1
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Rao S. Sex differences in HIV-1 persistence and the implications for a cure. Front Glob Womens Health 2022; 3:942345. [PMID: 36212905 PMCID: PMC9538461 DOI: 10.3389/fgwh.2022.942345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Of the 38 million people currently living with Human Immunodeficiency Virus type-1 (HIV-1), women, especially adolescents and young women, are disproportionally affected by the HIV-1 pandemic. Acquired immunodeficiency syndrome (AIDS) - related illnesses are the leading cause of death in women of reproductive age worldwide. Although combination antiretroviral therapy (cART) can suppress viral replication, cART is not curative due to the presence of a long-lived viral reservoir that persists despite treatment. Biological sex influences the characteristics of the viral reservoir as well as the immune responses to infection, factors that can have a significant impact on the design and quantification of HIV-1 curative interventions in which women are grossly underrepresented. This mini-review will provide an update on the current understanding of the impact of biological sex on the viral reservoir and will discuss the implications of these differences in the context of the development of potential HIV-1 curative strategies, with a focus on the shock and kill approach to an HIV-1 cure. This mini-review will also highlight the current gaps in the knowledge of sex-based differences in HIV-1 persistence and will speculate on approaches to address them to promote the development of more scalable, effective curative approaches for people living with HIV-1.
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2
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Scheller SH, Rashad Y, Saleh FM, Willingham KA, Reilich A, Lin D, Izadpanah R, Alt EU, Braun SE. Biallelic, Selectable, Knock-in Targeting of CCR5 via CRISPR-Cas9 Mediated Homology Directed Repair Inhibits HIV-1 Replication. Front Immunol 2022; 13:821190. [PMID: 35386712 PMCID: PMC8978527 DOI: 10.3389/fimmu.2022.821190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/22/2022] [Indexed: 01/17/2023] Open
Abstract
Transplanting HIV-1 positive patients with hematopoietic stem cells homozygous for a 32 bp deletion in the chemokine receptor type 5 (CCR5) gene resulted in a loss of detectable HIV-1, suggesting genetically disrupting CCR5 is a promising approach for HIV-1 cure. Targeting the CCR5-locus with CRISPR-Cas9 was shown to decrease the amount of CCR5 expression and HIV-1 susceptibility in vitro as well as in vivo. Still, only the individuals homozygous for the CCR5-Δ32 frameshift mutation confer complete resistance to HIV-1 infection. In this study we introduce a mechanism to target CCR5 and efficiently select for cells with biallelic frameshift insertion, using CRISPR-Cas9 mediated homology directed repair (HDR). We hypothesized that cells harboring two different selectable markers (double positive), each in one allele of the CCR5 locus, would carry a frameshift mutation in both alleles, lack CCR5 expression and resist HIV-1 infection. Inducing double-stranded breaks (DSB) via CRISPR-Cas9 leads to HDR and integration of a donor plasmid. Double-positive cells were selected via fluorescence-activated cell sorting (FACS), and CCR5 was analyzed genetically, phenotypically, and functionally. Targeted and selected populations showed a very high frequency of mutations and a drastic reduction in CCR5 surface expression. Most importantly, double-positive cells displayed potent inhibition to HIV-1 infection. Taken together, we show that targeting cells via CRISPR-Cas9 mediated HDR enables efficient selection of mutant cells that are deficient for CCR5 and highly resistant to HIV-1 infection.
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Affiliation(s)
- Stefan H Scheller
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States.,Department of Cardiology and Angiology, Faculty of Medicine, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Yasmine Rashad
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States
| | - Fayez M Saleh
- Division of Immunology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States.,Department of Medical Microbiology, Faculty of Medicine, University of Tabuk, Tabuk, Saudi Arabia
| | - Kurtis A Willingham
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States
| | - Antonia Reilich
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States
| | - Dong Lin
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States.,Department of Surgery, Tulane University Health Science Center, New Orleans, LA, United States
| | - Reza Izadpanah
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States.,Department of Surgery, Tulane University Health Science Center, New Orleans, LA, United States
| | - Eckhard U Alt
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States.,Isar Klinikum Munich, Munich, Germany
| | - Stephen E Braun
- Applied Stem Cell Laboratory, Medicine/Heart and Vascular Institute, Tulane University Health Sciences Center, New Orleans, LA, United States.,Division of Immunology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States.,Department of Pharmacology, Tulane University Health Science Center, New Orleans, LA, United States
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3
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Dubé K, Kanazawa J, Taylor J, Dee L, Jones N, Roebuck C, Sylla L, Louella M, Kosmyna J, Kelly D, Clanton O, Palm D, Campbell DM, Onaiwu MG, Patel H, Ndukwe S, Henley L, Johnson MO, Saberi P, Brown B, Sauceda JA, Sugarman J. Ethics of HIV cure research: an unfinished agenda. BMC Med Ethics 2021; 22:83. [PMID: 34193141 PMCID: PMC8243312 DOI: 10.1186/s12910-021-00651-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Background The pursuit of a cure for HIV is a high priority for researchers, funding agencies, governments and people living with HIV (PLWH). To date, over 250 biomedical studies worldwide are or have been related to discovering a safe, effective, and scalable HIV cure, most of which are early translational research and experimental medicine. As HIV cure research increases, it is critical to identify and address the ethical challenges posed by this research. Methods We conducted a scoping review of the growing HIV cure research ethics literature, focusing on articles published in English peer-reviewed journals from 2013 to 2021. We extracted and summarized key developments in the ethics of HIV cure research. Twelve community advocates actively engaged in HIV cure research provided input on this summary and suggested areas warranting further ethical inquiry and foresight via email exchange and video conferencing. Discussion Despite substantial scholarship related to the ethics of HIV cure research, additional attention should focus on emerging issues in six categories of ethical issues: (1) social value (ongoing and emerging biomedical research and scalability considerations); (2) scientific validity (study design issues, such as the use of analytical treatment interruptions and placebos); (3) fair selection of participants (equity and justice considerations); (4) favorable benefit/risk balance (early phase research, benefit-risk balance, risk perception, psychological risks, and pediatric research); (5) informed consent (attention to language, decision-making, informed consent processes and scientific uncertainty); and (6) respect for enrolled participants and community (perspectives of people living with HIV and affected communities and representation). Conclusion HIV cure research ethics has an unfinished agenda. Scientific research and bioethics should work in tandem to advance ethical HIV cure research. Because the science of HIV cure research will continue to rapidly advance, ethical considerations of the major themes we identified will need to be revisited and refined over time.
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Affiliation(s)
- Karine Dubé
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, 4108 McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7469, USA.
| | - John Kanazawa
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, 4108 McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7469, USA
| | - Jeff Taylor
- HIV + Aging Research Project - Palm Springs (HARP-PS), Palm Springs, CA, USA.,AntiViral Research Center (AVRC) Community Advisory Board (CAB), San Diego, CA, USA.,Collaboratory of AIDS Researchers for Eradication (CARE) CAB, Chapel Hill, NC, USA
| | - Lynda Dee
- AIDS Action Baltimore, Baltimore, MD, USA.,Delaney AIDS Research Enterprise (DARE) Community Advisory Board (CAB), San Francisco, CA, USA
| | - Nora Jones
- BEAT-HIV Collaboratory CAB, Philadelphia, PA, USA
| | | | | | | | - Jan Kosmyna
- AIDS Clinical Trials Group (ACTG) Community Scientific Subcommittee (CSS) Ethics Working Group, Nationwide, USA
| | - David Kelly
- AIDS Clinical Trials Group (ACTG) Community Scientific Subcommittee (CSS) Ethics Working Group, Nationwide, USA
| | - Orbit Clanton
- AIDS Clinical Trials Group Global CAB, Washington, D.C., USA
| | - David Palm
- Collaboratory of AIDS Researchers for Eradication (CARE) CAB, Chapel Hill, NC, USA.,Institute of Global Health and Infectious Diseases HIV Treatment and Prevention CAB, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Danielle M Campbell
- Delaney AIDS Research Enterprise (DARE) Community Advisory Board (CAB), San Francisco, CA, USA.,Charles R. Drew College of Medicine and Science, Los Angeles, CA, USA
| | - Morénike Giwa Onaiwu
- AIDS Clinical Trials Group (ACTG) Community Scientific Subcommittee (CSS) Ethics Working Group, Nationwide, USA.,Center for the Study of Women, Gender, and Sexuality (School of Humanities), Rice University, Houston, TX, USA
| | - Hursch Patel
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, 4108 McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7469, USA
| | - Samuel Ndukwe
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, 4108 McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7469, USA
| | - Laney Henley
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, 4108 McGavran-Greenberg Hall, Chapel Hill, NC, 27599-7469, USA
| | - Mallory O Johnson
- Center for AIDS Prevention Studies (CAPS), Division of Prevention Sciences, UCSF, San Francisco, CA, USA
| | - Parya Saberi
- Center for AIDS Prevention Studies (CAPS), Division of Prevention Sciences, UCSF, San Francisco, CA, USA
| | - Brandon Brown
- Department of Social Medicine, Population and Public Health, Center for Healthy Communities, University of California, Riverside, Riverside, CA, USA
| | - John A Sauceda
- Center for AIDS Prevention Studies (CAPS), Division of Prevention Sciences, UCSF, San Francisco, CA, USA
| | - Jeremy Sugarman
- Johns Hopkins Berman Institute for Bioethics, Baltimore, MD, USA
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4
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Ivanov S, Filimonov D, Tarasova O. A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression. Comput Struct Biotechnol J 2021; 19:2447-2459. [PMID: 34025935 PMCID: PMC8113781 DOI: 10.1016/j.csbj.2021.04.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 01/06/2023] Open
Abstract
Cytotoxic and noncytotoxic CD8+ T lymphocyte responses are essential for the control of HIV infection. Understanding the mechanisms underlying HIV control in elite controllers (ECs), which maintain undetectable viral load in the absence of antiretroviral therapy, may facilitate the development of new effective therapeutic strategies. We developed an original pipeline for an analysis of the transcriptional profiles of CD8+ cells from ECs, treated and untreated progressors. Hierarchical cluster analysis of CD8+ cells' transcription profiles allowed us to identify five distinct groups (EC groups 1-5) of ECs. The transcriptional profiles of EC group 1 were opposite to those of groups 2-4 and similar to those of the treated progressors, which can be associated with residual activation and dysfunction of CD8+ T-lymphocytes. The profiles of groups 2-4 were associated with different numbers of differentially expressed genes compared to healthy controls, but the corresponding genes shared the same cellular processes. These three groups were associated with increased metabolism, survival, proliferation, and the absence of an "exhausted" phenotype, compared to both untreated progressors and healthy controls. The CD8+ lymphocytes from these groups of ECs may contribute to the control under HIV replication and slower disease progression. The EC group 5 was indistinguishable from normal. Application of master regulator analysis allowed us to identify 22 receptors, including interferon-gamma, interleukin-2, and androgen receptors, which may be responsible for the observed expression changes and the functional states of CD8+ cells from ECs. These receptors can be considered potential targets of therapeutic intervention, which may decelerate disease progression.
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Affiliation(s)
- Sergey Ivanov
- 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
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5
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Tebas P, Jadlowsky JK, Shaw PA, Tian L, Esparza E, Brennan AL, Kim S, Naing SY, Richardson MW, Vogel AN, Maldini CR, Kong H, Liu X, Lacey SF, Bauer AM, Mampe F, Richman LP, Lee G, Ando D, Levine BL, Porter DL, Zhao Y, Siegel DL, Bar KJ, June CH, Riley JL. CCR5-edited CD4+ T cells augment HIV-specific immunity to enable post-rebound control of HIV replication. J Clin Invest 2021; 131:144486. [PMID: 33571163 PMCID: PMC8011906 DOI: 10.1172/jci144486] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
BackgroundWe conducted a phase I clinical trial that infused CCR5 gene-edited CD4+ T cells to determine how these T cells can better enable HIV cure strategies.MethodsThe aim of trial was to develop RNA-based approaches to deliver zinc finger nuclease (ZFN), evaluate the effect of CCR5 gene-edited CD4+ T cells on the HIV-specific T cell response, test the ability of infused CCR5 gene-edited T cells to delay viral rebound during analytical treatment interruption, and determine whether individuals heterozygous for CCR5 Δ32 preferentially benefit. We enrolled 14 individuals living with HIV whose viral load was well controlled by antiretroviral therapy (ART). We measured the time to viral rebound after ART withdrawal, the persistence of CCR5-edited CD4+ T cells, and whether infusion of 10 billion CCR5-edited CD4+ T cells augmented the HIV-specific immune response.ResultsInfusion of the CD4+ T cells was well tolerated, with no serious adverse events. We observed a modest delay in the time to viral rebound relative to historical controls; however, 3 of the 14 individuals, 2 of whom were heterozygous for CCR5 Δ32, showed post-viral rebound control of viremia, before ultimately losing control of viral replication. Interestingly, only these individuals had substantial restoration of HIV-specific CD8+ T cell responses. We observed immune escape for 1 of these reinvigorated responses at viral recrudescence, illustrating a direct link between viral control and enhanced CD8+ T cell responses.ConclusionThese findings demonstrate how CCR5 gene-edited CD4+ T cell infusion could aid HIV cure strategies by augmenting preexisting HIV-specific immune responses.REGISTRATIONClinicalTrials.gov NCT02388594.FundingNIH funding (R01AI104400, UM1AI126620, U19AI149680, T32AI007632) was provided by the National Institute of Allergy and Infectious Diseases (NIAID), the National Institute on Drug Abuse (NIDA), the National Institute of Mental Health (NIMH), and the National Institute of Neurological Disorders and Stroke (NINDS). Sangamo Therapeutics also provided funding for these studies.
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Affiliation(s)
| | | | - Pamela A. Shaw
- Department of Biostatistics, Epidemiology and Informatics, and
| | - Lifeng Tian
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erin Esparza
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrea L. Brennan
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Ashley N. Vogel
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Colby R. Maldini
- Department of Microbiology and Center for Cellular Immunotherapies
| | - Hong Kong
- Department of Microbiology and Center for Cellular Immunotherapies
| | - Xiaojun Liu
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Simon F. Lacey
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Gary Lee
- Sangamo Therapeutics Inc., Richmond, California, USA
| | - Dale Ando
- Sangamo Therapeutics Inc., Richmond, California, USA
| | - Bruce L. Levine
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Yangbing Zhao
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Don L. Siegel
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Carl H. June
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James L. Riley
- Department of Microbiology and Center for Cellular Immunotherapies
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6
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Schwarze LI, Sonntag T, Wild S, Schmitz S, Uhde A, Fehse B. Automated production of CCR5-negative CD4 +-T cells in a GMP-compatible, clinical scale for treatment of HIV-positive patients. Gene Ther 2021; 28:572-587. [PMID: 33867524 PMCID: PMC8455337 DOI: 10.1038/s41434-021-00259-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 02/02/2023]
Abstract
Ex-vivo gene editing in T lymphocytes paves the way for novel concepts of immunotherapy. One of those strategies is directed at the protection of CD4+-T helper cells from HIV infection in HIV-positive individuals. To this end, we have developed and optimised a CCR5-targeting TALE nuclease, CCR5-Uco-hetTALEN, mediating high-efficiency knockout of C-C motif chemokine receptor 5 (CCR5), the HIV co-receptor essential during initial infection. Clinical translation of the knockout approach requires up-scaling of the manufacturing process to clinically relevant cell numbers in accordance with good manufacturing practice (GMP). Here we present a GMP-compatible mRNA electroporation protocol for the automated production of CCR5-edited CD4+-T cells in the closed CliniMACS Prodigy system. The automated process reliably produced high amounts of CCR5-edited CD4+-T cells (>1.5 × 109 cells with >60% CCR5 editing) within 12 days. Of note, about 40% of total large-scale produced cells showed a biallelic CCR5 editing, and between 25 and 42% of produced cells had a central memory T-cell phenotype. In conclusion, transfection of primary T cells with CCR5-Uco-hetTALEN mRNA is readily scalable for GMP-compatible production and hence suitable for application in HIV gene therapy.
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Affiliation(s)
- Lea Isabell Schwarze
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site, Hamburg, Germany
| | - Tanja Sonntag
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Wild
- grid.59409.310000 0004 0552 5033Miltenyi Biotec, Bergisch Gladbach, Germany
| | - Sabrina Schmitz
- grid.59409.310000 0004 0552 5033Miltenyi Biotec, Bergisch Gladbach, Germany
| | - Almut Uhde
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Fehse
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site, Hamburg, Germany
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7
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Cary DC, Peterlin BM. Proteasomal Inhibition Potentiates Latent HIV Reactivation. AIDS Res Hum Retroviruses 2020; 36:800-807. [PMID: 32683901 DOI: 10.1089/aid.2020.0040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Despite the success of antiretroviral therapy (ART), ART fails to eradicate the virus and HIV cure has remained beyond the reach of current treatments. ART targets replicating virally infected but not latently infected cells, which have limited expression of factors important for proliferation and cellular activity, including positive transcription elongation factor b (P-TEFb) and nuclear factor κB (NF-κB). Levels of the cyclin T1 (CycT1) subunit of P-TEFb are low to absent in resting T cells, and treatment with proteasome inhibitors (PIs) increases CycT1 protein levels to those of proliferating T cells. In this study, the clinically approved PI bortezomib reactivated latent HIV in latently infected primary CD4+ T cells. Bortezomib not only increased levels of CycT1 but also activated NF-κB. Strikingly, as opposed to most currently researched latency reversing agents (LRAs), bortezomib did not require a second LRA to potently reactivate latent HIV. Effects of bortezomib on resting T cells and reactivation of HIV suggest a possible direction for future attempts to diminish the viral reservoir in HIV+ individuals.
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Affiliation(s)
- Daniele C. Cary
- Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - B. Matija Peterlin
- Department of Medicine, University of California at San Francisco, San Francisco, California, USA
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8
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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] [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.
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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
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9
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Frank AM, Buchholz CJ. Surface-Engineered Lentiviral Vectors for Selective Gene Transfer into Subtypes of Lymphocytes. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 12:19-31. [PMID: 30417026 PMCID: PMC6216101 DOI: 10.1016/j.omtm.2018.10.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Lymphocytes have always been among the prime targets in gene therapy, even more so since chimeric antigen receptor (CAR) T cells have reached the clinic. However, other gene therapeutic approaches hold great promise as well. The first part of this review provides an overview of current strategies in lymphocyte gene therapy. The second part highlights the importance of precise gene delivery into B and T cells as well as distinct subtypes of lymphocytes. This can be achieved with lentiviral vectors (LVs) pseudotyped with engineered glycoproteins recognizing lymphocyte surface markers as entry receptors. Different strategies for envelope glycoprotein engineering and selection of the targeting ligand are discussed. With a CD8-targeted LV that was recently used to achieve proof of principle for the in vivo reprogramming of CAR T cells, these vectors are becoming a key tool to genetically engineer lymphocytes directly in vivo.
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Affiliation(s)
- Annika M Frank
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Christian J Buchholz
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, 63225 Langen, Germany.,Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
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10
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Peterson TA, MacLean AG. Current and Future Therapeutic Strategies for Lentiviral Eradication from Macrophage Reservoirs. J Neuroimmune Pharmacol 2018; 14:68-93. [PMID: 30317409 DOI: 10.1007/s11481-018-9814-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/02/2018] [Indexed: 12/17/2022]
Abstract
Macrophages, one of the most abundant populations of leukocytes in the body, function as the first line of defense against pathogen invaders. Human Immunodeficiency virus 1 (HIV-1) remains to date one of the most extensively studied viral infections. Naturally occurring lentiviruses in domestic and primate species serve as valuable models to investigate lentiviral pathogenesis and novel therapeutics. Better understanding of the role macrophages play in HIV pathogenesis will aid in the advancement towards a cure. Even with current efficacy of first- and second-line Antiretroviral Therapy (ART) guidelines and future efficacy of Long Acting Slow Effective Release-ART (LASER-ART); ART alone does not lead to a cure. The major challenge of HIV eradication is viral latency. Latency Reversal Agents (LRAs) show promise as a possible means to eradicate HIV-1 from the body. It has become evident that complete eradication will need to include combinations of various effective therapeutic strategies such as LASER-ART, LRAs, and gene editing. Review of the current literature indicates the most promising HIV eradication strategy appears to be LASER-ART in conjunction with viral and receptor gene modifications via the CRISPR/Cas9 system. Graphical abstract A multimodal approach to HIV treatment including gene editing, LASER-ART, and latency reversal agents may provide a means to achieve HIV eradication.
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Affiliation(s)
- Tiffany A Peterson
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - Andrew G MacLean
- Department of Microbiology & Immunology, Division of Comparative Pathology, Tulane National Primate Research Center, Tulane Center for Aging, Tulane Brain Institute, 18703 Three Rivers Road, Covington, LA, 70433, USA.
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11
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Chen L, Keppler OT, Schölz C. Post-translational Modification-Based Regulation of HIV Replication. Front Microbiol 2018; 9:2131. [PMID: 30254620 PMCID: PMC6141784 DOI: 10.3389/fmicb.2018.02131] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) relies heavily on the host cellular machinery for production of viral progeny. To exploit cellular proteins for replication and to overcome host factors with antiviral activity, HIV has evolved a set of regulatory and accessory proteins to shape an optimized environment for its replication and to facilitate evasion from the immune system. Several cellular pathways are hijacked by the virus to modulate critical steps during the viral life cycle. Thereby, post-translational modifications (PTMs) of viral and cellular proteins gain increasingly attention as modifying enzymes regulate virtually every step of the viral replication cycle. This review summarizes the current knowledge of HIV-host interactions influenced by PTMs with a special focus on acetylation, ubiquitination, and phosphorylation of proteins linked to cellular signaling and viral replication. Insights into these interactions are surmised to aid development of new intervention strategies.
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Affiliation(s)
- Lin Chen
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christian Schölz
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
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