); (D.H.); (A.S.); (C.K.)
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (T.A.G.); (D.H.); (A.S.); (C.K.)
| | - Amit Sharma
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (T.A.G.); (D.H.); (A.S.); (C.K.)
| | - Caroline Kikawa
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (T.A.G.); (D.H.); (A.S.); (C.K.)
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (T.A.G.); (D.H.); (A.S.); (C.K.)
- Correspondence:
| |
Collapse
|
49
|
Adland E, Millar J, Bengu N, Muenchhoff M, Fillis R, Sprenger K, Ntlantsana V, Roider J, Vieira V, Govender K, Adamson J, Nxele N, Ochsenbauer C, Kappes J, Mori L, van Lobenstein J, Graza Y, Chinniah K, Kapongo C, Bhoola R, Krishna M, Matthews PC, Poderos RP, Lluch MC, Puertas MC, Prado JG, McKerrow N, Archary M, Ndung'u T, Groll A, Jooste P, Martinez-Picado J, Altfeld M, Goulder P. Sex-specific innate immune selection of HIV-1 in utero is associated with increased female susceptibility to infection. Nat Commun 2020; 11:1767. [PMID: 32286302 DOI: 10.1038/s41467-020-15632-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Female children and adults typically generate more efficacious immune responses to vaccines and infections than age-matched males, but also suffer greater immunopathology and autoimmune disease. We here describe, in a cohort of > 170 in utero HIV-infected infants from KwaZulu-Natal, South Africa, fetal immune sex differences resulting in a 1.5–2-fold increased female susceptibility to intrauterine HIV infection. Viruses transmitted to females have lower replicative capacity (p = 0.0005) and are more type I interferon-resistant (p = 0.007) than those transmitted to males. Cord blood cells from females of HIV-uninfected sex-discordant twins are more activated (p = 0.01) and more susceptible to HIV infection in vitro (p = 0.03). Sex differences in outcome include superior maintenance of aviraemia among males (p = 0.007) that is not explained by differential antiretroviral therapy adherence. These data demonstrate sex-specific innate immune selection of HIV associated with increased female susceptibility to in utero infection and enhanced functional cure potential among infected males. Sex differences in the immune response to vaccines and infections have been well described in children and adults. Here the authors describe, in a cohort of 177 HIV-infected infants, innate immune sex differences in fetal life that increase female susceptibility to intrauterine HIV infection and increase the chances of subsequent HIV remission in infected males.
Collapse
|
50
|
Prévost J, Edgar CR, Richard J, Trothen SM, Jacob RA, Mumby MJ, Pickering S, Dubé M, Kaufmann DE, Kirchhoff F, Neil SJD, Finzi A, Dikeakos JD. HIV-1 Vpu Downregulates Tim-3 from the Surface of Infected CD4 + T Cells. J Virol 2020; 94:e01999-19. [PMID: 31941771 PMCID: PMC7081912 DOI: 10.1128/jvi.01999-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/12/2020] [Indexed: 01/26/2023] Open
Abstract
Along with other immune checkpoints, T cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) is expressed on exhausted CD4+ and CD8+ T cells and is upregulated on the surface of these cells upon infection by human immunodeficiency virus type 1 (HIV-1). Recent reports have suggested an antiviral role for Tim-3. However, the molecular determinants of HIV-1 which modulate cell surface Tim-3 levels have yet to be determined. Here, we demonstrate that HIV-1 Vpu downregulates Tim-3 from the surface of infected primary CD4+ T cells, thus attenuating HIV-1-induced upregulation of Tim-3. We also provide evidence that the transmembrane domain of Vpu is required for Tim-3 downregulation. Using immunofluorescence microscopy, we determined that Vpu is in close proximity to Tim-3 and alters its subcellular localization by directing it to Rab 5-positive (Rab 5+) vesicles and targeting it for sequestration within the trans- Golgi network (TGN). Intriguingly, Tim-3 knockdown and Tim-3 blockade increased HIV-1 replication in primary CD4+ T cells, thereby suggesting that Tim-3 expression might represent a natural immune mechanism limiting viral spread.IMPORTANCE HIV infection modulates the surface expression of Tim-3, but the molecular determinants remain poorly understood. Here, we show that HIV-1 Vpu downregulates Tim-3 from the surface of infected primary CD4+ T cells through its transmembrane domain and alters its subcellular localization. Tim-3 blockade increases HIV-1 replication, suggesting a potential negative role of this protein in viral spread that is counteracted by Vpu.
Collapse
Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Cassandra R Edgar
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Steven M Trothen
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Rajesh Abraham Jacob
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Mitchell J Mumby
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Suzanne Pickering
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Mathieu Dubé
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Stuart J D Neil
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| |
Collapse
|