1
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Kuzmichev YV, Lackman-Smith C, Bakkour S, Wiegand A, Bale MJ, Musick A, Bernstein W, Aronson N, Ake J, Tovanabutra S, Stone M, Ptak RG, Kearney MF, Busch MP, Wonderlich ER, Kulpa DA. Application of ultrasensitive digital ELISA for p24 enables improved evaluation of HIV-1 reservoir diversity and growth kinetics in viral outgrowth assays. Sci Rep 2023; 13:10958. [PMID: 37414788 PMCID: PMC10326067 DOI: 10.1038/s41598-023-37223-9] [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] [Received: 08/22/2022] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
The advent of combined antiretroviral therapy (cART) has been instrumental in controlling HIV-1 replication and transmission and decreasing associated morbidity and mortality. However, cART alone is not able to cure HIV-1 due to the presence of long-lived, latently infected immune cells, which re-seed plasma viremia when cART is interrupted. Assessment of HIV-cure strategies using ex vivo culture methods for further understanding of the diversity of reactivated HIV, viral outgrowth, and replication dynamics are enhanced using ultrasensitive digital ELISA based on single-molecule array (Simoa) technology to increase the sensitivity of endpoint detection. In viral outgrowth assays (VOA), exponential HIV-1 outgrowth has been shown to be dependent upon initial virus burst size surpassing a critical growth threshold of 5100 HIV-1 RNA copies. Here, we show an association between ultrasensitive HIV-1 Gag p24 concentrations and HIV-1 RNA copy number that characterize viral dynamics below the exponential replication threshold. Single-genome sequencing (SGS) revealed the presence of multiple identical HIV-1 sequences, indicative of low-level replication occurring below the threshold of exponential outgrowth early during a VOA. However, SGS further revealed diverse related HIV variants detectable by ultrasensitive methods that failed to establish exponential outgrowth. Overall, our data suggest that viral outgrowth occurring below the threshold necessary for establishing exponential growth in culture does not preclude replication competence of reactivated HIV, and ultrasensitive detection of HIV-1 p24 may provide a method to detect previously unquantifiable variants. These data strongly support the use of the Simoa platform in a multi-prong approach to measuring latent viral burden and efficacy of therapeutic interventions aimed at an HIV-1 cure.
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Affiliation(s)
- Yury V Kuzmichev
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA.
| | - Carol Lackman-Smith
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ann Wiegand
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew Musick
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Wendy Bernstein
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Naomi Aronson
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Julie Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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2
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Sanders-Beer BE, Archin NM, Brumme ZL, Busch MP, Deleage C, O'Doherty U, Hughes SH, Jerome KR, Jones RB, Karn J, Kearney MF, Keele BF, Kulpa DA, Laird GM, Li JZ, Lichterfeld MD, Nussenzweig MC, Persaud D, Yukl SA, Siliciano RF, Mellors JW. Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary. AIDS Res Hum Retroviruses 2023; 40:7-21. [PMID: 37126090 DOI: 10.1089/aid.2022.0188] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Since the first HIV-cured person was reported in 2009, a strong interest in developing highly sensitive HIV and SIV reservoir assays has emerged. In particular, the question arose about the comparative value of state-of-the-art assays to measure and characterize the HIV reservoir, and how these assays can be applied to accurately detect changes in the reservoir during efforts to develop a cure for HIV infection. Second, it is important to consider the impact on the outcome of clinical trials if these relatively new HIV reservoir assays are incorporated into clinical trial endpoints and/or used for clinical decision-making. To understand the advantages and limitations and the regulatory implications of HIV reservoir assays, the National Institute of Allergy and Infectious Diseases (NIAID) sponsored and convened a meeting on September 16, 2022, to discuss the state of knowledge concerning these questions and best practices for selecting HIV reservoir assays for a particular research question or clinical trial protocol.
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Affiliation(s)
- Brigitte E Sanders-Beer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Vitalant Research Institute, University of California, San Francisco, California, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias D Lichterfeld
- Brigham and Women's Hospital and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Deborah Persaud
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven A Yukl
- Department of Medicine, University of California San Francisco (UCSF) and San Francisco VA Medical Center, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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3
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Mutascio S, Mota T, Franchitti L, Sharma AA, Willemse A, Bergstresser SN, Wang H, Statzu M, Tharp GK, Weiler J, Sékaly RP, Bosinger SE, Paiardini M, Silvestri G, Jones RB, Kulpa DA. CD8 + T cells promote HIV latency by remodeling CD4 + T cell metabolism to enhance their survival, quiescence, and stemness. Immunity 2023; 56:1132-1147.e6. [PMID: 37030290 PMCID: PMC10880039 DOI: 10.1016/j.immuni.2023.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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] [Received: 06/24/2022] [Revised: 11/16/2022] [Accepted: 03/15/2023] [Indexed: 04/10/2023]
Abstract
HIV infection persists during antiretroviral therapy (ART) due to a reservoir of latently infected cells that harbor replication-competent virus and evade immunity. Previous ex vivo studies suggested that CD8+ T cells from people with HIV may suppress HIV expression via non-cytolytic mechanisms, but the mechanisms responsible for this effect remain unclear. Here, we used a primary cell-based in vitro latency model and demonstrated that co-culture of autologous activated CD8+ T cells with HIV-infected memory CD4+ T cells promoted specific changes in metabolic and/or signaling pathways resulting in increased CD4+ T cell survival, quiescence, and stemness. Collectively, these pathways negatively regulated HIV expression and ultimately promoted the establishment of latency. As shown previously, we observed that macrophages, but not B cells, promoted latency in CD4+ T cells. The identification of CD8-specific mechanisms of pro-latency activity may favor the development of approaches to eliminate the viral reservoir in people with HIV.
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Affiliation(s)
- Simona Mutascio
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Talia Mota
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Ashish A Sharma
- Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Abigail Willemse
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | - Hong Wang
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Maura Statzu
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Gregory K Tharp
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jared Weiler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rafick-Pierre Sékaly
- Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Deanna A Kulpa
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
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4
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Druzak S, Iffrig E, Roberts BR, Zhang T, Fibben KS, Sakurai Y, Verkerke HP, Rostad CA, Chahroudi A, Schneider F, Wong AKH, Roberts AM, Chandler JD, Kim SO, Mosunjac M, Mosunjac M, Geller R, Albizua I, Stowell SR, Arthur CM, Anderson EJ, Ivanova AA, Ahn J, Liu X, Maner-Smith K, Bowen T, Paiardini M, Bosinger SE, Roback JD, Kulpa DA, Silvestri G, Lam WA, Ortlund EA, Maier CL. Multiplatform analyses reveal distinct drivers of systemic pathogenesis in adult versus pediatric severe acute COVID-19. Nat Commun 2023; 14:1638. [PMID: 37015925 PMCID: PMC10073144 DOI: 10.1038/s41467-023-37269-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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] [Received: 10/29/2022] [Accepted: 03/08/2023] [Indexed: 04/06/2023] Open
Abstract
The pathogenesis of multi-organ dysfunction associated with severe acute SARS-CoV-2 infection remains poorly understood. Endothelial damage and microvascular thrombosis have been identified as drivers of COVID-19 severity, yet the mechanisms underlying these processes remain elusive. Here we show alterations in fluid shear stress-responsive pathways in critically ill COVID-19 adults as compared to non-COVID critically ill adults using a multiomics approach. Mechanistic in-vitro studies, using microvasculature-on-chip devices, reveal that plasma from critically ill COVID-19 adults induces fibrinogen-dependent red blood cell aggregation that mechanically damages the microvascular glycocalyx. This mechanism appears unique to COVID-19, as plasma from non-COVID sepsis patients demonstrates greater red blood cell membrane stiffness but induces less significant alterations in overall blood rheology. Multiomics analyses in pediatric patients with acute COVID-19 or the post-infectious multi-inflammatory syndrome in children (MIS-C) demonstrate little overlap in plasma cytokine and metabolite changes compared to adult COVID-19 patients. Instead, pediatric acute COVID-19 and MIS-C patients show alterations strongly associated with cytokine upregulation. These findings link high fibrinogen and red blood cell aggregation with endotheliopathy in adult COVID-19 patients and highlight differences in the key mediators of pathogenesis between adult and pediatric populations.
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Grants
- T32 GM142617 NIGMS NIH HHS
- P51 OD011132 NIH HHS
- R35 HL145000 NHLBI NIH HHS
- K99 HL150626 NHLBI NIH HHS
- T32 GM135060 NIGMS NIH HHS
- F31 DK126435 NIDDK NIH HHS
- R01 DK115213 NIDDK NIH HHS
- R38 AI140299 NIAID NIH HHS
- A F31 training fellowship from the National Institutes of Health National Institute of Diabetes and Digestive and Kidney Diseases (NIH/NIDDK), F31DK126435, supported S.A.D during the duration of this work. Stimulating Access to Research in Residency of the National Institutes of Health under Award Number R38AI140299 supported E.I. R35HL145000 supported E.I, Y.S, K.S.F and W.A.L. National Institutes of Health National Heart, Lung, and Blood Institute (NIH/NHLBI) HL150658, awarded to J.D.C. A training grant supported by the Biochemistry and Cell Developmental Biology program (BCDB) at Emory university, T32GM135060-02S1, to S.O.K. NIH/NIDDK Grant R01-DK115213 and Winship Synergy Award to E.A.O. NIH/NHLBI K99 HL150626-01 awarded to C.L.M. The lipidomics and metabolomics experiments were supported by the Emory Integrated Metabolomics and Lipidomics Core, which is subsidized by the Emory University School of Medicine and is one of the Emory Integrated Core Facilities.
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Affiliation(s)
- Samuel Druzak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Elizabeth Iffrig
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Blaine R Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Tiantian Zhang
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Kirby S Fibben
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Yumiko Sakurai
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Frank Schneider
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew Kam Ho Wong
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Anne M Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua D Chandler
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Susan O Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Mario Mosunjac
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Marina Mosunjac
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rachel Geller
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Georgia Bureau of Investigation, Decatur, GA, USA
| | - Igor Albizua
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sean R Stowell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Connie M Arthur
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Evan J Anderson
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Anna A Ivanova
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Jun Ahn
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Xueyun Liu
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Kristal Maner-Smith
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas Bowen
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Mirko Paiardini
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Steve E Bosinger
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Emory Vaccine Center, Atlanta, GA, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Center for AIDS Research, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Emory Vaccine Center, Atlanta, GA, USA
- Center for AIDS Research, Emory University, Atlanta, GA, USA
| | - Wilbur A Lam
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Integrated Metabolomics and Lipidomics Core, Emory University School of Medicine, Atlanta, GA, USA.
| | - Cheryl L Maier
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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5
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Statzu M, Jin W, Fray EJ, Wong AKH, Kumar MR, Ferrer E, Docken SS, Pinkevych M, McBrien JB, Fennessey CM, Keele BF, Liang S, Harper JL, Mutascio S, Franchitti L, Wang H, Cicetti D, Bosinger SE, Carnathan DG, Vanderford TH, Margolis DM, Garcia-Martinez JV, Chahroudi A, Paiardini M, Siliciano J, Davenport MP, Kulpa DA, Siliciano RS, Silvestri G. CD8 + lymphocytes do not impact SIV reservoir establishment under ART. Nat Microbiol 2023; 8:299-308. [PMID: 36690860 PMCID: PMC9894752 DOI: 10.1038/s41564-022-01311-9] [Citation(s) in RCA: 3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/15/2022] [Indexed: 01/24/2023]
Abstract
Persistence of the human immunodeficiency virus type-1 (HIV-1) latent reservoir in infected individuals remains a problem despite fully suppressive antiretroviral therapy (ART). While reservoir formation begins during acute infection, the mechanisms responsible for its establishment remain unclear. CD8+ T cells are important during the initial control of viral replication. Here we examined the effect of CD8+ T cells on formation of the latent reservoir in simian immunodeficiency virus (SIV)-infected macaques by performing experimental CD8+ depletion either before infection or before early (that is, day 14 post-infection) ART initiation. We found that CD8+ depletion resulted in slower decline of viremia, indicating that CD8+ lymphocytes reduce the average lifespan of productively infected cells during acute infection and early ART, presumably through SIV-specific cytotoxic T lymphocyte (CTL) activity. However, CD8+ depletion did not change the frequency of infected CD4+ T cells in the blood or lymph node as measured by the total cell-associated viral DNA or intact provirus DNA assay. In addition, the size of the persistent reservoir remained the same when measuring the kinetics of virus rebound after ART interruption. These data indicate that during early SIV infection, the viral reservoir that persists under ART is established largely independent of CTL control.
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Grants
- P30 AI050409 NIAID NIH HHS
- 75N91019D00024 NCI NIH HHS
- P51 OD011132 NIH HHS
- R01 AI143414 NIAID NIH HHS
- HHSN261201500003C NCI NIH HHS
- HHSN261201500003I NCI NIH HHS
- UM1 AI164562 NIAID NIH HHS
- UM1 AI164567 NIAID NIH HHS
- R01 AI125064 NIAID NIH HHS
- CU | National Cancer Institute, Cairo University (NCI)
- National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024/HHSN261201500003I.
- This work was supported by UM1AI164562, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases (to G.S., D.A.K., M.P.1), and NIH NIAID R01-AI143414 (to G.S. and D.A.K), and R01-AI125064 (to G.S., A.C., D.A.K.).
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Affiliation(s)
- Maura Statzu
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Wang Jin
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Kam Ho Wong
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Ferrer
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steffen S Docken
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Mykola Pinkevych
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Julia B McBrien
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shan Liang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Justin L Harper
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Simona Mutascio
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Hong Wang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Davide Cicetti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Diane G Carnathan
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David M Margolis
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - J Victor Garcia-Martinez
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - Ann Chahroudi
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Janet Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Deanna A Kulpa
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Robert S Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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6
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Reece MD, Song C, Hancock SC, Pereira Ribeiro S, Kulpa DA, Gavegnano C. Repurposing BCL-2 and Jak 1/2 inhibitors: Cure and treatment of HIV-1 and other viral infections. Front Immunol 2022; 13:1033672. [PMID: 36569952 PMCID: PMC9782439 DOI: 10.3389/fimmu.2022.1033672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
B cell lymphoma 2 (BCL-2) family proteins are involved in the mitochondrial apoptotic pathway and are key modulators of cellular lifespan, which is dysregulated during human immunodeficiency virus type 1 (HIV-1) and other viral infections, thereby increasing the lifespan of cells harboring virus, including the latent HIV-1 reservoir. Long-lived cells harboring integrated HIV-1 DNA is a major barrier to eradication. Strategies reducing the lifespan of reservoir cells could significantly impact the field of cure research, while also providing insight into immunomodulatory strategies that can crosstalk to other viral infections. Venetoclax is a first-in-class orally bioavailable BCL-2 homology 3 (BH3) mimetic that recently received Food and Drug Administration (FDA) approval for treatment in myeloid and lymphocytic leukemia. Venetoclax has been recently investigated in HIV-1 and demonstrated anti-HIV-1 effects including a reduction in reservoir size. Another immunomodulatory strategy towards reduction in the lifespan of the reservoir is Jak 1/2 inhibition. The Jak STAT pathway has been implicated in BCL-2 and interleukin 10 (IL-10) expression, leading to a downstream effect of cellular senescence. Ruxolitinib and baricitinib are FDA-approved, orally bioavailable Jak 1/2 inhibitors that have been shown to indirectly decay the HIV-1 latent reservoir, and down-regulate markers of HIV-1 persistence, immune dysregulation and reservoir lifespan in vitro and ex vivo. Ruxolitinib recently demonstrated a significant decrease in BCL-2 expression in a human study of virally suppressed people living with HIV (PWH), and baricitinib recently received emergency use approval for the indication of coronavirus disease 2019 (COVID-19), underscoring their safety and efficacy in the viral infection setting. BCL-2 and Jak 1/2 inhibitors could be repurposed as immunomodulators for not only HIV-1 and COVID-19, but other viruses that upregulate BCL-2 anti-apoptotic proteins. This review examines potential routes for BCL-2 and Jak 1/2 inhibitors as immunomodulators for treatment and cure of HIV-1 and other viral infections.
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Affiliation(s)
- Monica D. Reece
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Colin Song
- Department of Chemistry, College of Arts and Sciences, Emory University, Atlanta, GA, United States
| | - Sarah C. Hancock
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA, United States
| | - Susan Pereira Ribeiro
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Deanna A. Kulpa
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Christina Gavegnano
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, United States,Center for the Study of Human Health, College of Arts and Sciences, Emory University, Atlanta, GA, United States,Department of Pathology and Laboratory Medicine, Atlanta Veterans Affairs Medical Center, Decatur, GA, United States,Center for Bioethics, Harvard Medical School, Boston, MA, United States,*Correspondence: Christina Gavegnano,
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7
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Strongin Z, Hoang TN, Tharp GK, Rahmberg AR, Harper JL, Nguyen K, Franchitti L, Cervasi B, Lee M, Zhang Z, Boritz EA, Silvestri G, Marconi VC, Bosinger SE, Brenchley JM, Kulpa DA, Paiardini M. The role of CD101-expressing CD4 T cells in HIV/SIV pathogenesis and persistence. PLoS Pathog 2022; 18:e1010723. [PMID: 35867722 PMCID: PMC9348691 DOI: 10.1371/journal.ppat.1010723] [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: 03/23/2022] [Revised: 08/03/2022] [Accepted: 07/01/2022] [Indexed: 11/18/2022] Open
Abstract
Despite the advent of effective antiretroviral therapy (ART), human immunodeficiency virus (HIV) continues to pose major challenges, with extensive pathogenesis during acute and chronic infection prior to ART initiation and continued persistence in a reservoir of infected CD4 T cells during long-term ART. CD101 has recently been characterized to play an important role in CD4 Treg potency. Using the simian immunodeficiency virus (SIV) model of HIV infection in rhesus macaques, we characterized the role and kinetics of CD101+ CD4 T cells in longitudinal SIV infection. Phenotypic analyses and single-cell RNAseq profiling revealed that CD101 marked CD4 Tregs with high immunosuppressive potential, distinct from CD101- Tregs, and these cells also were ideal target cells for HIV/SIV infection, with higher expression of CCR5 and α4β7 in the gut mucosa. Notably, during acute SIV infection, CD101+ CD4 T cells were preferentially depleted across all CD4 subsets when compared with their CD101- counterpart, with a pronounced reduction within the Treg compartment, as well as significant depletion in mucosal tissue. Depletion of CD101+ CD4 was associated with increased viral burden in plasma and gut and elevated levels of inflammatory cytokines. While restored during long-term ART, the reconstituted CD101+ CD4 T cells display a phenotypic profile with high expression of inhibitory receptors (including PD-1 and CTLA-4), immunsuppressive cytokine production, and high levels of Ki-67, consistent with potential for homeostatic proliferation. Both the depletion of CD101+ cells and phenotypic profile of these cells found in the SIV model were confirmed in people with HIV on ART. Overall, these data suggest an important role for CD101-expressing CD4 T cells at all stages of HIV/SIV infection and a potential rationale for targeting CD101 to limit HIV pathogenesis and persistence, particularly at mucosal sites.
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Affiliation(s)
- Zachary Strongin
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Timothy N. Hoang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Gregory K. Tharp
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Andrew R. Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH; Bethesda, Maryland, United States of America
| | - Justin L. Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Lavinia Franchitti
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Barbara Cervasi
- Flow Cytometry Core, Emory Vaccine Center, Emory University; Atlanta, Georgia, United States of America
| | - Max Lee
- Vaccine Research Center, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Zhan Zhang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Eli A. Boritz
- Vaccine Research Center, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Vincent C. Marconi
- Division of Infectious Diseases, Emory University School of Medicine; Atlanta, Georgia, United States of America
- Division of Infectious Diseases Research, Atlanta Veterans Affairs Medical Center; Atlanta, Georgia, United States of America
- Rollins School of Public Health, Emory University; Atlanta, Georgia, United States of America
- Emory Vaccine Center, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH; Bethesda, Maryland, United States of America
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
- * E-mail:
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8
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Harper J, Ribeiro SP, Chan CN, Aid M, Deleage C, Micci L, Pino M, Cervasi B, Raghunathan G, Rimmer E, Ayanoglu G, Wu G, Shenvi N, Barnard RJ, Del Prete GQ, Busman-Sahay K, Silvestri G, Kulpa DA, Bosinger SE, Easley KA, Howell BJ, Gorman D, Hazuda DJ, Estes JD, Sekaly RP, Paiardini M. Interleukin-10 contributes to reservoir establishment and persistence in SIV-infected macaques treated with antiretroviral therapy. J Clin Invest 2022; 132:155251. [PMID: 35230978 PMCID: PMC9012284 DOI: 10.1172/jci155251] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 09/22/2021] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Interleukin-10 (IL-10) is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper (Tfh) cell differentiation and germinal center formation. In SIV-infected macaques, levels of IL-10 in plasma and lymph nodes (LNs) were induced by infection and not normalized with antiretroviral therapy (ART). During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including Tfh cells, and predicted the frequency of CD4+ Tfh cells and their cell-associated SIV-DNA content during ART, respectively. In ART-treated rhesus macaques, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B cell follicle in proximity to IL-10. Finally, we demonstrated that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques reduced B cell follicle maintenance and, by extension, LN memory CD4+ T cells, including Tfh cells and those expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.
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Affiliation(s)
- Justin Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Susan P. Ribeiro
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Luca Micci
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Discovery Oncology, Merck & Co., Inc., Boston, Massachusetts, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Barbara Cervasi
- Flow Cytometry Core, Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | | | - Eric Rimmer
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., South San Francisco, California, USA
| | - Gulesi Ayanoglu
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., South San Francisco, California, USA
| | - Guoxin Wu
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Neeta Shenvi
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Richard J.O. Barnard
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kirk A. Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Bonnie J. Howell
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | | | - Daria J. Hazuda
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | | | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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9
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Abstract
During antiretroviral therapy (ART), HIV-1 persists as a latent reservoir in CD4+ T cell subsets in central (TCM), transitional (TTM) and effector memory (TEM) CD4+ T cells. Understanding the mechanisms that support HIV-1 latency in each of these subsets is essential to the identification of cure strategies to eliminate them. Due to the very low frequency of latently infected cells in vivo, model systems that can accurately reflect the heterogenous population of HIV-1 infected cells are a critical component in HIV cure discoveries. Here, we describe a novel primary cell-based model of HIV-1 latency that recapitulates the complex dynamics of the establishment and maintenance of the latent reservoir in different memory T cell subsets. The latency and reversion assay (LARA ) culture conditions uniquely retain phenotypically and transcriptionally distinct memory CD4+ T cell subsets that allow in a single assay to assess LRA activity in each memory subset and differential examination of the dynamics of HIV latency reversal.
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Affiliation(s)
- Sydney Bergstresser
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, and Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, and Yerkes National Primate Research Center, Atlanta, GA, USA.
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10
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Wonderlich ER, Reece MD, Kulpa DA. Ex Vivo Differentiation of Resting CD4+ T Lymphocytes Enhances Detection of Replication Competent HIV-1 in Viral Outgrowth Assays. Methods Mol Biol 2022; 2407:315-331. [PMID: 34985673 DOI: 10.1007/978-1-0716-1871-4_21] [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: 06/14/2023]
Abstract
Quantifying the number of cells harboring inducible and replication competent HIV-1 provirus is critical to evaluating HIV-1 cure interventions, but precise quantification of the latent reservoir has proven to be technically challenging. Existing protocols to quantify the frequency of replication-competent HIV-1 in resting CD4+ T cells from long-term ART treated individuals have helped to investigate the dynamics of reservoir stability, however these approaches have significant barriers to the induction of HIV-1 expression required to effectively evaluate the intact reservoir. Differentiation of CD4+ T cells to an effector memory phenotype is a successful strategy for promoting latency reversal in vitro, and significantly enhances the performance and sensitivity of viral outgrowth assays.
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Affiliation(s)
| | - Monica D Reece
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, and Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, and Yerkes National Primate Research Center, Atlanta, GA, USA.
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11
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Wong AKH, Kulpa DA, Silvestri G, Maier CL. A flow-cytometry-based protocol using diverse cell types for detecting autoantibodies from human plasma and serum samples. STAR Protoc 2021; 2:100924. [PMID: 34761236 PMCID: PMC8567435 DOI: 10.1016/j.xpro.2021.100924] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Here, we describe a protocol for cell-based detection of autoantibodies from human plasma and serum samples using a standard flow cytometer. The protocol allows detection of autoantibodies against a wide array of extracellular antigens. Antigen coverage is limited to the cell types tested, and researchers will need to further determine if autoantibody-positive samples correlate with cytotoxic or clinical outcomes. This protocol is less expensive and faster to perform when compared to protein microarrays and requires no prior knowledge of potential targets. For complete details on the use and execution of this protocol, please refer to Wong et al. (2021). A flow-cytometry-based protocol to detect the presence of autoantibodies Uses input cells to screen plasma or serum samples and identify hits Hits are samples reactive with cellular surface antigens, and may be studied further
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Affiliation(s)
- Andrew Kam Ho Wong
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Guido Silvestri
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cheryl L Maier
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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12
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Kulpa DA, Silvestri G. Introduction to the Special Issue: Immunology of HIV and SIV infection. Semin Immunol 2021; 51:101484. [PMID: 34340888 DOI: 10.1016/j.smim.2021.101484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Deanna A Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States.
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13
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Wong AKH, Woodhouse I, Schneider F, Kulpa DA, Silvestri G, Maier CL. Broad auto-reactive IgM responses are common in critically ill patients, including those with COVID-19. Cell Rep Med 2021; 2:100321. [PMID: 34075365 PMCID: PMC8160082 DOI: 10.1016/j.xcrm.2021.100321] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/09/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022]
Abstract
The pathogenesis of severe coronavirus disease 2019 (COVID-19) remains poorly understood. While several studies suggest that immune dysregulation plays a central role, the key mediators of this process are yet to be defined. Here, we demonstrate that plasma from a high proportion (93%) of critically ill COVID-19 patients, but not healthy controls, contains broadly auto-reactive immunoglobulin M (IgM) and less frequently auto-reactive IgG or IgA. Importantly, these auto-IgMs preferentially recognize primary human lung cells in vitro, including pulmonary endothelial and epithelial cells. By using a combination of flow cytometry, analytical proteome microarray technology, and lactose dehydrogenase (LDH)-release cytotoxicity assays, we identify high-affinity, complement-fixing, auto-reactive IgM directed against 260 candidate autoantigens, including numerous molecules preferentially expressed on the cellular membranes of pulmonary, vascular, gastrointestinal, and renal tissues. These findings suggest that broad IgM-mediated autoimmune reactivity may be involved in the pathogenesis of severe COVID-19, thereby identifying a potential target for therapeutic interventions.
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Affiliation(s)
- Andrew Kam Ho Wong
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Isaac Woodhouse
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frank Schneider
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deanna A. Kulpa
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheryl L. Maier
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Center for Transfusion and Cellular Therapies, Emory University School of Medicine, Atlanta, GA, USA
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14
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Zanoni M, Palesch D, Pinacchio C, Statzu M, Tharp GK, Paiardini M, Chahroudi A, Bosinger SE, Yoon J, Cox B, Silvestri G, Kulpa DA. Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription. PLoS Pathog 2020; 16:e1008821. [PMID: 32941545 PMCID: PMC7523993 DOI: 10.1371/journal.ppat.1008821] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 09/29/2020] [Accepted: 07/18/2020] [Indexed: 12/31/2022] Open
Abstract
MHC-I-restricted, virus-specific cytotoxic CD8+ T cells (CTLs) may control human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication via the recognition and killing of productively infected CD4+ T cells. Several studies in SIV-infected macaques suggest that CD8+ T cells may also decrease virus production by suppressing viral transcription. Here, we show that non-HIV-specific, TCR-activated non-cytolytic CD8+ T cells suppress HIV transcription via a virus- and MHC-independent immunoregulatory mechanism that modulates CD4+ T cell proliferation and activation. We also demonstrate that this CD8+ T cell-mediated effect promotes the survival of infected CD4+ T cells harboring integrated, inducible virus. Finally, we used RNA sequencing and secretome analyses to identify candidate cellular pathways that are involved in the virus-silencing mediated by these CD8+ T cells. This study characterizes a previously undescribed mechanism of immune-mediated HIV silencing that may be involved in the establishment and maintenance of the reservoir under antiretroviral therapy and therefore represent a major obstacle to HIV eradication.
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Affiliation(s)
- Michelle Zanoni
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - David Palesch
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Claudia Pinacchio
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Maura Statzu
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Gregory K. Tharp
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Jack Yoon
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Bryan Cox
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
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15
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McBrien JB, Mavigner M, Franchitti L, Smith SA, White E, Tharp GK, Walum H, Busman-Sahay K, Aguilera-Sandoval CR, Thayer WO, Spagnuolo RA, Kovarova M, Wahl A, Cervasi B, Margolis DM, Vanderford TH, Carnathan DG, Paiardini M, Lifson JD, Lee JH, Safrit JT, Bosinger SE, Estes JD, Derdeyn CA, Garcia JV, Kulpa DA, Chahroudi A, Silvestri G. Author Correction: Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8 + cells. Nature 2020; 578:E21. [PMID: 32015546 DOI: 10.1038/s41586-020-2002-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Julia Bergild McBrien
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lavinia Franchitti
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - S Abigail Smith
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Erick White
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Hasse Walum
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Christian R Aguilera-Sandoval
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William O Thayer
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rae Ann Spagnuolo
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martina Kovarova
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angela Wahl
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Barbara Cervasi
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - David M Margolis
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- University of North Carolina HIV Cure Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas H Vanderford
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Diane G Carnathan
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Steven E Bosinger
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Cynthia A Derdeyn
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Deanna A Kulpa
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory + Children's Center for Childhood Infections and Vaccines, Atlanta, GA, USA
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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16
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McBrien JB, Mavigner M, Franchitti L, Smith SA, White E, Tharp GK, Walum H, Busman-Sahay K, Aguilera-Sandoval CR, Thayer WO, Spagnuolo RA, Kovarova M, Wahl A, Cervasi B, Margolis DM, Vanderford TH, Carnathan DG, Paiardini M, Lifson JD, Lee JH, Safrit JT, Bosinger SE, Estes JD, Derdeyn CA, Garcia JV, Kulpa DA, Chahroudi A, Silvestri G. Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8 + cells. Nature 2020; 578:154-159. [PMID: 31969705 DOI: 10.1038/s41586-020-1946-0] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 12/12/2019] [Indexed: 11/09/2022]
Abstract
Human immunodeficiency virus (HIV) persists indefinitely in individuals with HIV who receive antiretroviral therapy (ART) owing to a reservoir of latently infected cells that contain replication-competent virus1-4. Here, to better understand the mechanisms responsible for latency persistence and reversal, we used the interleukin-15 superagonist N-803 in conjunction with the depletion of CD8+ lymphocytes in ART-treated macaques infected with simian immunodeficiency virus (SIV). Although N-803 alone did not reactivate virus production, its administration after the depletion of CD8+ lymphocytes in conjunction with ART treatment induced robust and persistent reactivation of the virus in vivo. We found viraemia of more than 60 copies per ml in all macaques (n = 14; 100%) and in 41 out of a total of 56 samples (73.2%) that were collected each week after N-803 administration. Notably, concordant results were obtained in ART-treated HIV-infected humanized mice. In addition, we observed that co-culture with CD8+ T cells blocked the in vitro latency-reversing effect of N-803 on primary human CD4+ T cells that were latently infected with HIV. These results advance our understanding of the mechanisms responsible for latency reversal and lentivirus reactivation during ART-suppressed infection.
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Affiliation(s)
- Julia Bergild McBrien
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lavinia Franchitti
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - S Abigail Smith
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Erick White
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Hasse Walum
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Christian R Aguilera-Sandoval
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William O Thayer
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rae Ann Spagnuolo
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martina Kovarova
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angela Wahl
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Barbara Cervasi
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - David M Margolis
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,University of North Carolina HIV Cure Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas H Vanderford
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Diane G Carnathan
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Steven E Bosinger
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA.,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Cynthia A Derdeyn
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Deanna A Kulpa
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.,Emory + Children's Center for Childhood Infections and Vaccines, Atlanta, GA, USA
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA. .,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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17
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Wonderlich ER, Subramanian K, Cox B, Wiegand A, Lackman-Smith C, Bale MJ, Stone M, Hoh R, Kearney MF, Maldarelli F, Deeks SG, Busch MP, Ptak RG, Kulpa DA. Effector memory differentiation increases detection of replication-competent HIV-l in resting CD4+ T cells from virally suppressed individuals. PLoS Pathog 2019; 15:e1008074. [PMID: 31609991 PMCID: PMC6812841 DOI: 10.1371/journal.ppat.1008074] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/24/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022] Open
Abstract
Studies have demonstrated that intensive ART alone is not capable of eradicating HIV-1, as the virus rebounds within a few weeks upon treatment interruption. Viral rebound may be induced from several cellular subsets; however, the majority of proviral DNA has been found in antigen experienced resting CD4+ T cells. To achieve a cure for HIV-1, eradication strategies depend upon both understanding mechanisms that drive HIV-1 persistence as well as sensitive assays to measure the frequency of infected cells after therapeutic interventions. Assays such as the quantitative viral outgrowth assay (QVOA) measure HIV-1 persistence during ART by ex vivo activation of resting CD4+ T cells to induce latency reversal; however, recent studies have shown that only a fraction of replication-competent viruses are inducible by primary mitogen stimulation. Previous studies have shown a correlation between the acquisition of effector memory phenotype and HIV-1 latency reversal in quiescent CD4+ T cell subsets that harbor the reservoir. Here, we apply our mechanistic understanding that differentiation into effector memory CD4+ T cells more effectively promotes HIV-1 latency reversal to significantly improve proviral measurements in the QVOA, termed differentiation QVOA (dQVOA), which reveals a significantly higher frequency of the inducible HIV-1 replication-competent reservoir in resting CD4+ T cells.
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Affiliation(s)
| | | | - Bryan Cox
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Ann Wiegand
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | | | - Michael J Bale
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | - Mars Stone
- Vitalant Research Institute, San Francisco, California, United States of America.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Rebecca Hoh
- University of California, San Francisco (UCSF), San Francisco, California, United States of America
| | - Mary F Kearney
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | - Frank Maldarelli
- HIV DRP, NCI at Frederick, NIH, Frederick, Maryland, United States of America
| | - Steven G Deeks
- University of California, San Francisco (UCSF), San Francisco, California, United States of America
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, California, United States of America.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Roger G Ptak
- Southern Research, Frederick, Maryland, United States of America
| | - Deanna A Kulpa
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
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18
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Rosenbloom DIS, Bacchetti P, Stone M, Deng X, Bosch RJ, Richman DD, Siliciano JD, Mellors JW, Deeks SG, Ptak RG, Hoh R, Keating SM, Dimapasoc M, Massanella M, Lai J, Sobolewski MD, Kulpa DA, Busch MP. Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size. PLoS Comput Biol 2019; 15:e1006849. [PMID: 30978183 PMCID: PMC6481870 DOI: 10.1371/journal.pcbi.1006849] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 04/24/2019] [Accepted: 02/06/2019] [Indexed: 12/27/2022] Open
Abstract
Quantitative viral outgrowth assays (QVOA) use limiting dilutions of CD4+ T cells to measure the size of the latent HIV-1 reservoir, a major obstacle to curing HIV-1. Efforts to reduce the reservoir require assays that can reliably quantify its size in blood and tissues. Although QVOA is regarded as a "gold standard" for reservoir measurement, little is known about its accuracy and precision or about how cell storage conditions or laboratory-specific practices affect results. Owing to this lack of knowledge, confidence intervals around reservoir size estimates-as well as judgments of the ability of therapeutic interventions to alter the size of the replication-competent but transcriptionally inactive latent reservoir-rely on theoretical statistical assumptions about dilution assays. To address this gap, we have carried out a Bayesian statistical analysis of QVOA reliability on 75 split samples of peripheral blood mononuclear cells (PBMC) from 5 antiretroviral therapy (ART)-suppressed participants, measured using four different QVOAs at separate labs, estimating assay precision and the effect of frozen cell storage on estimated reservoir size. We found that typical assay results are expected to differ from the true value by a factor of 1.6 to 1.9 up or down. Systematic assay differences comprised a 24-fold range between the assays with highest and lowest scales, likely reflecting differences in viral outgrowth readout and input cell stimulation protocols. We also found that controlled-rate freezing and storage of samples did not cause substantial differences in QVOA compared to use of fresh cells (95% probability of < 2-fold change), supporting continued use of frozen storage to allow transport and batched analysis of samples. Finally, we simulated an early-phase clinical trial to demonstrate that batched analysis of pre- and post-therapy samples may increase power to detect a three-fold reservoir reduction by 15 to 24 percentage points.
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Affiliation(s)
- Daniel I S Rosenbloom
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Douglas D Richman
- University of California San Diego, La Jolla, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Roger G Ptak
- Southern Research, Frederick, Maryland, United States of America
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Sheila M Keating
- Blood Systems Research Institute, San Francisco, California, United States of America
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Melanie Dimapasoc
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Marta Massanella
- University of California San Diego, La Jolla, California, United States of America
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Michele D Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Deanna A Kulpa
- Southern Research, Frederick, Maryland, United States of America
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Michael P Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
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19
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Gavegnano C, Brehm JH, Dupuy FP, Talla A, Ribeiro SP, Kulpa DA, Cameron C, Santos S, Hurwitz SJ, Marconi VC, Routy JP, Sabbagh L, Schinazi RF, Sékaly RP. Novel mechanisms to inhibit HIV reservoir seeding using Jak inhibitors. PLoS Pathog 2017; 13:e1006740. [PMID: 29267399 PMCID: PMC5739511 DOI: 10.1371/journal.ppat.1006740] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/09/2017] [Indexed: 11/18/2022] Open
Abstract
Despite advances in the treatment of HIV infection with ART, elucidating strategies to overcome HIV persistence, including blockade of viral reservoir establishment, maintenance, and expansion, remains a challenge. T cell homeostasis is a major driver of HIV persistence. Cytokines involved in regulating homeostasis of memory T cells, the major hub of the HIV reservoir, trigger the Jak-STAT pathway. We evaluated the ability of tofacitinib and ruxolitinib, two FDA-approved Jak inhibitors, to block seeding and maintenance of the HIV reservoir in vitro. We provide direct demonstration for involvement of the Jak-STAT pathway in HIV persistence in vivo, ex vivo, and in vitro; pSTAT5 strongly correlates with increased levels of integrated viral DNA in vivo, and in vitro Jak inhibitors reduce the frequency of CD4+ T cells harboring integrated HIV DNA. We show that Jak inhibitors block viral production from infected cells, inhibit γ-C receptor cytokine (IL-15)-induced viral reactivation from latent stores thereby preventing transmission of infectious particles to bystander activated T cells. These results show that dysregulation of the Jak-STAT pathway is associated with viral persistence in vivo, and that Jak inhibitors target key events downstream of γ-C cytokine (IL-2, IL-7 and IL-15) ligation to their receptors, impacting the magnitude of the HIV reservoir in all memory CD4 T cell subsets in vitro and ex vivo. Jak inhibitors represent a therapeutic modality to prevent key events of T cell activation that regulate HIV persistence and together, specific, potent blockade of these events may be integrated to future curative strategies.
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Affiliation(s)
- Christina Gavegnano
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Jessica H. Brehm
- Case Western Reserve University, Dept. of Pathology, Cleveland, OH, United States of America
| | | | - Aarthi Talla
- Case Western Reserve University, Dept. of Pathology, Cleveland, OH, United States of America
| | - Susan Pereira Ribeiro
- Case Western Reserve University, Dept. of Pathology, Cleveland, OH, United States of America
| | - Deanna A. Kulpa
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Cheryl Cameron
- Case Western Reserve University, Dept. of Pathology, Cleveland, OH, United States of America
| | | | - Selwyn J. Hurwitz
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Vincent C. Marconi
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Jean-Pierre Routy
- Chronic Viral Illnesses Service Research Institute, Division of Hematology, McGill University Health Centre, Montréal, QC, Canada
| | - Laurent Sabbagh
- Université de Montréal, Department of Microbiology, Infectiology, and Immunology, Montreal, QC, Canada
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University, Atlanta, GA, United States of America
- * E-mail: (RFS); (RPS)
| | - Rafick Pierre Sékaly
- Case Western Reserve University, Dept. of Pathology, Cleveland, OH, United States of America
- * E-mail: (RFS); (RPS)
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20
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Procopio FA, Fromentin R, Kulpa DA, Brehm JH, Bebin AG, Strain MC, Richman DD, O'Doherty U, Palmer S, Hecht FM, Hoh R, Barnard RJO, Miller MD, Hazuda DJ, Deeks SG, Sékaly RP, Chomont N. A Novel Assay to Measure the Magnitude of the Inducible Viral Reservoir in HIV-infected Individuals. EBioMedicine 2015; 2:874-83. [PMID: 26425694 PMCID: PMC4563128 DOI: 10.1016/j.ebiom.2015.06.019] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [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: 06/16/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Quantifying latently infected cells is critical to evaluate the efficacy of therapeutic strategies aimed at reducing the size of the long-lived viral reservoir, but the low frequency of these cells makes this very challenging. Methods We developed TILDA (Tat/rev Induced Limiting Dilution Assay) to measure the frequency of cells with inducible multiply-spliced HIV RNA, as these transcripts are usually absent in latently infected cells but induced upon viral reactivation. TILDA requires less than a million cells, does not require RNA extraction and can be completed in two days. Findings In suppressed individuals on ART, we found the median frequency of latently infected CD4 + T cells as estimated by TILDA to be 24 cells/million, which was 48 times more than the frequency measured by the quantitative viral outgrowth assay, and 6–27 times less than the frequencies of cells harbouring viral DNA measured by PCR-based assays. TILDA measurements strongly correlated with most HIV DNA assays. The size of the latent reservoir measured by TILDA was lower in subjects who initiated ART during the early compared to late stage of infection (p = 0.011). In untreated HIV disease, the frequency of CD4 + cells carrying latent but inducible HIV largely exceeded the frequency of actively producing cells, demonstrating that the majority of infected cells are transcriptionally silent even in the absence of ART. Interpretations Our results suggest that TILDA is a reproducible and sensitive approach to measure the frequency of productively and latently infected cells in clinical settings. We demonstrate that the latent reservoir represents a substantial fraction of all infected cells prior to ART initiation. Research in context In this manuscript, we describe the development of a novel assay that measures the magnitude of the latent HIV reservoir, the main barrier to HIV eradication. This novel assay, termed TILDA for Tat/rev Induced Limiting Dilution Assay, requires only 10 ml of blood, does not necessitate extraction of viral nucleic acids, is highly reproducible, covers a wide dynamic range of reservoir sizes and can be completed in two days. As such, TILDA may represent an alternative to existing assays used to evaluate the efficacy of therapeutic strategies aimed at reducing the size of the latent HIV reservoir. We developed TILDA (Tat/rev Induced Limiting Dilution Assay) to measure the frequency of cells with inducible multiply-spliced HIV RNA in HIV-infected individuals on suppressive ART. Our results suggest that TILDA is a reproducible and sensitive approach to measure the frequency of productively and latently infected cells in clinical settings. Using TILDA, We demonstrate that the latent reservoir represents a substantial fraction of all infected cells prior to ART initiation.
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Affiliation(s)
| | - Rémi Fromentin
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | - Deanna A Kulpa
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | - Jessica H Brehm
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | | | - Matthew C Strain
- University of California San Diego, La Jolla, California and Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Douglas D Richman
- University of California San Diego, La Jolla, California and Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Palmer
- Centre for Virus Research, Westmead Millennium Institute, Westmead, Australia ; Sydney Medical School, University of Sydney, Sydney, Australia
| | - Frederick M Hecht
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Michael D Miller
- Infectious Disease, Merck Research Laboratories, West Point, PA, USA
| | - Daria J Hazuda
- Infectious Disease, Merck Research Laboratories, West Point, PA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Nicolas Chomont
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
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21
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22
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Kulpa DA, Chomont N. HIV persistence in the setting of antiretroviral therapy: when, where and how does HIV hide? J Virus Erad 2015; 1:59-66. [PMID: 26448966 PMCID: PMC4593515] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Advances in the treatment of HIV infection have dramatically reduced the death rate from AIDS and improved the quality of life of many HIV-infected individuals. However, the possible long-term toxicity associated with antiretroviral therapy (ART), stigma and cost, all contribute to the necessity of finding a cure for HIV infection. In infected individuals taking ART, HIV persists in a small number of cells that can survive for the lifetime of the infected person. These persistently infected cells, usually referred as the 'reservoirs for HIV infection', are the main barriers to a cure. The diversity of the tissues and cellular types in which HIV persists, as well as the multiplicity of the molecular mechanisms contributing to HIV persistence, complicate the efforts to develop a safe, effective, and globally accessible cure for HIV. In this review, we summarise recent data that contribute to our understanding of HIV persistence during ART by addressing three questions pertaining to the HIV reservoir: (1) when is the reservoir established; (2) where is the reservoir maintained; and (3) how does the reservoir persist?
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Affiliation(s)
- Deanna A Kulpa
- Vaccine and Gene Therapy Institute Florida,
Port St Lucie,
Florida,
USA
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology,
Université de Montréal, Faculty of Medicine, and ,Centre de Recherche du CHUM,
Montréal,
Quebec,
Canada,Corresponding author: Nicolas Chomont,
Université de Montréal,
Centre de recherche du CHUM,
900 rue St-Denis, Tour Viger, R09 430,
Montréal,
QC,
H2X 0A,
Canada
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23
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Abstract
A major challenge in the development of a cure for human immunodeficiency virus (HIV) has been the incomplete understanding of the basic mechanisms underlying HIV persistence during antiretroviral therapy. It is now realized that the establishment of a latently infected reservoir refractory to immune system recognition has thus far hindered eradication efforts. Recent investigation into the innate immune response has shed light on signaling pathways downstream of the immunological synapse critical for T-cell activation and establishment of T-cell memory. This has led to the understanding that the cell-to-cell contacts observed in an immunological synapse that involve the CD4+ T cell and antigen-presenting cell or T-cell–T-cell interactions enhance efficient viral spread and facilitate the induction and maintenance of latency in HIV-infected memory T cells. This review focuses on recent work characterizing the immunological synapse and the signaling pathways involved in T-cell activation and gene regulation in the context of HIV persistence.
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Affiliation(s)
- Deanna A Kulpa
- Division of Infectious Diseases, Vaccine and Gene Therapy Institute-Florida (VGTI-FL), Port Saint Lucie, FL 34987, USA
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Kulpa DA, Lawani M, Cooper A, Peretz Y, Ahlers J, Sékaly RP. PD-1 coinhibitory signals: the link between pathogenesis and protection. Semin Immunol 2013; 25:219-27. [PMID: 23548749 DOI: 10.1016/j.smim.2013.02.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 02/15/2013] [Indexed: 12/31/2022]
Abstract
In the majority of HIV-1 infected individuals, the adaptive immune response drives virus escape resulting in persistent viremia and a lack of immune-mediated control. The expression of negative regulatory molecules such as PD-1 during chronic HIV infection provides a useful marker to differentiate functional memory T cell subsets and the frequency of T cells with an exhausted phenotype. In addition, cell-based measurements of virus persistence equate with activation markers and the frequency of CD4 T cells expressing PD-1. High-level expression of PD-1 and its ligands PD-L1 and PD-L2 are found on hematopoietic and non-hematopoietic cells, and are upregulated by chronic antigen stimulation, Type 1 and Type II interferons (IFNs), and homeostatic cytokines. In HIV infected subjects, PD-1 levels on CD4 and CD8 T cells continue to remain high following combination anti-retroviral therapy (cART). System biology approaches have begun to elucidate signal transduction pathways regulated by PD-1 expression in CD4 and CD8 T cell subsets that become dysfunctional through chronic TCR activation and PD-1 signaling. In this review, we summarize our current understanding of transcriptional signatures and signal transduction pathways associated with immune exhaustion with a focus on recent work in our laboratory characterizing the role of PD-1 in T cell dysfunction and HIV pathogenesis. We also highlight the therapeutic potential of blocking PD-1-PD-L1 and other immune checkpoints for activating potent cellular immune responses against chronic viral infections and cancer.
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Affiliation(s)
- Deanna A Kulpa
- Division of Infectious Diseases, Vaccine and Gene Therapy Institute-Florida (VGTI-FL), Port Saint Lucie, FL, United States
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25
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Abstract
Recently, genome-wide association studies have identified the major histocompatibility complex class I protein HLA-C as an important molecule that affects HIV disease progression. The association between HLA-C and HIV disease outcome was originally determined through a single nucleotide polymorphism (SNP) 35 kb upstream of the HLA-C locus. More recent work has focused on elucidating the functional significance of the -35 SNP, and several groups now have demonstrated HLA-C surface expression to be a key element in control of HIV viral load, with higher surface expression associating with slower disease progression. Most recently, control of HLA-C surface expression has been correlated with the presence of microRNA binding sites that affect HLA-C expression and control of HIV disease. This review highlights these results and explores the ways in which HLA-C surface expression could affect immune system function in the setting of HIV disease.
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Affiliation(s)
- Deanna A Kulpa
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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Schaefer MR, Williams M, Kulpa DA, Blakely PK, Yaffee AQ, Collins KL. A novel trafficking signal within the HLA-C cytoplasmic tail allows regulated expression upon differentiation of macrophages. J Immunol 2008; 180:7804-17. [PMID: 18523244 DOI: 10.4049/jimmunol.180.12.7804] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
MHC class I molecules (MHC-I) present peptides to CTLs. In addition, HLA-C allotypes are recognized by killer cell Ig-like receptors (KIR) found on NK cells and effector CTLs. Compared with other classical MHC-I allotypes, HLA-C has low cell surface expression and an altered intracellular trafficking pattern. We present evidence that this results from effects of both the extracellular domain and the cytoplasmic tail. Notably, we demonstrate that the cytoplasmic tail contains a dihydrophobic (LI) internalization and lysosomal targeting signal that is partially attenuated by an aspartic acid residue (DXSLI). In addition, we provide evidence that this signal is specifically inhibited by hypophosphorylation of the adjacent serine residue upon macrophage differentiation and that this allows high HLA-C expression in this cell type. We propose that tightly regulated HLA-C surface expression facilitates immune surveillance and allows HLA-C to serve a specialized role in macrophages.
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Affiliation(s)
- Malinda R Schaefer
- Graduate Program Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Kulpa DA, Moran JV. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 2006; 13:655-60. [PMID: 16783376 DOI: 10.1038/nsmb1107] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 05/11/2006] [Indexed: 11/09/2022]
Abstract
LINE-1 retrotransposons (L1s) constitute approximately 17% of human DNA, and their activity continues to affect genome evolution. Retrotransposition-competent human L1s encode two proteins required for their mobility (ORF1p and ORF2p); however, biochemical activities associated with ORF2p have been difficult to detect in cells. Here, we show for the first time the colocalization of L1 RNA, ORF1p and ORF2p to a putative ribonucleoprotein retrotransposition intermediate. We further demonstrate that ORF2p preferentially uses its encoding RNA as a template for reverse transcription. Thus, our data provide the first biochemical evidence supporting the cis-preferential action of the L1 reverse transcriptase.
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Affiliation(s)
- Deanna A Kulpa
- Department of Human Genetics 1241 E. Catherine St., University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA.
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28
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Abstract
Long interspersed elements (LINE-1s or L1s) are abundant non-LTR retrotransposons that mobilize through an RNA intermediate by target site primed reverse transcription. The L1-encoded proteins (ORF1p and ORF2p) preferentially associate with their encoding transcript to form a ribonucleoprotein particle (RNP), which is a proposed retrotransposition intermediate. Here, we have used epitope tagging to discriminate the proteins encoded by engineered L1s from those encoded by endogenously expressed L1s. We demonstrate that an L1 containing an epitope tag at the carboxyl terminus of ORF1p remains retrotransposition-competent and that tagged ORF1p and its encoding RNA localize to cytoplasmic RNPs. We also identified two classes of ORF1p mutants, one that severely decreased RNP formation and blocked retrotransposition, and another that allows RNP formation but reduces retrotransposition by 100-fold. Thus, these data indicate that RNP formation is important but not sufficient for L1 retrotransposition and suggest that ORF1p also may function at downstream steps in the L1 retrotransposition pathway.
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Affiliation(s)
- Deanna A Kulpa
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-0618, USA
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Rossbach S, Kulpa DA, Rossbach U, de Bruijn FJ. Molecular and genetic characterization of the rhizopine catabolism (mocABRC) genes of Rhizobium meliloti L5-30. Mol Gen Genet 1994; 245:11-24. [PMID: 7845353 DOI: 10.1007/bf00279746] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Rhizopine (L-3-O-methyl-scyllo-inosamine, 3-O-MSI) is a symbiosis-specific compound, which is synthesized in nitrogen-fixing nodules of Medicago sativa induced by Rhizobium meliloti strain L5-30. 3-O-MSI is thought to function as an unusual growth substrate for R. meliloti L5-30, which carries a locus (mos) responsible for its synthesis closely linked to a locus (moc) responsible for its degradation. Here, the essential moc genes were delimited by Tn5 mutagenesis and shown to be organized into two regions, separated by 3 kb of DNA. The DNA sequence of a 9-kb fragment spanning the two moc regions was determined, and four genes were identified that play an essential role in rhizopine catabolism (mocABC and mocR). The analysis of the DNA sequence and the amino acid sequence of the deduced protein products revealed that MocA resembles NADH-dependent dehydrogenases. MocB exhibits characteristic features of periplasmic-binding proteins that are components of high-affinity transport systems. MocC does not share significant homology with any protein in the database. MocR shows homology with the GntR class of bacterial regulator proteins. These results suggest that the mocABC genes are involved in the uptake and subsequent degradation of rhizopine, whereas mocR is likely to play a regulatory role.
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Affiliation(s)
- S Rossbach
- NSF Center for Microbial Ecology, Michigan State University, East Lansing 48824
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Roa BB, Garcia CA, Suter U, Kulpa DA, Wise CA, Mueller J, Welcher AA, Snipes GJ, Shooter EM, Patel PI, Lupski JR. Charcot-Marie-Tooth disease type 1A. Association with a spontaneous point mutation in the PMP22 gene. N Engl J Med 1993; 329:96-101. [PMID: 8510709 DOI: 10.1056/nejm199307083290205] [Citation(s) in RCA: 223] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. CMT type 1A is associated with a 1.5-megabase DNA duplication in region p11.2-p12 of chromosome 17 in most patients. An increased dosage of a gene within the duplicated segment appears to cause the disease. The PMP22 gene, which encodes a myelin protein, has been mapped within the duplication and proposed as a candidate gene for CMT type 1A. METHODS We analyzed DNA samples from a cohort of 32 unrelated patients with CMT type 1 who did not have the 1.5-Mb tandem duplication in 17p11.2-p12 for mutations within the PMP22 coding region. Molecular techniques included the polymerase chain reaction (PCR), heteroduplex analysis to detect point mutations, and direct nucleotide-sequence determination of amplified PCR products. RESULTS A 10-year-old boy was identified with a point mutation in PMP22, which resulted in the substitution of cysteine for serine in a putative transmembrane domain of PMP22. Analysis of family members revealed that the PMP22 point mutation arose spontaneously and segregated with the CMT type 1 phenotype in an autosomal dominant pattern. The patients with the PMP22 point mutation had clinical and electrophysiologic phenotypes that were similar to those of patients with the 1.5-Mb duplication. CONCLUSIONS The PMP22 gene has a causative role in CMT type 1. Either a point mutation in PMP22 or a duplication of the region including the PMP22 gene can result in the disease phenotype.
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Affiliation(s)
- B B Roa
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, TX 77030-3498
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