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Zani A, Messali S, Uggeri M, Bonfanti C, Caruso A, Caccuri F. Detection of HIV-1 matrix protein p17 in sera of viremic and aviremic patients. J Virol Methods 2024; 324:114858. [PMID: 38029970 DOI: 10.1016/j.jviromet.2023.114858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 12/01/2023]
Abstract
People living with human immunodeficiency virus type 1 (HIV-1), even if successfully treated with a combined antiretroviral therapy, display a persistent inflammation and chronic immune activation, and an increasing risk of developing cardiovascular and thrombotic events, cancers, and neurologic disorders. Accumulating evidence reveals that biologically active HIV-1 proteins may play a role in the development of these HIV-1-associated conditions. The HIV-1 matrix protein p17 (p17) is released and accumulates in different organs and tissue where it may exert multiple biological activities on different target cells. To assess a role of p17 in different HIV-1-related pathological processes, it is central to definitively ascertain and quantitate its expression in a large number of sera obtained from HIV-1-infected (HIV-1+) patients. To this aim, we developed a specific and highly sensitive p17 capture immunoenzymatic assay. Data obtained highlight a heterogeneous expression of p17 in blood of tested patients, with patients who were negative or displayed from low to relatively high p17 blood concentrations (range from 0.05 to 7.29 nM). Moreover, we found that blood p17 concentration was totally independent from the viremic status of the patient. This finding calls for monitoring HIV-1+ patients in order to evaluate a possible correlation between p17 amount in blood and the likelihood of developing HIV-1-related pathological conditions.
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Affiliation(s)
- Alberto Zani
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Piazzale Spedali Civili, 1, 25123 Brescia, Italy
| | - Serena Messali
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Piazzale Spedali Civili, 1, 25123 Brescia, Italy
| | - Matteo Uggeri
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Piazzale Spedali Civili, 1, 25123 Brescia, Italy
| | - Carlo Bonfanti
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Piazzale Spedali Civili, 1, 25123 Brescia, Italy
| | - Arnaldo Caruso
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Piazzale Spedali Civili, 1, 25123 Brescia, Italy
| | - Francesca Caccuri
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Piazzale Spedali Civili, 1, 25123 Brescia, Italy.
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2
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Haddaji A, Ouladlahsen A, Lkhider M, Bensghir R, Jebbar S, Hilmi S, Abbadi I, Sodqi M, Marih L, Pineau P, El Filali KM, Ezzikouri S. Impact of the first-line antiretroviral therapy on soluble markers of inflammation in cohort of human immunodeficiency virus type 1 in Moroccan patients: a prospective study. Arch Microbiol 2023; 205:223. [PMID: 37154966 DOI: 10.1007/s00203-023-03574-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/04/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
Chronic inflammation and immune activation are a hallmark of HIV-1 infection. In this study, we assessed inflammation biomarkers in a cohort of people living with HIV-1 (PLWH) before and after long-term suppressive combined antiretroviral therapy (cART). A single-center prospective cohort study was conducted to assess inflammatory biomarkers in 86 cART-naive PLWH and after receiving suppressive cART and 50 uninfected controls. Tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and soluble CD14 (sCD14) were measured using enzyme-linked immunosorbent assay (ELISA). No significant difference was found in IL-6 levels between cART-naïve PLWH and controls (p = 0.753). In contrast, TNF-α level showed a significant difference between cART naïve-PLWH and controls (p = 0.019). Interestingly, IL-6 and TNF-α levels were significantly decreased in PLWH after cART (p < 0.0001). The sCD14 showed no significant difference between cART-naïve patients and controls (p = 0.839) and similar levels were observed in pre- and post-treatment (p = 0.719). Our results highlight the critical importance of early treatment to reduce inflammation and its consequences during HIV infection.
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Affiliation(s)
- Asmaa Haddaji
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco
- Laboratory of Virology, Oncology, Biosciences, Environment and New Energies, Faculty of Sciences and Techniques of Mohammedia, Hassan II University of Casablanca, Mohammedia, Morocco
| | - Ahd Ouladlahsen
- Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco
- Service Des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Mustapha Lkhider
- Laboratory of Virology, Oncology, Biosciences, Environment and New Energies, Faculty of Sciences and Techniques of Mohammedia, Hassan II University of Casablanca, Mohammedia, Morocco
| | - Rajaa Bensghir
- Service Des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Sanaa Jebbar
- Service Des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Soufiane Hilmi
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Islam Abbadi
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco
- Laboratory of Virology, Oncology, Biosciences, Environment and New Energies, Faculty of Sciences and Techniques of Mohammedia, Hassan II University of Casablanca, Mohammedia, Morocco
| | - Mustapha Sodqi
- Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco
- Service Des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Latifa Marih
- Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco
- Service Des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Pascal Pineau
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, Paris, France
| | - Kamal Marhoum El Filali
- Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco
- Service Des Maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco.
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3
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Znaidia M, de Souza-Angelo Y, Létoffé S, Staropoli I, Grzelak L, Ghigo JM, Schwartz O, Casartelli N. Exposure to Secreted Bacterial Factors Promotes HIV-1 Replication in CD4 + T Cells. Microbiol Spectr 2023; 11:e0431322. [PMID: 36853052 PMCID: PMC10100953 DOI: 10.1128/spectrum.04313-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
Microbial translocation is associated with systemic immune activation in HIV-1 disease. Circulating T cells can encounter microbial products in the bloodstream and lymph nodes, where viral replication takes place. The mechanisms by which bacteria contribute to HIV-associated pathogenesis are not completely deciphered. Here, we examined how bacteria may impact T cell function and viral replication. We established cocultures between a panel of live bacteria and uninfected or HIV-1-infected activated peripheral blood CD4-positive (CD4+) T cells. We show that some bacteria, such as Escherichia coli and Acinetobacter baumannii, sustain lymphocyte activation and enhance HIV-1 replication. Bacteria secrete soluble factors that upregulate CD25 and ICAM-1 cell surface levels and activate NF-κB nuclear translocation. Our data also demonstrate that CD25 polarizes at the virological synapse, suggesting a previously unappreciated role of CD25 during viral replication. These findings highlight how interactions between bacterial factors and T cells may promote T cell activation and HIV-1 replication. IMPORTANCE People living with HIV suffer from chronic immune activation despite effective antiretroviral therapy. Early after infection, HIV-1 actively replicates in the gut, causing the breakage of the intestinal epithelial barrier and microbial translocation. Microbial translocation and chronic immune activation have been proven linked; however, gaps in our knowledge on how bacteria contribute to the development of HIV-related diseases remain. Whether T cells in the peripheral blood react to bacterial products and how this affects viral replication are unknown. We show that some bacteria enriched in people living with HIV activate T cells and favor HIV-1's spread. Bacteria release soluble factors that cause the overexpression of cellular molecules related to their activation state. T cells overexpressing these molecules also replicate HIV-1 more efficiently. These results help us learn more about how HIV-1, T cells, and bacteria interact with each other, as well as the mechanisms behind chronic immune activation.
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Affiliation(s)
- M. Znaidia
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - Y. de Souza-Angelo
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - S. Létoffé
- Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - I. Staropoli
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - L. Grzelak
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - J. M. Ghigo
- Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - O. Schwartz
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
- Vaccine Research Institute, Créteil, France
| | - N. Casartelli
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
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Diakite M, Shaw-Saliba K, Lau CY. Malignancy and viral infections in Sub-Saharan Africa: A review. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2023; 3:1103737. [PMID: 37476029 PMCID: PMC10358275 DOI: 10.3389/fviro.2023.1103737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The burden of malignancy related to viral infection is increasing in Sub-Saharan Africa (SSA). In 2018, approximately 2 million new cancer cases worldwide were attributable to infection. Prevention or treatment of these infections could reduce cancer cases by 23% in less developed regions and about 7% in developed regions. Contemporaneous increases in longevity and changes in lifestyle have contributed to the cancer burden in SSA. African hospitals are reporting more cases of cancer related to infection (e.g., cervical cancer in women and stomach and liver cancer in men). SSA populations also have elevated underlying prevalence of viral infections compared to other regions. Of 10 infectious agents identified as carcinogenic by the International Agency for Research on Cancer, six are viruses: hepatitis B and C viruses (HBV and HCV, respectively), Epstein-Barr virus (EBV), high-risk types of human papillomavirus (HPV), Human T-cell lymphotropic virus type 1 (HTLV-1), and Kaposi's sarcoma herpesvirus (KSHV, also known as human herpesvirus type 8, HHV-8). Human immunodeficiency virus type 1 (HIV) also facilitates oncogenesis. EBV is associated with lymphomas and nasopharyngeal carcinoma; HBV and HCV are associated with hepatocellular carcinoma; KSHV causes Kaposi's sarcoma; HTLV-1 causes T-cell leukemia and lymphoma; HPV causes carcinoma of the oropharynx and anogenital squamous cell cancer. HIV-1, for which SSA has the greatest global burden, has been linked to increasing risk of malignancy through immunologic dysregulation and clonal hematopoiesis. Public health approaches to prevent infection, such as vaccination, safer injection techniques, screening of blood products, antimicrobial treatments and safer sexual practices could reduce the burden of cancer in Africa. In SSA, inequalities in access to cancer screening and treatment are exacerbated by the perception of cancer as taboo. National level cancer registries, new screening strategies for detection of viral infection and public health messaging should be prioritized in SSA's battle against malignancy. In this review, we discuss the impact of carcinogenic viruses in SSA with a focus on regional epidemiology.
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Affiliation(s)
- Mahamadou Diakite
- University Clinical Research Center, University of Sciences, Techniques, and Technologies, Bamako, Mali
| | - Kathryn Shaw-Saliba
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Chuen-Yen Lau
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
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5
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Qi H, Qin L, Li Y, Jin F, Kang Z, Hou J, Wang Y. A 16-color full spectrum flow cytometric analysis for comprehensive evaluation of T-cell reconstitution in SIV-infected rhesus macaques. J Immunol Methods 2023; 514:113404. [PMID: 36496008 DOI: 10.1016/j.jim.2022.113404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
T-cell reconstitution is central in human immunodeficiency virus (HIV) infection/disease progression. Simian immunodeficiency virus (SIV)-infected rhesus macaques (Macaca mulatta) have been the most widely used animal model for HIV research so far. An effective flow cytometry panel is crucial for monitoring the T cell reconstitution in SIV infection progression. We developed this sixteen-color flow cytometry-based panel for a T cell subsets analysis by manual gating and, once successfully gated, to characterize T cells function in-depth in rhesus macaques. This panel included markers to characterize CD4+ T cells and CD8+ T cells, T regulatory cells (Tregs), and T cell differentiation status (CD45RA and CCR7). Additionally, we included antibodies that measure T cell activation and proliferation molecules (CD69, HLA-DR, CD38 and Ki67), antibodies that examine the expressions of key PD-1 pathway molecule (PD-1), SIV potential target (CD32) and the primary SIV co-receptor CCR5 (CD195). High-dimensional single cell analysis was also performed to identify CD3+ T cells immunophenotypes of SIV-infected rhesus macaques. We designed this panel to evaluate the responses of different T cell subsets to SIV in whole blood from SIV-infected rhesus macaques.
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Affiliation(s)
- Hemei Qi
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Li Qin
- CAS Lamvac (Guangzhou) Biomedical Technology CO.,Ltd., Guangzhou 510663, China
| | - Yuefeng Li
- Landao Biotech Co., Ltd, Guangzhou 510555, China
| | - Fujun Jin
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhongkui Kang
- CAS Lamvac (Guangzhou) Biomedical Technology CO.,Ltd., Guangzhou 510663, China
| | - Jianghou Hou
- Kunming City Matermal and Child Health Hospital, Kunming 650013, China.
| | - Yifei Wang
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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6
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Cocaine Self-Administration Influences Central Nervous System Immune Responses in Male HIV-1 Transgenic Rats. Cells 2022; 11:cells11152405. [PMID: 35954251 PMCID: PMC9368446 DOI: 10.3390/cells11152405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/25/2022] [Accepted: 07/30/2022] [Indexed: 01/19/2023] Open
Abstract
Cocaine use increases the neurotoxic severity of human immunodeficiency virus-1 (HIV-1) infection and the development of HIV-associated neurocognitive disorders (HAND). Among the studied cellular mechanisms promoting neurotoxicity in HIV-1 and cocaine use, central nervous system (CNS) immunity, such as neuroimmune signaling and reduced antiviral activity, are risk determinants; however, concrete evidence remains elusive. In the present study, we tested the hypothesis that cocaine self-administration by transgenic HIV-1 (HIV-1Tg) rats promotes CNS inflammation. To test this hypothesis, we measured cytokine, chemokine, and growth factor protein levels in the frontal cortex (fCTX) and caudal striatum (cSTR). Our results demonstrated that cocaine self-administration significantly increased fCTX inflammation in HIV-1Tg rats, but not in the cSTR. Accordingly, we postulate that cocaine synergizes with HIV-1 proteins to increase neuroinflammation in a region-selective manner, including the fCTX. Given the fCTX role in cognition, this interaction may contribute to the hyperimmunity and reduced antiviral activity associated with cocaine-mediated enhancement of HAND.
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7
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HIV-Related Immune Activation and Inflammation: Current Understanding and Strategies. J Immunol Res 2021; 2021:7316456. [PMID: 34631899 PMCID: PMC8494587 DOI: 10.1155/2021/7316456] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 02/07/2023] Open
Abstract
Although antiretroviral therapy effectively controls human immunodeficiency virus (HIV) replication, a residual chronic immune activation/inflammation persists throughout the disease. This aberrant immune activation and inflammation are considered an accelerator of non-AIDS-related events and one of the driving forces of CD4+ T cell depletion. Unfortunately, HIV-associated immune activation is driven by various factors, while the mechanism of excessive inflammation has not been formally clarified. To date, several clinical interventions or treatment candidates undergoing clinical trials have been proposed to combat this systemic immune activation/inflammation. However, these strategies revealed limited results, or their nonspecific anti-inflammatory properties are similar to previous interventions. Here, we reviewed recent learnings of immune activation and persisting inflammation associated with HIV infection, as well as the current directions to overcome it. Of note, a more profound understanding of the specific mechanisms for aberrant inflammation is still imperative for identifying an effective clinical intervention strategy.
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8
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Venanzi Rullo E, Pinzone MR, Cannon L, Weissman S, Ceccarelli M, Zurakowski R, Nunnari G, O'Doherty U. Persistence of an intact HIV reservoir in phenotypically naive T cells. JCI Insight 2020; 5:133157. [PMID: 33055422 PMCID: PMC7605525 DOI: 10.1172/jci.insight.133157] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/10/2020] [Indexed: 12/25/2022] Open
Abstract
Despite the efficacy of antiretroviral therapy (ART), HIV persists in a latent form and remains a hurdle to eradication. CD4+ T lymphocytes harbor the majority of the HIV reservoir, but the role of individual subsets remains unclear. CD4+ T cells were sorted into central, transitional, effector memory, and naive T cells. We measured HIV DNA and performed proviral sequencing of more than 1900 proviruses in 2 subjects at 2 and 9 years after ART initiation to estimate the contribution of each subset to the reservoir. Although our study was limited to 2 subjects, we obtained comparable findings with publicly available sequences. While the HIV integration levels were lower in naive compared with memory T cells, naive cells were a major contributor to the intact proviral reservoir. Notably, proviral sequences isolated from naive cells appeared to be unique, while those retrieved from effector memory cells were mainly clonal. The number of clones increased as cells differentiated from a naive to an effector memory phenotype, suggesting naive cells repopulate the effector memory reservoir as previously shown for central memory cells. Naive T cells contribute substantially to the intact HIV reservoir and represent a significant hurdle for HIV eradication.
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Affiliation(s)
- Emmanuele Venanzi Rullo
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, Messina, Italy
| | - Marilia Rita Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - LaMont Cannon
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Virginia, USA
| | - Sam Weissman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Manuela Ceccarelli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, Messina, Italy
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, USA
| | - Giuseppe Nunnari
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, Messina, Italy
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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9
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Zerbato JM, McMahon DK, Sobolewski MD, Mellors JW, Sluis-Cremer N. Naive CD4+ T Cells Harbor a Large Inducible Reservoir of Latent, Replication-competent Human Immunodeficiency Virus Type 1. Clin Infect Dis 2020; 69:1919-1925. [PMID: 30753360 DOI: 10.1093/cid/ciz108] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/31/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The latent human immunodeficiency virus type 1 (HIV-1) reservoir represents a major barrier to a cure. Based on the levels of HIV-1 DNA in naive (TN) vs resting memory CD4+ T cells, it is widely hypothesized that this reservoir resides primarily within memory cells. Here, we compared virus production from TN and central memory (TCM) CD4+ T cells isolated from HIV-1-infected individuals on suppressive therapy. METHODS CD4+ TN and TCM cells were purified from the blood of 7 HIV-1-infected individuals. We quantified total HIV-1 DNA in the CD4+ TN and TCM cells. Extracellular virion-associated HIV-1 RNA or viral outgrowth assays were used to assess latency reversal following treatment with anti-CD3/CD28 monoclonal antibodies (mAbs), phytohaemagglutinin/interleukin-2, phorbol 12-myristate 13-acetate/ionomycin, prostratin, panobinostat, or romidepsin. RESULTS HIV-1 DNA was significantly higher in TCM compared to TN cells (2179 vs 684 copies/106 cells, respectively). Following exposure to anti-CD3/CD28 mAbs, virion-associated HIV-1 RNA levels were similar between TCM and TN cells (15 135 vs 18 290 copies/mL, respectively). In 4/7 donors, virus production was higher for TN cells independent of the latency reversing agent used. Replication-competent virus was recovered from both TN and TCM cells. CONCLUSIONS Although the frequency of HIV-1 infection is lower in TN compared to TCM cells, as much virus is produced from the TN population after latency reversal. This finding suggests that quantifying HIV-1 DNA alone may not predict the size of the inducible latent reservoir and that TN cells may be an important reservoir of latent HIV-1.
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Affiliation(s)
- Jennifer M Zerbato
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pennsylvania
| | - Deborah K McMahon
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pennsylvania
| | - Michelle D Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pennsylvania
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pennsylvania
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pennsylvania
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10
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Agan BK, Ganesan A, Byrne M, Deiss R, Schofield C, Maves RC, Okulicz J, Chu X, O'Bryan T, Lalani T, Kronmann K, Ferguson T, Robb ML, Whitman TJ, Burgess TH, Michael N, Tramont E. The US Military HIV Natural History Study: Informing Military HIV Care and Policy for Over 30 Years. Mil Med 2020; 184:6-17. [PMID: 31778201 DOI: 10.1093/milmed/usy430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION In October 1985, 4 years after the initial descriptions of the acquired immunodeficiency syndrome (AIDS), the U.S. Department of Defense (DoD) began routine screening for human immunodeficiency virus (HIV) infection to prevent infected recruits from exposure to live virus vaccines, implemented routine active-duty force screening to ensure timely care and help protect the walking blood bank, and initiated the U.S. Military HIV Natural History Study (NHS) to develop epidemiologic, clinical, and basic science evidence to inform military HIV policy and establish a repository of data and specimens for future research. Here, we have reviewed accomplishments of the NHS over the past 30 years and sought to describe relevant trends among NHS subjects over this time, with emphasis on combination antiretroviral therapy (cART) use and non-AIDS comorbidities. METHODS Subjects who were prospectively enrolled in the NHS from 1986 through 2015 were included in this analysis. Time periods were classified by decade of study conduct, 1986-1995, 1996-2005, and 2006-2015, which also correlate approximately with pre-, early-, and late-combination ART (cART) eras. Analyses included descriptive statistics and comparisons among decades. We also evaluated mean community log10 HIV viral load (CVL) and CD4 counts for each year. RESULTS A total of 5,758 subjects were enrolled between 1986 and 2015, of whom 92% were male with a median age of 28 years, and 45% were African-American, 42% Caucasian, and 13% Hispanic/other. The proportion of African-Americans remained stable over the decades (45%, 47%, and 42%, respectively), while the proportion of Hispanic/other increased (10%, 13%, and 24%, respectively). The CD4 count at HIV diagnosis has remained high (median 496 cells/uL), while the occurrence of AIDS-defining conditions (excluding low CD4 count) has decreased by decade (36.7%, 5.4%, and 2.9%, respectively). Following the introduction of effective cART in 1996, CVL declined through 2000 as use increased and then plateaued until guidelines changed. After 2004, cART use again increased and CVL declined further until 2012-15 when the vast majority of subjects achieved viral suppression. Non-AIDS comorbidities have remained common, with approximately half of subjects experiencing one or more new diagnoses overall and nearly half of subjects diagnosed between 2006 and 2015, in spite of their relatively young age, shorter median follow-up, and wide use of cART. CONCLUSIONS The US Military HIV NHS has been critical to understanding the impact of HIV infection among active-duty service members and military beneficiaries, as well as producing insights that are broadly relevant. In addition, the rich repository of NHS data and specimens serves as a resource to investigators in the DoD, NIH, and academic community, markedly increasing scientific yield and identifying novel associations. Looking forward, the NHS remains relevant to understanding host factor correlates of virologic and immunologic control, biologic pathways of HIV pathogenesis, causes and consequences of residual inflammation in spite of effective cART, identifying predictors of and potential approaches to mitigation of excess non-AIDS comorbidities, and helping to understand the latent reservoir.
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Affiliation(s)
- Brian K Agan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817.,Division of Infectious Diseases, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20852
| | - Morgan Byrne
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817
| | - Robert Deiss
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817.,Division of Infectious Diseases, Naval Medical Center San Diego, 34800 Bob Wilson Drive, San Diego, CA 92134
| | - Christina Schofield
- Division of Infectious Diseases, Madigan Army Medical Center, 9040A Jackson Avenue, Joint Base Lewis McChord, WA 98431
| | - Ryan C Maves
- Division of Infectious Diseases, Naval Medical Center San Diego, 34800 Bob Wilson Drive, San Diego, CA 92134
| | - Jason Okulicz
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Infectious Disease Service, San Antonio Military Medical Center, 3551 Roger Brooke Drive, Fort Sam Houston, TX 78234
| | - Xiuping Chu
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817
| | - Thomas O'Bryan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817.,Infectious Disease Service, San Antonio Military Medical Center, 3551 Roger Brooke Drive, Fort Sam Houston, TX 78234
| | - Tahaniyat Lalani
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817.,Division of Infectious Diseases, Naval Medical Center Portsmouth, 620 John Paul Jones Circle, Portsmouth, VA 23708
| | - Karl Kronmann
- Division of Infectious Diseases, Naval Medical Center Portsmouth, 620 John Paul Jones Circle, Portsmouth, VA 23708
| | - Tomas Ferguson
- Division of Infectious Diseases, Madigan Army Medical Center, 9040A Jackson Avenue, Joint Base Lewis McChord, WA 98431
| | - Merlin L Robb
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910
| | - Timothy J Whitman
- Division of Infectious Diseases, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20852
| | - Timothy H Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814
| | - Nelson Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910
| | - Edmund Tramont
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, Bethesda, MD 20892
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11
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Eller MA, Hong T, Creegan M, Nau ME, Sanders-Buell E, Slike BM, Krebs SJ, Ratto-Kim S, McElrath MJ, Katabira ET, Bolton DL, Michael NL, Robb ML, Tovanabutra S, Baeten JM, Sandberg JK. Activated PD-1+ CD4+ T cells represent a short-lived part of the viral reservoir and predict poor immunologic recovery upon initiation of ART. AIDS 2020; 34:197-202. [PMID: 31764072 DOI: 10.1097/qad.0000000000002432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Activated (CD38HLA-DR) PD-1 CD4 T cells are strongly associated with virus replication and disease progression in untreated HIV-1 infection, and viral persistence in individuals on ART. Few studies have examined cell-associated viral load (CAVL) in different activated CD4 T-cell populations to measure relative contributions to viral reservoirs. DESIGN Longitudinal assessment of HIV-1 chronically infected Ugandans initiating ART, to investigate activated CD4 T-cell populations and their contribution to viral reservoirs. METHODS We followed 32 HIV-1 chronically infected individuals from Kampala, Uganda, and determined their CD4 T-cell counts and viral load at baseline, 6, and 12 months after the initiation of ART. T-cell populations were sorted based on activation profiles and gag DNA was measured to determine CAVL within these populations. Soluble factors associated with inflammation were measured in plasma using a multiplexed platform. RESULTS Concomitant with viral load decline and CD4 T-cell count rebound, the activated PD-1 CD4 T-cell population contracted upon initiation of ART. Baseline levels of activated PD-1 CD4 T cells correlated with plasma levels of IP-10 and TNFRII. Interestingly, a higher baseline level of activated PD-1 CD4 T cells was associated with poorer CD4 T-cell recovery after 12 months of ART. This population contributed significantly to the cell-associated HIV DNA load at baseline, whereas their contribution declined on ART, indicating high turnover. CONCLUSION Activated PD-1 CD4 T cells are predictors of poor immunologic recovery on ART and may represent a short-lived component of HIV-1 reservoirs.
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Affiliation(s)
- Michael A Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Ting Hong
- Departments of Global Health, Medicine, and Epidemiology, University of Washington, Seattle, Washington
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Martin E Nau
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Bonnie M Slike
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Silvia Ratto-Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Elly T Katabira
- Faculty of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Diane L Bolton
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Jared M Baeten
- Departments of Global Health, Medicine, and Epidemiology, University of Washington, Seattle, Washington
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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12
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Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP. GateFinder: projection-based gating strategy optimization for flow and mass cytometry. Bioinformatics 2019; 34:4131-4133. [PMID: 29850785 DOI: 10.1093/bioinformatics/bty430] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/22/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging. Results Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology. Availability and implementation The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nima Aghaeepour
- Baxter Laboratory in Stem Cell Biology.,Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | - Erin F Simonds
- Department of Neurology, University of California, San Francisco, CA, USA
| | - David J H F Knapp
- Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | | | | | - Anthony Culos
- Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | | | | | | | - Sean C Bendall
- Baxter Laboratory in Stem Cell Biology.,Department of Pathology
| | - Brice Gaudilliere
- Baxter Laboratory in Stem Cell Biology.,Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | - Martin S Angst
- Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Wendy J Fantl
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
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13
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Chattopadhyay PK, Winters AF, Lomas WE, Laino AS, Woods DM. High-Parameter Single-Cell Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:411-430. [PMID: 30699035 DOI: 10.1146/annurev-anchem-061417-125927] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Thousands of transcripts and proteins confer function and discriminate cell types in the body. Using high-parameter technologies, we can now measure many of these markers at once, and multiple platforms are now capable of analysis on a cell-by-cell basis. Three high-parameter single-cell technologies have particular potential for discovering new biomarkers, revealing disease mechanisms, and increasing our fundamental understanding of cell biology. We review these three platforms (high-parameter flow cytometry, mass cytometry, and a new class of technologies called integrated molecular cytometry platforms) in this article. We describe the underlying hardware and instrumentation, the reagents involved, and the limitations and advantages of each platform. We also highlight the emerging field of high-parameter single-cell data analysis, providing an accessible overview of the data analysis process and choice of tools.
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Affiliation(s)
- Pratip K Chattopadhyay
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Aidan F Winters
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Woodrow E Lomas
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Andressa S Laino
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - David M Woods
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
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14
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Delgado-Vélez M, Lasalde-Dominicci JA. The Cholinergic Anti-Inflammatory Response and the Role of Macrophages in HIV-Induced Inflammation. Int J Mol Sci 2018; 19:ijms19051473. [PMID: 29772664 PMCID: PMC5983673 DOI: 10.3390/ijms19051473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/11/2018] [Accepted: 04/29/2018] [Indexed: 12/20/2022] Open
Abstract
Macrophages are phagocytic immune cells that protect the body from foreign invaders and actively support the immune response by releasing anti- and proinflammatory cytokines. A seminal finding revolutionized the way macrophages are seen. The expression of the neuronal alpha7 nicotinic acetylcholine receptor (α7-nAChR) in macrophages led to the establishment of the cholinergic anti-inflammatory response (CAR) in which the activation of this receptor inactivates macrophage production of proinflammatory cytokines. This novel neuroimmune response soon began to emerge as a potential target to counteract inflammation during illness and infection states. Human immunodeficiency virus (HIV)-infected individuals suffer from chronic inflammation that persists even under antiretroviral therapy. Despite the CAR’s importance, few studies involving macrophages have been performed in the HIV field. Evidence demonstrates that monocyte-derived macrophages (MDMs) recovered from HIV-infected individuals are upregulated for α7-nAChR. Moreover, in vitro studies demonstrate that addition of an HIV viral constituent, gp120IIIB, to uninfected MDMs also upregulates the α7-nAChR. Importantly, contrary to what was expected, activation of upregulated α7-nAChRs in macrophages does not reduce inflammation, suggesting a CAR disruption. Although it is reasonable to consider this receptor as a pharmacological target, additional studies are necessary since its activity seems to differ from that observed in neurons.
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Affiliation(s)
- Manuel Delgado-Vélez
- Molecular Sciences Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico.
| | - José A Lasalde-Dominicci
- Molecular Sciences Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico.
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan 00931, Puerto Rico.
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan 00931, Puerto Rico.
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15
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Exploring viral reservoir: The combining approach of cell sorting and droplet digital PCR. Methods 2017; 134-135:98-105. [PMID: 29197654 DOI: 10.1016/j.ymeth.2017.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/24/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022] Open
Abstract
Combined antiretroviral therapy (cART) blocks different steps of HIV replication and maintains plasma viral RNA at undetectable levels. The virus can remain in long-living cells and create a reservoir where HIV can restart replicating after cART discontinuation. A persistent viral production triggers and maintains a persistent immune activation, which is a well-known feature of chronic HIV infection, and contributes either to precocious aging, or to the increased incidence of morbidity and mortality of HIV positive patients. The new frontier of the treatment of HIV infection is nowadays eradication of the virus from all host cells and tissues. For this reason, it is crucial to have a clear and precise idea of where the virus hides, and which are the cells that keep it silent. Important efforts have been made to improve the detection of viral reservoirs, and new techniques are now giving the opportunity to characterize viral reservoirs. Among these techniques, a strategic approach based upon cell sorting and droplet digital PCR (ddPCR) is opening new horizons and opportunities of research. This review provides an overview of the methods that combine cell sorting and ddPCR for the quantification of HIV DNA in different cell types, and for the detection of its maintenance.
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16
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Khan S, Telwatte S, Trapecar M, Yukl S, Sanjabi S. Differentiating Immune Cell Targets in Gut-Associated Lymphoid Tissue for HIV Cure. AIDS Res Hum Retroviruses 2017; 33:S40-S58. [PMID: 28882067 PMCID: PMC5685216 DOI: 10.1089/aid.2017.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The single greatest challenge to an HIV cure is the persistence of latently infected cells containing inducible, replication-competent proviral genomes, which constitute only a small fraction of total or infected cells in the body. Although resting CD4+ T cells in the blood are a well-known source of viral rebound, more than 90% of the body's lymphocytes reside elsewhere. Many are in gut tissue, where HIV DNA levels per million CD4+ T cells are considerably higher than in the blood. Despite the significant contribution of gut tissue to viral replication and persistence, little is known about the cell types that support persistence of HIV in the gut; importantly, T cells in the gut have phenotypic, functional, and survival properties that are distinct from T cells in other tissues. The mechanisms by which latency is established and maintained will likely depend on the location and cytokine milieu surrounding the latently infected cells in each compartment. Therefore, successful HIV cure strategies require identification and characterization of the exact cell types that support viral persistence, particularly in the gut. In this review, we describe the seeding of the latent HIV reservoir in the gut mucosa; highlight the evidence for compartmentalization and depletion of T cells; summarize the immunologic consequences of HIV infection within the gut milieu; propose how the damaged gut environment may promote the latent HIV reservoir; and explore several immune cell targets in the gut and their place on the path toward HIV cure.
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Affiliation(s)
- Shahzada Khan
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
| | - Sushama Telwatte
- San Francisco VA Health Care System and University of California, San Francisco (UCSF), San Francisco, California
| | - Martin Trapecar
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
| | - Steven Yukl
- San Francisco VA Health Care System and University of California, San Francisco (UCSF), San Francisco, California
| | - Shomyseh Sanjabi
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, California
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California
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17
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Pouyan MB, Nourani M. Identifying Cell Populations in Flow Cytometry Data Using Phenotypic Signatures. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:880-891. [PMID: 27076456 DOI: 10.1109/tcbb.2016.2550428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-cell flow cytometry is a technology that measures the expression of several cellular markers simultaneously for a large number of cells. Identification of homogeneous cell populations, currently done by manual biaxial gating, is highly subjective and time consuming. To overcome the shortcomings of manual gating, automatic algorithms have been proposed. However, the performance of these methods highly depends on the shape of populations and the dimension of the data. In this paper, we have developed a time-efficient method that accurately identifies cellular populations. This is done based on a novel technique that estimates the initial number of clusters in high dimension and identifies the final clusters by merging clusters using their phenotypic signatures in low dimension. The proposed method is called SigClust. We have applied SigClust to four public datasets and compared it with five well known methods in the field. The results are promising and indicate higher performance and accuracy compared to similar approaches reported in literature.
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18
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Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications. Clin Microbiol Rev 2017; 29:859-80. [PMID: 27559075 DOI: 10.1128/cmr.00015-16] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis.
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19
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Sensitive detection of rare disease-associated cell subsets via representation learning. Nat Commun 2017; 8:14825. [PMID: 28382969 PMCID: PMC5384229 DOI: 10.1038/ncomms14825] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 02/02/2017] [Indexed: 01/20/2023] Open
Abstract
Rare cell populations play a pivotal role in the initiation and progression of diseases such as cancer. However, the identification of such subpopulations remains a difficult task. This work describes CellCnn, a representation learning approach to detect rare cell subsets associated with disease using high-dimensional single-cell measurements. Using CellCnn, we identify paracrine signalling-, AIDS onset- and rare CMV infection-associated cell subsets in peripheral blood, and extremely rare leukaemic blast populations in minimal residual disease-like situations with frequencies as low as 0.01%.
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20
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CD25+ FoxP3+ Memory CD4 T Cells Are Frequent Targets of HIV Infection In Vivo. J Virol 2016; 90:8954-67. [PMID: 27384654 DOI: 10.1128/jvi.00612-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/17/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Interleukin 2 (IL-2) signaling through the IL-2 receptor alpha chain (CD25) facilitates HIV replication in vitro and facilitates homeostatic proliferation of CD25(+) FoxP3(+) CD4(+) T cells. CD25(+) FoxP3(+) CD4(+) T cells may therefore constitute a suitable subset for HIV infection and plasma virion production. CD25(+) FoxP3(+) CD4(+) T cell frequencies, absolute numbers, and the expression of CCR5 and cell cycle marker Ki67 were studied in peripheral blood from HIV(+) and HIV(-) study volunteers. Different memory CD4(+) T cell subsets were then sorted for quantification of cell-associated HIV DNA and phylogenetic analyses of the highly variable EnvV1V3 region in comparison to plasma-derived virus sequences. In HIV(+) subjects, 51% (median) of CD25(+) FoxP3(+) CD4(+) T cells expressed the HIV coreceptor CCR5. Very high frequencies of Ki67(+) cells were detected in CD25(+) FoxP3(+) memory CD4(+) T cells (median, 27.6%) in comparison to CD25(-) FoxP3(-) memory CD4(+) T cells (median, 4.1%; P < 0.0001). HIV DNA content was 15-fold higher in CD25(+) FoxP3(+) memory CD4(+) T cells than in CD25(-) FoxP3(-) T cells (P = 0.003). EnvV1V3 sequences derived from CD25(+) FoxP3(+) memory CD4(+) T cells did not preferentially cluster with plasma-derived sequences. Quasi-identical cell-plasma sequence pairs were rare, and their proportion decreased with the estimated HIV infection duration. These data suggest that specific cellular characteristics of CD25(+) FoxP3(+) memory CD4(+) T cells might facilitate efficient HIV infection in vivo and passage of HIV DNA to cell progeny in the absence of active viral replication. The contribution of this cell population to plasma virion production remains unclear. IMPORTANCE Despite recent advances in the understanding of AIDS virus pathogenesis, which cell subsets support HIV infection and replication in vivo is incompletely understood. In vitro, the IL-2 signaling pathway and IL-2-dependent cell cycle induction are essential for HIV infection of stimulated T cells. CD25(+) FoxP3(+) memory CD4 T cells, often referred to as regulatory CD4 T cells, depend on IL-2 signaling for homeostatic proliferation in vivo Our results show that CD25(+) FoxP3(+) memory CD4(+) T cells often express the HIV coreceptor CCR5, are significantly more proliferative, and contain more HIV DNA than CD25(-) FoxP3(-) memory CD4 T cell subsets. The specific cellular characteristics of CD25(+) FoxP3(+) memory CD4(+) T cells probably facilitate efficient HIV infection in vivo and passage of HIV DNA to cell progeny in the absence of active viral replication. However, the contribution of this cell subset to plasma viremia remains unclear.
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21
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Beddall M, Chattopadhyay PK, Kao SF, Foulds K, Roederer M. A simple tube adapter to expedite and automate thawing of viably frozen cells. J Immunol Methods 2016; 439:74-78. [PMID: 27594593 DOI: 10.1016/j.jim.2016.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 08/27/2016] [Accepted: 08/29/2016] [Indexed: 11/29/2022]
Abstract
Although cryopreserved cell specimens are used throughout biomedical research, the process for thawing samples is labor-intensive and prone to error. Here we describe a small laboratory device that couples an uncapped vial of frozen cells to a conical tube containing warm cell culture media. The entire complex is loaded directly into a centrifuge; within 5min, cells are thawed and diluted out of toxic cryopreservation medium. The recovery and viability of cells are slightly reduced compared to the common (traditional) method. However, antigen-specific T-cell function is not affected. Since no technician time is required (beyond uncapping of vials), our device allows the parallel processing of as many samples as a centrifuge can hold (up to 96, in some models). Moreover, since the samples are not thawed manually in a water bath, the problems associated with technician-to-technician differences in sample handling are minimized, as is the potential for contamination. Importantly, the elimination of substantial labor involving subjective decisions standardizes this process and can reduce variability in results from cryopreserved specimens.
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Affiliation(s)
- Margaret Beddall
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892, United States
| | - Pratip K Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892, United States.
| | - Shing-Fen Kao
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892, United States
| | - Kathy Foulds
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892, United States
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892, United States
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22
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Establishment and Reversal of HIV-1 Latency in Naive and Central Memory CD4+ T Cells In Vitro. J Virol 2016; 90:8059-73. [PMID: 27356901 DOI: 10.1128/jvi.00553-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/21/2016] [Indexed: 01/02/2023] Open
Abstract
UNLABELLED The latent HIV-1 reservoir primarily resides in resting CD4(+) T cells which are a heterogeneous population composed of both naive (TN) and memory cells. In HIV-1-infected individuals, viral DNA has been detected in both naive and memory CD4(+) T cell subsets although the frequency of HIV-1 DNA is typically higher in memory cells, particularly in the central memory (TCM) cell subset. TN and TCM cells are distinct cell populations distinguished by many phenotypic and physiological differences. In this study, we used a primary cell model of HIV-1 latency that utilizes direct infection of highly purified TN and TCM cells to address differences in the establishment and reversal of HIV-1 latency. Consistent with what is seen in vivo, we found that HIV-1 infected TN cells less efficiently than TCM cells. However, when the infected TN cells were treated with latency-reversing agents, including anti-CD3/CD28 antibodies, phorbol myristate acetate/phytohemagglutinin, and prostratin, as much (if not more) extracellular virion-associated HIV-1 RNA was produced per infected TN cell as per infected TCM cell. There were no major differences in the genomic distribution of HIV-1 integration sites between TN and TCM cells that accounted for these observed differences. We observed decay of the latent HIV-1 cells in both T cell subsets after exposure to each of the latency-reversing agents. Collectively, these data highlight significant differences in the establishment and reversal of HIV-1 latency in TN and TCM CD4(+) T cells and suggest that each subset should be independently studied in preclinical and clinical studies. IMPORTANCE The latent HIV-1 reservoir is frequently described as residing within resting memory CD4(+) T cells. This is largely due to the consistent finding that memory CD4(+) T cells, specifically the central (TCM) and transitional memory compartments, harbor the highest levels of HIV-1 DNA in individuals on suppressive therapy. This has yielded little research into the contribution of CD4(+) naive T (TN) cells to the latent reservoir. In this study, we show that although TN cells harbor significantly lower levels of HIV-1 DNA, following latency reversal, they produced as many virions as did the TCM cells (if not more virions). This suggests that latently infected TN cells may be a major source of virus following treatment interruption or failure. These findings highlight the need for a better understanding of the establishment and reversal of HIV-1 latency in TN cells in evaluating therapeutic approaches to eliminate the latent reservoir.
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Modification of the HIV-specific CD8+ T-cell response in an HIV elite controller after chikungunya virus infection. AIDS 2016; 30:1905-11. [PMID: 27124898 DOI: 10.1097/qad.0000000000001129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To evaluate the impact of chikungunya virus (CHIKV) infection on the quality of the HIV-specific CD8 T-cell (CTL) response in an HIV elite controller. DESIGN Three blood samples were obtained from an elite controller at 27 days (EC-CHIKV, Sample 1, S1), 41 days (S2) and 1 year (S3) after CHIKV infection. Additionally, samples from another nine elite controllers and nine viremic chronics were obtained. METHODS CD4 T-cell counts, viral load and immune activation were recorded. Natural killer (NK) cells and HIV-specific CTL quality were evaluated. Data were analyzed using nonparametric statistics. RESULTS A male HIV elite controller was confirmed for CHIKV infection. At S1, he presented 211 cells/μl CD4 T-cell count, a HIV viral load blip (145 copies/ml) and high T-cell activation. NK cell percentage and activation were higher at S2. All parameters were recovered by S3. CTLs at S1 were exclusively monofunctional with a high proportion (>80%) of degranulating CTLs. By S3, CTL polyfunctionality was more similar to that of a typical elite controller. The distribution of CTL memory subsets also displayed altered profiles. CONCLUSION The results showed that the phenotype and function of HIV-specific CTLs were modified in temporal association with an HIV viral load blip that followed CHIKV infection. This might have helped to control the transient HIV rebound. Additionally, NK cells could have been involved in this control. These results provide useful information to help understand how elite controllers maintain their status, control HIV infection and alert about the negative impact to the immune function of HIV-infected individuals living in CHIKV endemic areas.
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Yu YRA, Hotten DF, Malakhau Y, Volker E, Ghio AJ, Noble PW, Kraft M, Hollingsworth JW, Gunn MD, Tighe RM. Flow Cytometric Analysis of Myeloid Cells in Human Blood, Bronchoalveolar Lavage, and Lung Tissues. Am J Respir Cell Mol Biol 2016; 54:13-24. [PMID: 26267148 DOI: 10.1165/rcmb.2015-0146oc] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Clear identification of specific cell populations by flow cytometry is important to understand functional roles. A well-defined flow cytometry panel for myeloid cells in human bronchoalveolar lavage (BAL) and lung tissue is currently lacking. The objective of this study was to develop a flow cytometry-based panel for human BAL and lung tissue. We obtained and performed flow cytometry/sorting on human BAL cells and lung tissue. Confocal images were obtained from lung tissue using antibodies for cluster of differentiation (CD)206, CD169, and E cadherin. We defined a multicolor flow panel for human BAL and lung tissue that identifies major leukocyte populations. These include macrophage (CD206(+)) subsets and other CD206(-) leukocytes. The CD206(-) cells include: (1) three monocyte (CD14(+)) subsets, (2) CD11c(+) dendritic cells (CD14(-), CD11c(+), HLA-DR(+)), (3) plasmacytoid dendritic cells (CD14(-), CD11c(-), HLA-DR(+), CD123(+)), and (4) other granulocytes (neutrophils, mast cells, eosinophils, and basophils). Using this panel on human lung tissue, we defined two populations of pulmonary macrophages: CD169(+) and CD169(-) macrophages. In lung tissue, CD169(-) macrophages were a prominent cell type. Using confocal microscopy, CD169(+) macrophages were located in the alveolar space/airway, defining them as alveolar macrophages. In contrast, CD169(-) macrophages were associated with airway/alveolar epithelium, consistent with interstitial-associated macrophages. We defined a flow cytometry panel in human BAL and lung tissue that allows identification of multiple immune cell types and delineates alveolar from interstitial-associated macrophages. This study has important implications for defining myeloid cells in human lung samples.
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Affiliation(s)
- Yen-Rei A Yu
- 1 Department of Medicine, Duke University, Durham, North Carolina
| | | | - Yuryi Malakhau
- 1 Department of Medicine, Duke University, Durham, North Carolina
| | - Ellen Volker
- 1 Department of Medicine, Duke University, Durham, North Carolina
| | - Andrew J Ghio
- 2 National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Chapel Hill, North Carolina
| | - Paul W Noble
- 3 Department of Medicine, Cedar Sinai Medical Center, Los Angeles, California; and
| | - Monica Kraft
- 1 Department of Medicine, Duke University, Durham, North Carolina
| | | | - Michael D Gunn
- 1 Department of Medicine, Duke University, Durham, North Carolina
| | - Robert M Tighe
- 1 Department of Medicine, Duke University, Durham, North Carolina
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Drylewicz J, Vrisekoop N, Mugwagwa T, de Boer AB, Otto SA, Hazenberg MD, Tesselaar K, de Boer RJ, Borghans JAM. Reconciling Longitudinal Naive T-Cell and TREC Dynamics during HIV-1 Infection. PLoS One 2016; 11:e0152513. [PMID: 27010200 PMCID: PMC4806918 DOI: 10.1371/journal.pone.0152513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/15/2016] [Indexed: 12/14/2022] Open
Abstract
Naive T cells in untreated HIV-1 infected individuals have a reduced T-cell receptor excision circle (TREC) content. Previous mathematical models have suggested that this is due to increased naive T-cell division. It remains unclear, however, how reduced naive TREC contents can be reconciled with a gradual loss of naive T cells in HIV-1 infection. We performed longitudinal analyses in humans before and after HIV-1 seroconversion, and used a mathematical model to investigate which processes could explain the observed changes in naive T-cell numbers and TRECs during untreated HIV-1 disease progression. Both CD4+ and CD8+ naive T-cell TREC contents declined biphasically, with a rapid loss during the first year and a much slower loss during the chronic phase of infection. While naive CD8+ T-cell numbers hardly changed during follow-up, naive CD4+ T-cell counts continually declined. We show that a fine balance between increased T-cell division and loss in the peripheral naive T-cell pool can explain the observed short- and long-term changes in TRECs and naive T-cell numbers, especially if T-cell turnover during the acute phase is more increased than during the chronic phase of infection. Loss of thymic output, on the other hand, does not help to explain the biphasic loss of TRECs in HIV infection. The observed longitudinal changes in TRECs and naive T-cell numbers in HIV-infected individuals are most likely explained by a tight balance between increased T-cell division and death, suggesting that these changes are intrinsically linked in HIV infection.
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Affiliation(s)
- Julia Drylewicz
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Nienke Vrisekoop
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tendai Mugwagwa
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anne Bregje de Boer
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sigrid A. Otto
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mette D. Hazenberg
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - José A. M. Borghans
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan G, Scheuermann RH, Brinkman RR. A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry A 2016; 89:16-21. [PMID: 26447924 PMCID: PMC4874734 DOI: 10.1002/cyto.a.22732] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/20/2015] [Accepted: 07/16/2015] [Indexed: 11/07/2022]
Abstract
The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of computational methods for identifying cell populations in multidimensional flow cytometry data. Here we report the results of FlowCAP-IV where algorithms from seven different research groups predicted the time to progression to AIDS among a cohort of 384 HIV+ subjects, using antigen-stimulated peripheral blood mononuclear cell (PBMC) samples analyzed with a 14-color staining panel. Two approaches (FlowReMi.1 and flowDensity-flowType-RchyOptimyx) provided statistically significant predictive value in the blinded test set. Manual validation of submitted results indicated that unbiased analysis of single cell phenotypes could reveal unexpected cell types that correlated with outcomes of interest in high dimensional flow cytometry datasets.
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Affiliation(s)
- Nima Aghaeepour
- British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - Pratip Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Health, Washington, DC, USA
| | - Maria Chikina
- Department Computational and Systems Biology, University of Pittsburgh, Pittsburg, USA
| | - Tom Dhaene
- Department of Information Technology, Ghent University - iMinds, Ghent, Belgium
| | - Sofie Van Gassen
- Department of Information Technology, Ghent University - iMinds, Ghent, Belgium
- Inflammation Research Center, VIB, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Miron Kursa
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
| | - Bart N. Lambrecht
- Inflammation Research Center, VIB, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Yu Qian
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University
| | - Yvan Saeys
- Inflammation Research Center, VIB, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Dong Tong
- The John van Geest Cancer Research Centre, Nottingham Trent University, UK & Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Celine Vens
- Inflammation Research Center, VIB, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Public Health and Primary Care, KU Leuven Kulak, Kortrijk, Belgium
| | - Sławomir Walkowiak
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
| | - Kui Wang
- Department of Mathematics, University of Queensland, St. Lucia, Brisbane, Australia
- School of Medicine, Shihezi University, Xinjiang 832000, China
| | - Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim Mosmann
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Garry Nolan
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
| | - Ryan R. Brinkman
- British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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Van Gassen S, Vens C, Dhaene T, Lambrecht BN, Saeys Y. FloReMi: Flow density survival regression using minimal feature redundancy. Cytometry A 2015; 89:22-9. [DOI: 10.1002/cyto.a.22734] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 05/29/2015] [Accepted: 07/16/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Sofie Van Gassen
- Department of Information Technology; Ghent University-iMinds; Ghent Belgium
- Inflammation Research Center, VIB; Ghent Belgium
- Department of Respiratory Medicine; Ghent University Hospital; Ghent Belgium
| | - Celine Vens
- Inflammation Research Center, VIB; Ghent Belgium
- Department of Respiratory Medicine; Ghent University Hospital; Ghent Belgium
- Department of Public Health and Primary Care; kU Leuven Kulak; Kortrijk Belgium
| | - Tom Dhaene
- Department of Information Technology; Ghent University-iMinds; Ghent Belgium
| | - Bart N. Lambrecht
- Inflammation Research Center, VIB; Ghent Belgium
- Department of Respiratory Medicine; Ghent University Hospital; Ghent Belgium
| | - Yvan Saeys
- Inflammation Research Center, VIB; Ghent Belgium
- Department of Respiratory Medicine; Ghent University Hospital; Ghent Belgium
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Chisenga CC, Filteau S, Siame J, Chisenga M, Prendergast AJ, Kelly P. T-Cell Subsets Predict Mortality in Malnourished Zambian Adults Initiating Antiretroviral Therapy. PLoS One 2015; 10:e0129928. [PMID: 26083409 PMCID: PMC4470912 DOI: 10.1371/journal.pone.0129928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/14/2015] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVE To estimate the prognostic value of T-cell subsets in Zambian patients initiating antiretroviral therapy (ART), and to assess the impact of a nutritional intervention on T-cell subsets. METHODS This was a sub-study of a randomised clinical trial of a nutritional intervention for malnourished adults initiating ART. Participants in a randomised controlled trial (NUSTART trial) were enrolled between April and December 2012. Participants received lipid-based nutritional supplement either with or without additional vitamins and minerals. Immunophenotyping was undertaken at baseline and, in survivors, after 12 weeks of ART to characterize T-cell subsets using the markers CD3, CD4, CD8, CD45RA, CCR7, CD28, CD57, CD31, α4β7, Ki67, CD25 and HLA-DR. Univariate and multivariate survival analysis was performed, and responses to treatment were analysed using the Wicoxon rank-sum test. RESULTS Among 181 adults, 36 (20%) died by 12 weeks after starting ART. In univariate analysis, patients who died had fewer proliferating, more naïve and fewer gut homing CD4+ T-cells compared to survivors; and more senescent and fewer proliferating CD8+ T-cells. In a multivariate Cox regression model high naïve CD4+, low proliferating CD4+, high senescent CD8+ and low proliferating CD8+ subsets were independently associated with increased risk of death. Recent CD4+ thymic emigrants increased less between recruitment and 12 weeks of ART in the intervention group compared to the control group. CONCLUSIONS Specific CD4+ T-cell subsets are of considerable prognostic significance for patients initiating ART in Zambia, but only thymic output responded to this nutritional intervention.
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Affiliation(s)
- Caroline C. Chisenga
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Lusaka, Zambia
- NUSTART project, University Teaching Hospital, Lusaka, Zambia
| | - Suzanne Filteau
- NUSTART project, University Teaching Hospital, Lusaka, Zambia
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joshua Siame
- NUSTART project, University Teaching Hospital, Lusaka, Zambia
| | - Molly Chisenga
- NUSTART project, University Teaching Hospital, Lusaka, Zambia
| | - Andrew J. Prendergast
- Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Paul Kelly
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Lusaka, Zambia
- NUSTART project, University Teaching Hospital, Lusaka, Zambia
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom
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Chattopadhyay PK, Roederer M. A mine is a terrible thing to waste: high content, single cell technologies for comprehensive immune analysis. Am J Transplant 2015; 15:1155-61. [PMID: 25708158 DOI: 10.1111/ajt.13193] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 01/25/2023]
Abstract
In recent years, an incredible variety of single cell technologies have become available to analyze immune responses. These technologies include polychromatic flow cytometry, mass cytometry, highly multiplexed single cell qPCR, RNA sequencing, microtools, and high-resolution imaging. In this article, we review these platforms, describing their power and limitations for comprehensive analysis of the immune system. We relate the properties of these technologies to the various cellular states relevant to an immune response, in order to address which technologies are most appropriate for which settings.
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Affiliation(s)
- P K Chattopadhyay
- Vaccine Research Center, National Institutes of Health, Bethesda, MD
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Chéret A, Bacchus-Souffan C, Avettand-Fenoël V, Mélard A, Nembot G, Blanc C, Samri A, Sáez-Cirión A, Hocqueloux L, Lascoux-Combe C, Allavena C, Goujard C, Valantin MA, Leplatois A, Meyer L, Rouzioux C, Autran B. Combined ART started during acute HIV infection protects central memory CD4+ T cells and can induce remission. J Antimicrob Chemother 2015; 70:2108-20. [PMID: 25900157 DOI: 10.1093/jac/dkv084] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/13/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Therapeutic control of HIV replication reduces the size of the viral reservoir, particularly among central memory CD4+ T cells, and this effect might be accentuated by early treatment. METHODS We examined the effect of ART initiated at the time of the primary HIV infection (early ART), lasting 2 and 6 years in 11 and 10 patients, respectively, on the HIV reservoir in peripheral resting CD4+ T cells, sorted into naive (TN), central memory (TCM), transitional memory (TTM) and effector memory (TEM) cells, by comparison with 11 post-treatment controllers (PTCs). RESULTS Between baseline and 2 years, CD4+ T cell subset numbers increased markedly (P < 0.004) and HIV DNA levels decreased in all subsets (P < 0.009). TTM cells represented the majority of reservoir cells at both timepoints, T cell activation status normalized and viral diversity remained stable over time. The HIV reservoir was smaller after 6 years of early ART than after 2 years (P < 0.019), and did not differ between PTCs and patients treated for 6 years. One patient, who had low reservoir levels in all T cell subsets after 2 years of treatment similar to the levels in PTCs, spontaneously controlled viral replication during 18 months off treatment. CONCLUSIONS Early prolonged ART thus limits the size of the HIV reservoir, protects long-lived cells from persistent infection and may enhance post-treatment control.
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Affiliation(s)
- Antoine Chéret
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Charline Bacchus-Souffan
- Pierre & Marie Curie University Paris VI, INSERM UMR-S 945 Immunity & Infection, Pitié-Salpêtrière Hospital, Paris, France
| | - Veronique Avettand-Fenoël
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Adeline Mélard
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Georges Nembot
- Epidemiology and Public Health Department, Inserm U1018, AP-HP, Le Kremlin-Bicêtre Hospital, University Paris Sud, Le Kremlin-Bicêtre, France
| | - Catherine Blanc
- CyPS Flow Cytometry Platform, Pierre & Marie Curie University, Pitié-Salpêtrière Hospital, Paris, France
| | - Assia Samri
- Pierre & Marie Curie University Paris VI, INSERM UMR-S 945 Immunity & Infection, Pitié-Salpêtrière Hospital, Paris, France
| | - Asier Sáez-Cirión
- Pasteur Institute, Regulation of Retroviral Infections Unit, Paris, France
| | | | | | | | - Cécile Goujard
- Internal Medicine Department, AP-HP, Le Kremlin-Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Marc Antoine Valantin
- Infectious Diseases Department, AP-HP, Pitié-Salpêtrière Hospital, University Paris XII, Paris, France
| | - Anne Leplatois
- Infectious Diseases Department, l'Archet Hospital, Nice, France
| | - Laurence Meyer
- Epidemiology and Public Health Department, Inserm U1018, AP-HP, Le Kremlin-Bicêtre Hospital, University Paris Sud, Le Kremlin-Bicêtre, France
| | - Christine Rouzioux
- EA 7327 Paris-Descartes University, Sorbonne Paris-Cité, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France Infectious Diseases Department, Dron Hospital, Tourcoing, France
| | - Brigitte Autran
- Pierre & Marie Curie University Paris VI, INSERM UMR-S 945 Immunity & Infection, Pitié-Salpêtrière Hospital, Paris, France
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Holst PJ, Jensen BAH, Ragonnaud E, Thomsen AR, Christensen JP. Targeting of non-dominant antigens as a vaccine strategy to broaden T-cell responses during chronic viral infection. PLoS One 2015; 10:e0117242. [PMID: 25679375 PMCID: PMC4334508 DOI: 10.1371/journal.pone.0117242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 12/22/2014] [Indexed: 12/26/2022] Open
Abstract
In this study, we compared adenoviral vaccine vectors with the capacity to induce equally potent immune responses against non-dominant and immunodominant epitopes of murine lymphocytic choriomeningitis virus (LCMV). Our results demonstrate that vaccination targeting non-dominant epitopes facilitates potent virus-induced T-cell responses against immunodominant epitopes during subsequent challenge with highly invasive virus. In contrast, when an immunodominant epitope was included in the vaccine, the T-cell response associated with viral challenge remained focussed on that epitope. Early after challenge with live virus, the CD8+ T cells specific for vaccine-encoded epitopes, displayed a phenotype typically associated with prolonged/persistent antigenic stimulation marked by high levels of KLRG-1, as compared to T cells reacting to epitopes not included in the vaccine. Notably, this association was lost over time in T cells specific for the dominant T cell epitopes, and these cells were fully capable of expanding in response to a new viral challenge. Overall, our data suggests a potential for broadening of the antiviral CD8+ T-cell response by selecting non-dominant antigens to be targeted by vaccination. In addition, our findings suggest that prior adenoviral vaccination is not likely to negatively impact the long-term and protective immune response induced and maintained by a vaccine-attenuated chronic viral infection.
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Affiliation(s)
- Peter J. Holst
- Department of International Health, Immunology and Microbiology, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Benjamin A. H. Jensen
- Department of International Health, Immunology and Microbiology, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
| | - Emeline Ragonnaud
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan R. Thomsen
- Department of International Health, Immunology and Microbiology, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
| | - Jan P. Christensen
- Department of International Health, Immunology and Microbiology, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
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Alidjinou EK, Bocket L, Hober D. Quantification of viral DNA during HIV-1 infection: A review of relevant clinical uses and laboratory methods. ACTA ACUST UNITED AC 2014; 63:53-9. [PMID: 25201144 DOI: 10.1016/j.patbio.2014.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/15/2014] [Indexed: 01/25/2023]
Abstract
Effective antiretroviral therapy usually leads to undetectable HIV-1 RNA in the plasma. However, the virus persists in some cells of infected patients as various DNA forms, both integrated and unintegrated. This reservoir represents the greatest challenge to the complete cure of HIV-1 infection and its characteristics highly impact the course of the disease. The quantification of HIV-1 DNA in blood samples constitutes currently the most practical approach to measure this residual infection. Real-time quantitative PCR (qPCR) is the most common method used for HIV-DNA quantification and many strategies have been developed to measure the different forms of HIV-1 DNA. In the literature, several "in-house" PCR methods have been used and there is a need for standardization to have comparable results. In addition, qPCR is limited for the precise quantification of low levels by background noise. Among new assays in development, digital PCR was shown to allow an accurate quantification of HIV-1 DNA. Total HIV-1 DNA is most commonly measured in clinical routine. The absolute quantification of proviruses and unintegrated forms is more often used for research purposes.
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Affiliation(s)
- E K Alidjinou
- Laboratoire de virologie EA3610, faculté de médecine, institut Hippocrate, université Lille 2, CHRU Lille, 152, rue du Dr-Yersin, 59120 Loos-lez-Lille, France
| | - L Bocket
- Laboratoire de virologie EA3610, faculté de médecine, institut Hippocrate, université Lille 2, CHRU Lille, 152, rue du Dr-Yersin, 59120 Loos-lez-Lille, France
| | - D Hober
- Laboratoire de virologie EA3610, faculté de médecine, institut Hippocrate, université Lille 2, CHRU Lille, 152, rue du Dr-Yersin, 59120 Loos-lez-Lille, France.
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Early skewed distribution of total and HIV-specific CD8+ T-cell memory phenotypes during primary HIV infection is related to reduced antiviral activity and faster disease progression. PLoS One 2014; 9:e104235. [PMID: 25093660 PMCID: PMC4122399 DOI: 10.1371/journal.pone.0104235] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/08/2014] [Indexed: 11/19/2022] Open
Abstract
The important role of the CD8+ T-cells on HIV control is well established. However, correlates of immune protection remain elusive. Although the importance of CD8+ T-cell specificity and functionality in virus control has been underscored, further unraveling the link between CD8+ T-cell differentiation and viral control is needed. Here, an immunophenotypic analysis (in terms of memory markers and Programmed cell death 1 (PD-1) expression) of the CD8+ T-cell subset found in primary HIV infection (PHI) was performed. The aim was to seek for associations with functional properties of the CD8+ T-cell subsets, viral control and subsequent disease progression. Also, results were compared with samples from Chronics and Elite Controllers. It was found that normal maturation of total and HIV-specific CD8+ T-cells into memory subsets is skewed in PHI, but not at the dramatic level observed in Chronics. Within the HIV-specific compartment, this alteration was evidenced by an accumulation of effector memory CD8+ T (TEM) cells over fully differentiated terminal effector CD8+ T (TTE) cells. Furthermore, higher proportions of total and HIV-specific CD8+ TEM cells and higher HIV-specific TEM/(TEM+TTE) ratio correlated with markers of faster progression. Analysis of PD-1 expression on total and HIV-specific CD8+ T-cells from PHI subjects revealed not only an association with disease progression but also with skewed memory CD8+ T-cell differentiation. Most notably, significant direct correlations were obtained between the functional capacity of CD8+ T-cells to inhibit viral replication in vitro with higher proportions of fully-differentiated HIV-specific CD8+ TTE cells, both at baseline and at 12 months post-infection. Thus, a relationship between preservation of CD8+ T-cell differentiation pathway and cell functionality was established. This report presents evidence concerning the link among CD8+ T-cell function, phenotype and virus control, hence supporting the instauration of early interventions to prevent irreversible immune damage.
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Nissen SK, Højen JF, Andersen KLD, Kofod-Olsen E, Berg RK, Paludan SR, Østergaard L, Jakobsen MR, Tolstrup M, Mogensen TH. Innate DNA sensing is impaired in HIV patients and IFI16 expression correlates with chronic immune activation. Clin Exp Immunol 2014; 177:295-309. [PMID: 24593816 DOI: 10.1111/cei.12317] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2014] [Indexed: 02/03/2023] Open
Abstract
The innate immune system has been recognized to play a role in the pathogenesis of HIV infection, both by stimulating protective activities and through a contribution to chronic immune activation, the development of immunodeficiency and progression to AIDS. A role for DNA sensors in HIV recognition has been suggested recently, and the aim of the present study was to describe the influence of HIV infection on expression and function of intracellular DNA sensing. Here we demonstrate impaired expression of interferon-stimulated genes in responses to DNA in peripheral blood monuclear cells from HIV-positive individuals, irrespective of whether patients receive anti-retroviral treatment. Furthermore, we show that expression levels of the DNA sensors interferon-inducible protein 16 (IFI16) and cyclic guanosine monophosphate-adenosine monophosphate synthase were increased in treatment-naive patients, and for IFI16 expression was correlated with high viral load and low CD4 cell count. Finally, our data demonstrate a correlation between IFI16 and CD38 expression, a marker of immune activation, in CD4(+) central and effector memory T cells, which may indicate that IFI16-mediated DNA sensing and signalling contributes to chronic immune activation. Altogether, the present study demonstrates abnormal expression and function of cytosolic DNA sensors in HIV patients, which may have implications for control of opportunistic infections, chronic immune activation and T cell death.
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Affiliation(s)
- S K Nissen
- Department of Infectious Diseases, Aarhus University Hospital Skejby, Aarhus, Denmark
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36
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Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci U S A 2014; 111:E2770-7. [PMID: 24979804 DOI: 10.1073/pnas.1408792111] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Elucidation and examination of cellular subpopulations that display condition-specific behavior can play a critical contributory role in understanding disease mechanism, as well as provide a focal point for development of diagnostic criteria linking such a mechanism to clinical prognosis. Despite recent advancements in single-cell measurement technologies, the identification of relevant cell subsets through manual efforts remains standard practice. As new technologies such as mass cytometry increase the parameterization of single-cell measurements, the scalability and subjectivity inherent in manual analyses slows both analysis and progress. We therefore developed Citrus (cluster identification, characterization, and regression), a data-driven approach for the identification of stratifying subpopulations in multidimensional cytometry datasets. The methodology of Citrus is demonstrated through the identification of known and unexpected pathway responses in a dataset of stimulated peripheral blood mononuclear cells measured by mass cytometry. Additionally, the performance of Citrus is compared with that of existing methods through the analysis of several publicly available datasets. As the complexity of flow cytometry datasets continues to increase, methods such as Citrus will be needed to aid investigators in the performance of unbiased--and potentially more thorough--correlation-based mining and inspection of cell subsets nested within high-dimensional datasets.
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Mohan T, Bhatnagar S, Gupta DL, Rao DN. Current understanding of HIV-1 and T-cell adaptive immunity: progress to date. Microb Pathog 2014; 73:60-9. [PMID: 24930593 DOI: 10.1016/j.micpath.2014.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 12/11/2022]
Abstract
The cellular immune response to human immunodeficiency virus (HIV) has different components originating from both the adaptive and innate immune systems. HIV cleverly utilizes the host machinery to survive by its intricate nature of interaction with the host immune system. HIV evades the host immune system at innate ad adaptive, allows the pathogen to replicate and transmit from one host to another. Researchers have shown that HIV has multipronged effects especially on the adaptive immunity, with CD4(+) cells being the worst effect T-cell populations. Various analyses have revealed that, the exposure to HIV results in clonal expansion and excessive activation of the immune system. Also, an abnormal process of differentiation has been observed suggestive of an alteration and blocks in the maturation of various T-cell subsets. Additionally, HIV has shown to accelerate immunosenescence and exhaustion of the overtly activated T-cells. Apart from causing phenotypic changes, HIV has adverse effects on the functional aspect of the immune system, with evidences implicating it in the loss of the capacity of T-cells to secrete various antiviral cytokines and chemokines. However, there continues to be many aspects of the immune- pathogenesis of HIV that are still unknown and thus required further research in order to convert the malaise of HIV into a manageable epidemic.
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Affiliation(s)
- Teena Mohan
- Department of Biochemistry, All India Institute of Medical Sciences (A.I.I.M.S.), Ansari Nagar, New Delhi 110029, India.
| | - Santwana Bhatnagar
- Department of Biochemistry, All India Institute of Medical Sciences (A.I.I.M.S.), Ansari Nagar, New Delhi 110029, India
| | - Dablu L Gupta
- Department of Biochemistry, All India Institute of Medical Sciences (A.I.I.M.S.), Ansari Nagar, New Delhi 110029, India
| | - D N Rao
- Department of Biochemistry, All India Institute of Medical Sciences (A.I.I.M.S.), Ansari Nagar, New Delhi 110029, India.
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Autran B, Hamimi C, Katlama C. One Step Closer to HIV Eradication? CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2014. [DOI: 10.1007/s40506-014-0017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Miedema F, Hazenberg MD, Tesselaar K, van Baarle D, de Boer RJ, Borghans JAM. Immune activation and collateral damage in AIDS pathogenesis. Front Immunol 2013; 4:298. [PMID: 24133492 PMCID: PMC3783946 DOI: 10.3389/fimmu.2013.00298] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
In the past decade, evidence has accumulated that human immunodeficiency virus (HIV)-induced chronic immune activation drives progression to AIDS. Studies among different monkey species have shown that the difference between pathological and non-pathological infection is determined by the response of the immune system to the virus, rather than its cytopathicity. Here we review the current understanding of the various mechanisms driving chronic immune activation in HIV infection, the cell types involved, its effects on HIV-specific immunity, and how persistent inflammation may cause AIDS and the wide spectrum of non-AIDS related pathology. We argue that therapeutic relief of inflammation may be beneficial to delay HIV-disease progression and to reduce non-AIDS related pathological side effects of HIV-induced chronic immune stimulation.
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Affiliation(s)
- Frank Miedema
- Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Mette D. Hazenberg
- Department of Internal Medicine and Hematology, Academic Medical Center, Amsterdam, Netherlands
| | - Kiki Tesselaar
- Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Debbie van Baarle
- Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - José A. M. Borghans
- Department of Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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40
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Abstract
PURPOSE OF REVIEW To discuss the recent major advances in the understanding of how host immune defenses contribute to HIV reservoir control. RECENT FINDINGS Immune control of HIV-1 reservoirs is a two-step process: viral replication activation from latent reservoirs followed by elimination of virus-expressing cells by the host. Environmental factors, such as pro-inflammatory type-I interferon, chemokines or cytokines, can facilitate HIV-1 replication, confer dormancy in CD4 cells or confer resistance to cytopathogenic effects of cytotoxic CD8 T cells. Therefore, they constitute a double-edged sword for immune control of HIV reservoirs. Concomitantly, adaptive immunity takes advantage of CD4 T-cell homeostatic mechanisms and can expose HIV-1 antigen-expressing cells to HIV-specific cytotoxic CD8 T cells, and limit virus spreading. These highly interconnected phenomena can lead to quasi-equilibrium between the HIV-1 reservoirs and host immune control that can serve as a model for the 'shock and kill' immune-based therapeutic strategies in play in the course of finding an HIV cure. SUMMARY Immune control of HIV reservoirs in CD4 T cells involves modulation of both HIV-1 latency and the continuous reseeding of the reservoir offering conceptual models that may advance HIV cure strategies.
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Bacchus C, Cheret A, Avettand-Fenoël V, Nembot G, Mélard A, Blanc C, Lascoux-Combe C, Slama L, Allegre T, Allavena C, Yazdanpanah Y, Duvivier C, Katlama C, Goujard C, Seksik BCP, Leplatois A, Molina JM, Meyer L, Autran B, Rouzioux C. A single HIV-1 cluster and a skewed immune homeostasis drive the early spread of HIV among resting CD4+ cell subsets within one month post-infection. PLoS One 2013; 8:e64219. [PMID: 23691172 PMCID: PMC3653877 DOI: 10.1371/journal.pone.0064219] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/10/2013] [Indexed: 12/30/2022] Open
Abstract
Optimizing therapeutic strategies for an HIV cure requires better understanding the characteristics of early HIV-1 spread among resting CD4+ cells within the first month of primary HIV-1 infection (PHI). We studied the immune distribution, diversity, and inducibility of total HIV-DNA among the following cell subsets: monocytes, peripheral blood activated and resting CD4 T cells, long-lived (naive [TN] and central-memory [TCM]) and short-lived (transitional-memory [TTM] and effector-memory cells [TEM]) resting CD4+T cells from 12 acutely-infected individuals recruited at a median 36 days from infection. Cells were sorted for total HIV-DNA quantification, phylogenetic analysis and inducibility, all studied in relation to activation status and cell signaling. One month post-infection, a single CCR5-restricted viral cluster was massively distributed in all resting CD4+ subsets from 88% subjects, while one subject showed a slight diversity. High levels of total HIV-DNA were measured among TN (median 3.4 log copies/million cells), although 10-fold less (p = 0.0005) than in equally infected TCM (4.5), TTM (4.7) and TEM (4.6) cells. CD3−CD4+ monocytes harbored a low viral burden (median 2.3 log copies/million cells), unlike equally infected resting and activated CD4+ T cells (4.5 log copies/million cells). The skewed repartition of resting CD4 subsets influenced their contribution to the pool of resting infected CD4+T cells, two thirds of which consisted of short-lived TTM and TEM subsets, whereas long-lived TN and TCM subsets contributed the balance. Each resting CD4 subset produced HIV in vitro after stimulation with anti-CD3/anti-CD28+IL-2 with kinetics and magnitude varying according to subset differentiation, while IL-7 preferentially induced virus production from long-lived resting TN cells. In conclusion, within a month of infection, a clonal HIV-1 cluster is massively distributed among resting CD4 T-cell subsets with a flexible inducibility, suggesting that subset activation and skewed immune homeostasis determine the conditions of viral dissemination and early establishment of the HIV reservoir.
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Affiliation(s)
- Charline Bacchus
- Pierre-and-Marie-Curie University Paris 06, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
| | - Antoine Cheret
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
- Infectious Diseases Department, Gustave Dron Hospital, Tourcoing, France
| | - Véronique Avettand-Fenoël
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
| | - Georges Nembot
- Epidemiology and Public Health Department, Inserm U1018, Le Kremlin-Bicêtre Hospital, Paris, France
| | - Adeline Mélard
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
| | - Catherine Blanc
- CyPS Flow Cytometry Platform, Pierre & Marie Curie University, Pitié-Salpêtrière Hospital, Paris, France
| | - Caroline Lascoux-Combe
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Saint-Louis Hospital, Paris, France
| | - Laurence Slama
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Tenon Hospital, Paris, France
| | - Thierry Allegre
- Department of Hematology, Aix-en-Provence Hospital, Aix-en-Provence, France
| | | | - Yazdan Yazdanpanah
- Infectious Diseases Department, Gustave Dron Hospital, Tourcoing, France
| | - Claudine Duvivier
- Pasteur Institute, Medical Center, Necker-Pasteur Infectious Diseases Center, Paris, France
| | - Christine Katlama
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France
| | - Cécile Goujard
- Internal Medicine and Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre Hospital, Paris, France
| | - Bao Chau Phung Seksik
- Infectious Diseases Department, Assistance Publique - Hôpitaux de Paris, Bichat Hospital, Paris, France
| | - Anne Leplatois
- Infectious Diseases Department, L’Archet Hospital, Nice, France
| | - Jean-Michel Molina
- Sorbonne Paris-Cité University, Institut National de la Santé et de la Recherche Médicale U941, Infectious Diseases Unit, Saint-Louis Hospital, Paris, France
| | - Laurence Meyer
- Epidemiology and Public Health Department, Inserm U1018, Le Kremlin-Bicêtre Hospital, Paris, France
| | - Brigitte Autran
- Pierre-and-Marie-Curie University Paris 06, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Laboratory Immunity and Infection UMR_S 945, F-75013, Paris, France
- * E-mail:
| | - Christine Rouzioux
- Paris-Descartes University, Sorbonne Paris-Cité, EA 3620, Virology Laboratory, Necker Enfants-Malades Hospital, Paris, France
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Abstract
PURPOSE OF REVIEW The persistence of HIV within infected CD4 T cells is a major obstacle to eradication, and assessment of the strategies to reduce HIV reservoirs is one of the major challenges. Measuring HIV reservoirs accurately will be necessary to assess those strategies. The objective of this review is to present the most recent studies that may help to define the best markers to measure HIV reservoirs. RECENT FINDINGS Recent findings have shown that multiple assays can be used to quantify the different analytes that reflect the HIV reservoirs. They have provided new insights, but lack of standardization has made cross-comparisons of data difficult. No single best assay for measuring HIV reservoirs has been identified and these assays often address different questions, such as the size of the reservoirs, the composition of the reservoirs, or the capacity of latent reservoirs to produce virus. A consensus on what values reflect robust conclusions will have to wait for the generation of additional results. SUMMARY In conclusion, there is a compelling need for investigators to optimize assays and share protocol reagents and specimens to permit the validation, comparison, and standardization of techniques. There is an important need for validated, high-throughput, sensitive, and accurate assays that can detect changes in HIV reservoir size in order to assess the impact of candidate therapies.
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Affiliation(s)
- Christine Rouzioux
- Department of Virology, Necker Hospital, Paris Descartes University, Paris-Sorbonne-Cité, Paris, France.
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Zaunders J, van Bockel D. Innate and Adaptive Immunity in Long-Term Non-Progression in HIV Disease. Front Immunol 2013; 4:95. [PMID: 23630526 PMCID: PMC3633949 DOI: 10.3389/fimmu.2013.00095] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 04/09/2013] [Indexed: 12/20/2022] Open
Abstract
Long-term non-progressors (LTNP) were identified after 10-15 years of the epidemic, and have been the subject of intense investigation ever since. In a small minority of cases, infection with nef/3'LTR deleted attenuated viral strains allowed control over viral replication. A common feature of LTNP is the readily detected proliferation of CD4 T-cells in vitro, in response to p24. In some cases, the responding CD4 T-cells have cytotoxic effector function and may target conserved p24 epitopes, similar to the CD8 T-cells described below. LTNP may also carry much lower HIV DNA burden in key CD4 subsets, presumably resulting from lower viral replication during primary infection. Some studies, but not others, suggest that LTNP have CD4 T-cells that are relatively resistant to HIV infection in vitro. One possible mechanism may involve up-regulation of the cell cycle regulator p21/waf in CD4 T-cells from LTNP. Delayed progression in Caucasian LTNP is also partly associated with heterozygosity of the Δ32 CCR5 allele, probably through decreased expression of CCR5 co-receptor on CD4 T-cells. However, in approximately half of Caucasian LTNP, two host genotypes, namely HLA-B57 and HLA-B27, are associated with viral control. Immunodominant CD8 T-cells from these individuals target epitopes in p24 that are highly conserved, and escape mutations have significant fitness costs to the virus. Furthermore, recent studies have suggested that these CD8 T-cells from LTNP, but not from HLA-B27 or HLA-B57 progressors, can cross-react with intermediate escape mutations, preventing full escape via compensatory mutations. Humoral immunity appears to play little part in LTNP subjects, since broadly neutralizing antibodies are rare, even amongst slow progressors. Recent genome-wide comparisons between LTNP and progressors have confirmed the HLA-B57, HLA-B27, and delta32 CCR5 allelic associations, plus indicated a role for HLA-C/KIR interactions, but have not revealed any new genotypes so far. Nevertheless, it is hoped that studying the mechanisms of intracellular restriction factors, such as the recently identified SAMHD1, will lead to a better understanding of non-progression.
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Affiliation(s)
- John Zaunders
- Centre for Applied Medical Research, St Vincent's Hospital Darlinghurst, NSW, Australia
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Early Gag immunodominance of the HIV-specific T-cell response during acute/early infection is associated with higher CD8+ T-cell antiviral activity and correlates with preservation of the CD4+ T-cell compartment. J Virol 2013; 87:7445-62. [PMID: 23616666 DOI: 10.1128/jvi.00865-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The important role of the CD8(+) T-cell response on HIV control is well established. Moreover, the acute phase of infection represents a proper scenario to delineate the antiviral cellular functions that best correlate with control. Here, multiple functional aspects (specificity, ex vivo viral inhibitory activity [VIA] and polyfunctionality) of the HIV-specific CD8(+) T-cell subset arising early after infection, and their association with disease progression markers, were examined. Blood samples from 44 subjects recruited within 6 months from infection (primary HIV infection [PHI] group), 16 chronically infected subjects, 11 elite controllers (EC), and 10 healthy donors were obtained. Results indicated that, although Nef dominated the anti-HIV response during acute/early infection, a higher proportion of early anti-Gag T cells correlated with delayed progression. Polyfunctional HIV-specific CD8(+) T cells were detected at early time points but did not associate with virus control. Conversely, higher CD4(+) T-cell set points were observed in PHI subjects with higher HIV-specific CD8(+) T-cell VIA at baseline. Importantly, VIA levels correlated with the magnitude of the anti-Gag cellular response. The advantage of Gag-specific cells may result from their enhanced ability to mediate lysis of infected cells (evidenced by a higher capacity to degranulate and to mediate VIA) and to simultaneously produce IFN-γ. Finally, Gag immunodominance was associated with elevated plasma levels of interleukin 2 (IL-2) and macrophage inflammatory protein 1β (MIP-1β). All together, this study underscores the importance of CD8(+) T-cell specificity in the improved control of disease progression, which was related to the capacity of Gag-specific cells to mediate both lytic and nonlytic antiviral mechanisms at early time points postinfection.
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Abstract
OBJECTIVE To identify early determinants of HIV-1 disease progression, which could potentially enable individualized patient treatment, and provide correlates of progression applicable as reference phenotypes to evaluate breakthrough infections in vaccine development. DESIGN High-throughput technologies were employed to interrogate multiple parameters on cryopreserved, retrospective peripheral blood mononuclear cell (PBMC) samples from 51 individuals from São Paulo, Brazil, obtained within 1 year of diagnosing early Clade B HIV-1 infection. Fast Progressors, Slow Progressors, and Controllers were identified based on a 2-year clinical follow-up. METHODS Phenotypic and functional T-cell parameters were tested by flow cytometry and qPCR to identify potential early determinants of subsequent HIV-1 disease progression. RESULTS Major differences were observed between Controllers and Progressors, especially in cell-associated viral load (CAVL), the differentiation pattern and CD38 expression of CD8 T cells, and the cytokine pattern and activation phenotype of HIV-1-specific CD8 T cells. Despite remarkably few other differences between the two Progressor groups, the CAVL had predictive power independent of plasma viral load. CONCLUSION Analysis of three parameters (% CD38 CD8 T cells, total CAVL, % CCR5 CD8 T cells) was sufficient to predict subsequent disease progression (P < 0.001). Use of such prognostic correlates may be crucial when early CD4 T-cell counts and plasma viral load levels fail to discriminate among groups with differing subsequent clinical progression.
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46
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Sáez-Cirión A, Bacchus C, Hocqueloux L, Avettand-Fenoel V, Girault I, Lecuroux C, Potard V, Versmisse P, Melard A, Prazuck T, Descours B, Guergnon J, Viard JP, Boufassa F, Lambotte O, Goujard C, Meyer L, Costagliola D, Venet A, Pancino G, Autran B, Rouzioux C. Post-treatment HIV-1 controllers with a long-term virological remission after the interruption of early initiated antiretroviral therapy ANRS VISCONTI Study. PLoS Pathog 2013; 9:e1003211. [PMID: 23516360 PMCID: PMC3597518 DOI: 10.1371/journal.ppat.1003211] [Citation(s) in RCA: 803] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/09/2013] [Indexed: 02/06/2023] Open
Abstract
Combination antiretroviral therapy (cART) reduces HIV-associated morbidities and mortalities but cannot cure the infection. Given the difficulty of eradicating HIV-1, a functional cure for HIV-infected patients appears to be a more reachable short-term goal. We identified 14 HIV patients (post-treatment controllers [PTCs]) whose viremia remained controlled for several years after the interruption of prolonged cART initiated during the primary infection. Most PTCs lacked the protective HLA B alleles that are overrepresented in spontaneous HIV controllers (HICs); instead, they carried risk-associated HLA alleles that were largely absent among the HICs. Accordingly, the PTCs had poorer CD8+ T cell responses and more severe primary infections than the HICs did. Moreover, the incidence of viral control after the interruption of early antiretroviral therapy was higher among the PTCs than has been reported for spontaneous control. Off therapy, the PTCs were able to maintain and, in some cases, further reduce an extremely low viral reservoir. We found that long-lived HIV-infected CD4+ T cells contributed poorly to the total resting HIV reservoir in the PTCs because of a low rate of infection of naïve T cells and a skewed distribution of resting memory CD4+ T cell subsets. Our results show that early and prolonged cART may allow some individuals with a rather unfavorable background to achieve long-term infection control and may have important implications in the search for a functional HIV cure.
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Affiliation(s)
- Asier Sáez-Cirión
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, Paris, France
| | - Charline Bacchus
- Université Pierre et Marie Curie, INSERM UMR-S 945 Immunité et Infection, Hôpital Pitié-Salpêtrière, Paris, France
| | - Laurent Hocqueloux
- Centre Hospitalier Régional d'Orléans, Service des Maladies Infectieuses et Tropicales, Orléans, France
| | - Véronique Avettand-Fenoel
- AP-HP, CHU Necker-Enfants Malades, Laboratoire de Virologie, Paris, France
- EA 3620, Université Paris-Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Girault
- INSERM U1012, Université Paris-Sud 11, Le Kremlin Bicêtre, France
| | - Camille Lecuroux
- INSERM U1012, Université Paris-Sud 11, Le Kremlin Bicêtre, France
| | - Valerie Potard
- UPMC Univ Paris 06, UMR_S 943, Paris, France
- INSERM, U943, Paris, France
| | - Pierre Versmisse
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, Paris, France
| | - Adeline Melard
- AP-HP, CHU Necker-Enfants Malades, Laboratoire de Virologie, Paris, France
| | - Thierry Prazuck
- Centre Hospitalier Régional d'Orléans, Service des Maladies Infectieuses et Tropicales, Orléans, France
| | - Benjamin Descours
- Université Pierre et Marie Curie, INSERM UMR-S 945 Immunité et Infection, Hôpital Pitié-Salpêtrière, Paris, France
| | - Julien Guergnon
- Université Pierre et Marie Curie, INSERM UMR-S 945 Immunité et Infection, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Paul Viard
- EA 3620, Université Paris-Descartes, Sorbonne Paris Cité, Paris, France
- AP-HP, Hôtel-Dieu, Paris, France
| | - Faroudy Boufassa
- INSERM U1018, Université Paris-Sud 11, Le Kremlin Bicêtre, France
| | - Olivier Lambotte
- INSERM U1012, Université Paris-Sud 11, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Service de Médecine Interne, Le Kremlin Bicêtre, France
| | - Cécile Goujard
- INSERM U1018, Université Paris-Sud 11, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Service de Médecine Interne, Le Kremlin Bicêtre, France
| | - Laurence Meyer
- INSERM U1018, Université Paris-Sud 11, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Département d'épidémiologie, Le Kremlin Bicêtre, France
| | - Dominique Costagliola
- UPMC Univ Paris 06, UMR_S 943, Paris, France
- INSERM, U943, Paris, France
- AP-HP, Groupe hospitalier Pitié-Salpétrière, Service de Maladies Infectieuses et Tropicales, Paris, France
| | - Alain Venet
- INSERM U1012, Université Paris-Sud 11, Le Kremlin Bicêtre, France
| | - Gianfranco Pancino
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, Paris, France
| | - Brigitte Autran
- Université Pierre et Marie Curie, INSERM UMR-S 945 Immunité et Infection, Hôpital Pitié-Salpêtrière, Paris, France
| | - Christine Rouzioux
- AP-HP, CHU Necker-Enfants Malades, Laboratoire de Virologie, Paris, France
- EA 3620, Université Paris-Descartes, Sorbonne Paris Cité, Paris, France
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Roche S, El Garch H, Brunet S, Poulet H, Iwaz J, Ecochard R, Vanhems P. Diversity of trends of viremia and T-cell markers in experimental acute feline immunodeficiency virus infection. PLoS One 2013; 8:e56135. [PMID: 23409138 PMCID: PMC3567045 DOI: 10.1371/journal.pone.0056135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/05/2013] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE The early events of human immunodeficiency virus infection seem critical for progression toward disease and antiretroviral therapy initiation. We wanted to clarify some still unknown prognostic relationships between inoculum size and changes in various immunological and virological markers. Feline immunodeficiency virus infection could be a helpful model. METHODS Viremia and T-cell markers (number of CD4, CD8, CD8β(low)CD62L(neg) T-cells, CD4/CD8 ratio, and percentage of CD8β(low)CD62L(neg) cells among CD8 T-cells) were measured over 12 weeks in 102 cats infected with different feline immunodeficiency virus strains and doses. Viremia and T-cell markers trajectory groups were determined and the dose-response relationships between inoculum titres and trajectory groups investigated. RESULTS Cats given the same inoculum showed different patterns of changes in viremia and T-cell markers. A statistically significant positive dose-response relationship was observed between inoculum titre and i) viremia trajectory-groups (r = 0.80, p<0.01), ii) CD8β(low)CD62L(neg) cell-fraction trajectory-groups (r = 0.56, p<0.01). Significant correlations were also found between viremia and the CD4/CD8 ratio and between seven out of ten T-cell markers. CONCLUSIONS In cats, the infectious dose determines early kinetics of viremia and initial CD8+ T-cell activation. An expansion of the CD8β(low)CD62L(neg) T-cells might be an early predictor of progression toward disease. The same might be expected in humans but needs confirmation.
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Affiliation(s)
- Sylvain Roche
- Service de Biostatistique, Hospices Civils de Lyon, Lyon, France.
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48
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HIV infection and acquired immunodeficiency syndrome. Clin Immunol 2013. [DOI: 10.1016/b978-0-7234-3691-1.00053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Aghaeepour N, Jalali A, O’Neill K, Chattopadhyay PK, Roederer M, Hoos HH, Brinkman RR. RchyOptimyx: cellular hierarchy optimization for flow cytometry. Cytometry A 2012; 81:1022-30. [PMID: 23044634 PMCID: PMC3726344 DOI: 10.1002/cyto.a.22209] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/07/2012] [Accepted: 09/05/2012] [Indexed: 12/19/2022]
Abstract
Analysis of high-dimensional flow cytometry datasets can reveal novel cell populations with poorly understood biology. Following discovery, characterization of these populations in terms of the critical markers involved is an important step, as this can help to both better understand the biology of these populations and aid in designing simpler marker panels to identify them on simpler instruments and with fewer reagents (i.e., in resource poor or highly regulated clinical settings). However, current tools to design panels based on the biological characteristics of the target cell populations work exclusively based on technical parameters (e.g., instrument configurations, spectral overlap, and reagent availability). To address this shortcoming, we developed RchyOptimyx (cellular hieraRCHY OPTIMization), a computational tool that constructs cellular hierarchies by combining automated gating with dynamic programming and graph theory to provide the best gating strategies to identify a target population to a desired level of purity or correlation with a clinical outcome, using the simplest possible marker panels. RchyOptimyx can assess and graphically present the trade-offs between marker choice and population specificity in high-dimensional flow or mass cytometry datasets. We present three proof-of-concept use cases for RchyOptimyx that involve 1) designing a panel of surface markers for identification of rare populations that are primarily characterized using their intracellular signature; 2) simplifying the gating strategy for identification of a target cell population; 3) identification of a non-redundant marker set to identify a target cell population.
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Affiliation(s)
- Nima Aghaeepour
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Adrin Jalali
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Kieran O’Neill
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Mario Roederer
- Vaccine Research Center, National Institute of Health, Bethesda, Massachusetts
| | - Holger H. Hoos
- Department of Computer Science, University of British Columbia, British Columbia, Canada
| | - Ryan R. Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, British Columbia, Canada
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50
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Yang X, Jiao YM, Wang R, Ji YX, Zhang HW, Zhang YH, Chen DX, Zhang T, Wu H. High CCR5 density on central memory CD4+ T cells in acute HIV-1 infection is mostly associated with rapid disease progression. PLoS One 2012. [PMID: 23185351 PMCID: PMC3504013 DOI: 10.1371/journal.pone.0049526] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
CD4+ central memory T cells play a critical role in the pathogenesis of simian immunodeficiency virus disease, and the CCR5 density on the surface of CD4 T cells is an important factor in human immunodeficiency virus (HIV)-1 disease progression. We hypothesized that quantifying central memory cells and CCR5 expression in the early stages of HIV-infection could provide useful prognostic information. We enrolled two different groups of acute HIV-infected subjects. One group progressed to CD4 T cell numbers below 250 cells/µl within 2 years (CD4 Low group), while the other group maintained CD4 cell counts above 450 cells/µl over 2 years (CD4 High group). We compared the CCR5 levels and percentage of CD4 subsets between the two groups during the 1st year of HIV infection. We found no differences between the two groups regarding the percentage of naïve, central memory and effector memory subsets of CD4 cells during the 1st year of HIV-1 infection. CCR5 levels on CD4+ CM subset was higher in the CD4 Low group compared with the CD4 High group during the 1st year of HIV-1 infection. High CCR5 levels on CD4 central memory cells in acute HIV infection are mostly associated with rapid disease progression. Our data suggest that low CCR5 expression on CD4 central memory cells protects CD4 cells from direct virus infection and favors the preservation of CD4+ T cell homeostasis.
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Affiliation(s)
- Xue Yang
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
| | - Yan-mei Jiao
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
- * E-mail: (HW); (Y. Jiao)
| | - Rui Wang
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
| | - Yun-xia Ji
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
| | - Hong-wei Zhang
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
| | - Yong-hong Zhang
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
| | - De-xi Chen
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
| | - Tong Zhang
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
| | - Hao Wu
- Center for Infectious Diseases, Beijing You’an Hospital, Capital Medical University, Beijng, China
- * E-mail: (HW); (Y. Jiao)
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