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Li K, Chen H, Li J, Feng Y, Liang S, Rashid A, Liu M, Li S, Chu Q, Ruan Y, Xing H, Lan G, Qiao W, Shao Y. Distinct genetic clusters in HIV-1 CRF01_AE-infected patients induced variable degrees of CD4 + T-cell loss. mBio 2024; 15:e0334923. [PMID: 38385695 PMCID: PMC10936439 DOI: 10.1128/mbio.03349-23] [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: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 02/23/2024] Open
Abstract
CRF01_AE strains have been shown to form multiple transmission clusters in China, and some clusters have disparate pathogenicity in Chinese men who have sex with men. This study focused on other CRF01_AE clusters prevalent in heterosexual populations. The CD4+ T-cell counts from both cross-section data in National HIV Molecular Epidemiology Survey and seropositive cohort data were used to evaluate the pathogenicity of the CRF01_AE clusters and other HIV-1 sub-types. Their mechanisms of pathogenicity were evaluated by co-receptor tropisms, predicted by genotyping and confirmed with virus isolate phenotyping, as well as inflammation parameters. Our research elucidated that individuals infected with CRF01_AE clusters 1 and 2 exhibited significantly lower baseline CD4+ T-cell counts and greater CD4+ T-cell loss in cohort follow-up, compared with other HIV-1 sub-types and CRF01_AE clusters. The increased pathogenesis of cluster 1 or 2 was associated with higher CXCR4 tropisms, higher inflammation/immune activation, and increased pyroptosis. The protein structure modeling analysis revealed that the envelope V3 loop of clusters 1 and 2 viruses is favorable for CXCR4 co-receptor usage. Imbedded with the most mutating reverse transcriptase, HIV-1 is one of the most variable viruses. CRF01_AE clusters 1 and 2 have been found to have evolved into more virulent strains in regions with predominant heterosexual infections. The virulent strains increased the pressure for early diagnosis and treatment in HIV patients. To save more lives, HIV-1 surveillance systems should be upgraded from serology and genotyping to phenotyping, which could support precision interventions for those infected by virulent viruses. IMPORTANCE Retroviruses swiftly adapt, employing error-prone enzymes for genetic and phenotypic evolution, optimizing survival strategies, and enhancing virulence levels. HIV-1 CRF01_AE has persistently undergone adaptive selection, and cluster 1 and 2 infections display lower counts and fast loss of CD4+ T cells than other HIV-1 sub-types and CRF01_AE clusters. Its mechanisms are associated with increased CXCR4 tropism due to an envelope structure change favoring a tropism shift from CCR5 to CXCR4, thereby shaping viral phenotype features and impacting pathogenicity. This underscores the significance of consistently monitoring HIV-1 genetic evolution and phenotypic transfer to see whether selection bias across risk groups alters the delicate balance of transmissible versus toxic trade-offs, since virulent strains such as CRF01_AE clusters 1 and 2 could seriously compromise the efficacy of antiviral treatment. Only through such early warning and diagnostic services can precise antiviral treatments be administered to those infected with more virulent HIV-1 strains.
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Affiliation(s)
- Kang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huanhuan Chen
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Jianjun Li
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Yi Feng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shujia Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Abdur Rashid
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Meiliang Liu
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Sisi Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuhua Ruan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guanghua Lan
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Wentao Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yiming Shao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Zhejiang University, Hangzhou, China
- Changping Laboratory, Beijing, China
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Bose D, Deb Adhikary N, Xiao P, Rogers KA, Ferrell DE, Cheng-Mayer C, Chang TL, Villinger F. SHIV-C109p5 NHP induces rapid disease progression in elderly macaques with extensive GI viral replication. J Virol 2024; 98:e0165223. [PMID: 38299866 PMCID: PMC10878093 DOI: 10.1128/jvi.01652-23] [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: 10/23/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
CCR5-tropic simian/human immunodeficiency viruses (SHIV) with clade C transmitted/founder envelopes represent a critical tool for the investigation of HIV experimental vaccines and microbicides in nonhuman primates, although many such isolates lead to spontaneous viral control post infection. Here, we generated a high-titer stock of pathogenic SHIV-C109p5 by serial passage in two rhesus macaques (RM) and tested its virulence in aged monkeys. The co-receptor usage was confirmed before infecting five geriatric rhesus macaques (four female and one male). Plasma viral loads were monitored by reverse transcriptase-quantitative PCR (RT-qPCR), cytokines by multiplex analysis, and biomarkers of gastrointestinal damage by enzyme-linked immunosorbent assay. Antibodies and cell-mediated responses were also measured. Viral dissemination into tissues was determined by RNAscope. Intravenous SHIV-C109p5 infection of aged RMs leads to high plasma viremia and rapid disease progression; rapid decrease in CD4+ T cells, CD4+CD8+ T cells, and plasmacytoid dendritic cells; and wasting necessitating euthanasia between 3 and 12 weeks post infection. Virus-specific cellular immune responses were detected only in the two monkeys that survived 4 weeks post infection. These were Gag-specific TNFα+CD8+, MIP1β+CD4+, Env-specific IFN-γ+CD4+, and CD107a+ T cell responses. Four out of five monkeys had elevated intestinal fatty acid binding protein levels at the viral peak, while regenerating islet-derived protein 3α showed marked increases at later time points in the three animals surviving the longest, suggesting gut antimicrobial peptide production in response to microbial translocation post infection. Plasma levels of monocyte chemoattractant protein-1, interleukin-15, and interleukin-12/23 were also elevated. Viral replication in gut and secondary lymphoid tissues was extensive.IMPORTANCESimian/human immunodeficiency viruses (SHIV) are important reagents to study prevention of virus acquisition in nonhuman primate models of HIV infection, especially those representing transmitted/founder (T/F) viruses. However, many R5-tropic SHIV have limited fitness in vivo leading to many monkeys spontaneously controlling the virus post acute infection. Here, we report the generation of a pathogenic SHIV clade C T/F stock by in vivo passage leading to sustained viral load set points, a necessity to study pathogenicity. Unexpectedly, administration of this SHIV to elderly rhesus macaques led to extensive viral replication and fast disease progression, despite maintenance of a strict R5 tropism. Such age-dependent rapid disease progression had previously been reported for simian immunodeficiency virus but not for R5-tropic SHIV infections.
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Affiliation(s)
- Deepanwita Bose
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, Louisiana, USA
| | - Nihar Deb Adhikary
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, Louisiana, USA
| | - Peng Xiao
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, Louisiana, USA
| | - Kenneth A. Rogers
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, Louisiana, USA
| | - Douglas E. Ferrell
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, Louisiana, USA
| | | | - Theresa L. Chang
- The Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Francois Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, Louisiana, USA
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Chvatal-Medina M, Lopez-Guzman C, Diaz FJ, Gallego S, Rugeles MT, Taborda NA. Molecular mechanisms by which the HIV-1 latent reservoir is established and therapeutic strategies for its elimination. Arch Virol 2023; 168:218. [PMID: 37530901 DOI: 10.1007/s00705-023-05800-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/12/2023] [Indexed: 08/03/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) reservoir, composed of cells harboring the latent, integrated virus, is not eliminated by antiretroviral therapy. It therefore represents a significant barrier to curing the infection. The biology of HIV-1 reservoirs, the mechanisms of their persistence, and effective strategies for their eradication are not entirely understood. Here, we review the molecular mechanisms by which HIV-1 reservoirs develop, the cells and compartments where the latent virus resides, and advancements in curative therapeutic strategies. We first introduce statistics and relevant data on HIV-1 infection, aspects of pathogenesis, the role of antiretroviral therapy, and the general features of the latent HIV reservoir. Then, the article is built on three main pillars: The molecular mechanisms related to latency, the different strategies for targeting the reservoir to obtain a cure, and the current progress in immunotherapy to counteract said reservoirs.
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Affiliation(s)
- Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Carolina Lopez-Guzman
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Francisco J Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Salomon Gallego
- Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Natalia A Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
- Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia.
- Universidad Cooperativa de Colombia, Campus Medellin, Envigado, Colombia.
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Johnson MM, Jones CE, Clark DN. The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles. Viruses 2022; 15:107. [PMID: 36680147 PMCID: PMC9861436 DOI: 10.3390/v15010107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.
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Affiliation(s)
- Madison M. Johnson
- Department of Microbiology, Weber State University, Ogden, UT 84408, USA
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5
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Rudd H, Toborek M. Pitfalls of Antiretroviral Therapy: Current Status and Long-Term CNS Toxicity. Biomolecules 2022; 12:biom12070894. [PMID: 35883450 PMCID: PMC9312798 DOI: 10.3390/biom12070894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
HIV can traverse the BBB using a Trojan horse-like mechanism. Hidden within infected immune cells, HIV can infiltrate the highly safeguarded CNS and propagate disease. Once integrated within the host genome, HIV becomes a stable provirus, which can remain dormant, evade detection by the immune system or antiretroviral therapy (ART), and result in rebound viraemia. As ART targets actively replicating HIV, has low BBB penetrance, and exposes patients to long-term toxicity, further investigation into novel therapeutic approaches is required. Viral proteins can be produced by latent HIV, which may play a synergistic role alongside ART in promoting neuroinflammatory pathophysiology. It is believed that the ability to specifically target these proviral reservoirs would be a vital driving force towards a cure for HIV infection. A novel drug design platform, using the in-tandem administration of several therapeutic approaches, can be used to precisely target the various components of HIV infection, ultimately leading to the eradication of active and latent HIV and a functional cure for HIV. The aim of this review is to explore the pitfalls of ART and potential novel therapeutic alternatives.
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Affiliation(s)
- Harrison Rudd
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Michal Toborek
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
- Institute of Physiotherapy and Health Sciences, The Jerzy Kukuczka Academy of Physical Education, 40-065 Katowice, Poland
- Correspondence: ; Tel.: +1-(305)-243-0230
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6
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Mohamed H, Gurrola T, Berman R, Collins M, Sariyer IK, Nonnemacher MR, Wigdahl B. Targeting CCR5 as a Component of an HIV-1 Therapeutic Strategy. Front Immunol 2022; 12:816515. [PMID: 35126374 PMCID: PMC8811197 DOI: 10.3389/fimmu.2021.816515] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Globally, human immunodeficiency virus type 1 (HIV-1) infection is a major health burden for which successful therapeutic options are still being investigated. Challenges facing current drugs that are part of the established life-long antiretroviral therapy (ART) include toxicity, development of drug resistant HIV-1 strains, the cost of treatment, and the inability to eradicate the provirus from infected cells. For these reasons, novel anti-HIV-1 therapeutics that can prevent or eliminate disease progression including the onset of the acquired immunodeficiency syndrome (AIDS) are needed. While development of HIV-1 vaccination has also been challenging, recent advancements demonstrate that infection of HIV-1-susceptible cells can be prevented in individuals living with HIV-1, by targeting C-C chemokine receptor type 5 (CCR5). CCR5 serves many functions in the human immune response and is a co-receptor utilized by HIV-1 for entry into immune cells. Therapeutics targeting CCR5 generally involve gene editing techniques including CRISPR, CCR5 blockade using antibodies or antagonists, or combinations of both. Here we review the efficacy of these approaches and discuss the potential of their use in the clinic as novel ART-independent therapies for HIV-1 infection.
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Affiliation(s)
- Hager Mohamed
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore Gurrola
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Berman
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Mackenzie Collins
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, School of Medicine, Temple University, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- *Correspondence: Brian Wigdahl,
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7
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Sherpa C, Rausch JW, Le Grice SFJ. HIV Genetic Diversity - Superpower of a Formidable Virus. Curr HIV Res 2021; 18:69-73. [PMID: 32223727 DOI: 10.2174/1570162x1802200311104204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Chringma Sherpa
- Basic Research Laboratory Center for Cancer Research National Cancer Institute National Institute of Health Frederick, Maryland, 21702, United States
| | - Jason W Rausch
- Basic Research Laboratory Center for Cancer Research National Cancer Institute National Institute of Health Frederick, MD, 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory Center for Cancer Research National Cancer Institute National Institute of Health Frederick, MD, 21702, United States
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8
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Winichakoon P, Tongjai S. The Emerging of CRF01_AE: A Clinical Story and Future HIV/AIDS Situation in Thailand. Curr HIV Res 2021; 18:74-84. [PMID: 31995011 DOI: 10.2174/1570162x18666200129160723] [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: 10/09/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 11/22/2022]
Abstract
The HIV epidemic in Thailand in the 1980's compromised the country's socio-economic development. The epidemic first became evident in the community of men with male sexual partners (MSM), and subsequently spread to intravenous drug users (IVDU), female commercial sex workers (CSW) and their male clients, and, ultimately, to their partners and children. The HIV epidemic has devastated the country's working-age population. The extensive negative impact and social stigma associated with the disease do not only have an impact on the victims of HIV but also on their descendants and relatives. An epicenter of the HIV epidemic has been in the northern provinces of Thailand. An HIV-1 subtype CRF01_AE, a complex chimeric virus composed of both A and E subtypes, is prevalent in Northern Thailand. The virus has quickly become a predominant viral strain circulating in Thailand, other neighboring Southeast Asian countries, and China as well as some other countries throughout the world. The epidemiology, evolution, and biology of CRF01_AE offer a unique model for further scientific investigations which would advance the knowledge of and curative strategies against HIV. In addition, Thailand has developed suitable national guidelines on HIV/AIDS treatment and prevention in order to control the epidemic. Effective antiretroviral drugs are, therefore, able to be made available to those who live with HIV. The national surveillance system has also been effective. The great efforts and resources which Thailand has dedicated to the fight against the epidemic have eventually paid off. In 2010, a plan was proposed to eliminate mother-to-child HIV transmission and Thailand has become the first country to be effective in this objective. Thailand therefore has become recognized as being the global leader in HIV prevention and treatment. The experience which Thailand has gained from the past and the current research and management strategies of the HIV epidemic has prepared the country for emerging strains of HIV-1 in the future.
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Affiliation(s)
- Poramed Winichakoon
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Tambon Sriphum, Amphoe Muang, Thailand
| | - Siripong Tongjai
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Tambon Sriphum, Amphoe Muang, Thailand
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9
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Yandrapally S, Mohareer K, Arekuti G, Vadankula GR, Banerjee S. HIV co-receptor-tropism: cellular and molecular events behind the enigmatic co-receptor switching. Crit Rev Microbiol 2021; 47:499-516. [PMID: 33900141 DOI: 10.1080/1040841x.2021.1902941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recognition of cell-surface receptors and co-receptors is a crucial molecular event towards the establishment of HIV infection. HIV exists as several variants that differentially recognize the principal co-receptors, CCR5 and CXCR4, in different cell types, known as HIV co-receptor-tropism. The relative levels of these variants dynamically adjust to the changing host selection pressures to infect a vast repertoire of cells in a stage-specific manner. HIV infection sets in through immune cells such as dendritic cells, macrophages, and T-lymphocytes in the acute stage, while a wide range of other cells, including astrocytes, glial cells, B-lymphocytes, and epithelial cells, are infected during chronic stages. A change in tropism occurs during the transition from acute to a chronic phase, termed as co-receptor switching marked by a change in disease severity. The cellular and molecular events leading to co-receptor switching are poorly understood. This review aims to collate our present understanding of the dynamics of HIV co-receptor-tropism vis-à-vis host and viral factors, highlighting the cellular and molecular events involved therein. We present the possible correlations between virus entry, cell tropism, and co-receptor switching, speculating its consequences on disease progression, and proposing new scientific pursuits to help in an in-depth understanding of HIV biology.
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Affiliation(s)
| | | | - Geethika Arekuti
- Department of Biochemistry, University of Hyderabad, Hyderabad, India
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Differential recognition of HIV-stimulated IL-1β and IL-18 secretion through NLR and NAIP signalling in monocyte-derived macrophages. PLoS Pathog 2021; 17:e1009417. [PMID: 33861800 PMCID: PMC8109768 DOI: 10.1371/journal.ppat.1009417] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 05/10/2021] [Accepted: 02/22/2021] [Indexed: 12/29/2022] Open
Abstract
Macrophages are important drivers of pathogenesis and progression to AIDS in HIV infection. The virus in the later phases of the infection is often predominantly macrophage-tropic and this tropism contributes to a chronic inflammatory and immune activation state that is observed in HIV patients. Pattern recognition receptors of the innate immune system are the key molecules that recognise HIV and mount the inflammatory responses in macrophages. The innate immune response against HIV-1 is potent and elicits caspase-1-dependent pro-inflammatory cytokine production of IL-1β and IL-18. Although, NLRP3 has been reported as an inflammasome sensor dictating this response little is known about the pattern recognition receptors that trigger the “priming” signal for inflammasome activation, the NLRs involved or the HIV components that trigger the response. Using a combination of siRNA knockdowns in monocyte derived macrophages (MDMs) of different TLRs and NLRs as well as chemical inhibition, it was demonstrated that HIV Vpu could trigger inflammasome activation via TLR4/NLRP3 leading to IL-1β/IL-18 secretion. The priming signal is triggered via TLR4, whereas the activation signal is triggered by direct effects on Kv1.3 channels, causing K+ efflux. In contrast, HIV gp41 could trigger IL-18 production via NAIP/NLRC4, independently of priming, as a one-step inflammasome activation. NAIP binds directly to the cytoplasmic tail of HIV envelope protein gp41 and represents the first non-bacterial ligand for the NAIP/NLRC4 inflammasome. These divergent pathways represent novel targets to resolve specific inflammatory pathologies associated with HIV-1 infection in macrophages. It has been previously shown that inflammasome activation can be triggered during viral infection to produce the active cytokines IL-1β and IL-18. Our study represents a significant advance, as we now show that in fact there are distinct NLR inflammasome complexes and viral ligands for IL-1β secretion (Vpu) compared to IL-18 secretion (gp41) in response to HIV-1. Most importantly, we show that the HIV envelope protein gp41 represents the first non-bacterial ligand for the assembly of the NAIP/NLRC4 inflammasome. HIV gp41 is a viroporin, and thus our data demonstrates for the first time that the NAIP/NLRC4 inflammasome assembles for all pore-forming proteins, irrespective of whether they have a viral or bacterial origin. This is critical for the host antiviral response and has broad implications for innate immunity in general.
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11
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Existence of Replication-Competent Minor Variants with Different Coreceptor Usage in Plasma from HIV-1-Infected Individuals. J Virol 2020; 94:JVI.00193-20. [PMID: 32295903 DOI: 10.1128/jvi.00193-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/04/2020] [Indexed: 12/20/2022] Open
Abstract
Cell entry by HIV-1 is mediated by its principal receptor, CD4, and a coreceptor, either CCR5 or CXCR4, with viral envelope glycoprotein gp120. Generally, CCR5-using HIV-1 variants, called R5, predominate over most of the course of infection, while CXCR4-using HIV-1 variants (variants that utilize both CCR5 and CXCR4 [R5X4, or dual] or CXCR4 alone [X4]) emerge at late-stage infection in half of HIV-1-infected individuals and are associated with disease progression. Although X4 variants also appear during acute-phase infection in some cases, these variants apparently fall to undetectable levels thereafter. In this study, replication-competent X4 variants were isolated from plasma of drug treatment-naive individuals infected with HIV-1 strain CRF01_AE, which dominantly carries viral RNA (vRNA) of R5 variants. Next-generation sequencing (NGS) confirmed that sequences of X4 variants were indeed present in plasma vRNA from these individuals as a minor population. On the other hand, in one individual with a mixed infection in which X4 variants were dominant, only R5 replication-competent variants were isolated from plasma. These results indicate the existence of replication-competent variants with different coreceptor usage as minor populations.IMPORTANCE The coreceptor switch of HIV-1 from R5 to CXCR4-using variants (R5X4 or X4) has been observed in about half of HIV-1-infected individuals at late-stage infection with loss of CD4 cell count and disease progression. However, the mechanisms that underlie the emergence of CXCR4-using variants at this stage are unclear. In the present study, CXCR4-using X4 variants were isolated from plasma samples of HIV-1-infected individuals that dominantly carried vRNA of R5 variants. The sequences of the X4 variants were detected as a minor population using next-generation sequencing. Taken together, CXCR4-using variants at late-stage infection are likely to emerge when replication-competent CXCR4-using variants are maintained as a minor population during the course of infection. The present study may support the hypothesis that R5-to-X4 switching is mediated by the expansion of preexisting X4 variants in some cases.
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de Carvalho Lima EN, Lima RSA, Arif MS, Piqueira JRC, Diaz RS. Evolutive Temporal Footprint of an HIV-1 Envelope Protein in an Epidemiologically Linked Cluster. Open AIDS J 2020. [DOI: 10.2174/1874613602014010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
The C2V3C3 region of gp 120, encoded by the HIV-1 envelope gene (env), is an important antigenic target, a key determinant for viral evolution and essential for determining epitopes for vaccines.
Methods:
The relationships among genetic sequence diversity, selective pressure, constraints on HIV-1 envelope protein were explored and also correlated this analysis with information entropy; hypermutation; HIV tropism; CD4+ T cell counts or HIV viral load. A total of 179 HIV-1 C2V3C3 sequences derived from cell-free plasma were used, determined from serial samples, in four epidemiologically linked individuals (one infected blood donor, two transfusion recipients and a sexual partner infected by one of the recipients) over a maximum period of 8 years. This study is important because it considers the analysis of patterns in genomic sequences, without drugs and over time.
Results:
A temporal relationship among information entropy, hypermutation, tropism switch, viral load, and CD4+ T cell count was determined. Changes in information entropy were time-dependent, and an increase in entropy was observed in the C2V3C3 region at amino acids G313 and F317-I320 (related to the GPGR-motif and coreceptor tropism), and at amino acids A281 in C2 and A346 in C3, related to immune escape.
Conclusion:
The increase of information entropy over time was correlated with hypermutation and the emergence of nonR5- strains, which are both associated with more variable genomes.
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Meås HZ, Haug M, Beckwith MS, Louet C, Ryan L, Hu Z, Landskron J, Nordbø SA, Taskén K, Yin H, Damås JK, Flo TH. Sensing of HIV-1 by TLR8 activates human T cells and reverses latency. Nat Commun 2020; 11:147. [PMID: 31919342 PMCID: PMC6952430 DOI: 10.1038/s41467-019-13837-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/02/2019] [Indexed: 12/31/2022] Open
Abstract
During HIV infection, cell-to-cell transmission results in endosomal uptake of the virus by target CD4+ T cells and potential exposure of the viral ssRNA genome to endosomal Toll-like receptors (TLRs). TLRs are instrumental in activating inflammatory responses in innate immune cells, but their function in adaptive immune cells is less well understood. Here we show that synthetic ligands of TLR8 boosted T cell receptor signaling, resulting in increased cytokine production and upregulation of surface activation markers. Adjuvant TLR8 stimulation, but not TLR7 or TLR9, further promoted T helper cell differentiation towards Th1 and Th17. In addition, we found that endosomal HIV induced cytokine secretion from CD4+ T cells in a TLR8-specific manner. TLR8 engagement also enhanced HIV-1 replication and potentiated the reversal of latency in patient-derived T cells. The adjuvant TLR8 activity in T cells can contribute to viral dissemination in the lymph node and low-grade inflammation in HIV patients. In addition, it can potentially be exploited for therapeutic targeting and vaccine development.
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Affiliation(s)
- Hany Zekaria Meås
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Infectious Diseases, St. Olavs Hospital, Trondheim, Norway
| | - Markus Haug
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Infectious Diseases, St. Olavs Hospital, Trondheim, Norway
| | - Marianne Sandvold Beckwith
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Claire Louet
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Liv Ryan
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Zhenyi Hu
- School of Pharmaceutical Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100082, Beijing, China.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Johannes Landskron
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Svein Arne Nordbø
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Medical Microbiology, St. Olavs Hospital, Trondheim, Norway
| | - Kjetil Taskén
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Cancer Immunology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Centre for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100082, Beijing, China
| | - Jan Kristian Damås
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Infectious Diseases, St. Olavs Hospital, Trondheim, Norway
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway. .,Department of Infectious Diseases, St. Olavs Hospital, Trondheim, Norway. .,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
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Abstract
Human Immunodeficiency Virus 1 (HIV-1) co-receptor usage, called tropism, is associated with disease progression towards AIDS. Furthermore, the recently developed and developing drugs against co-receptors CCR5 or CXCR4 open a new thought for HIV-1 therapy. Thus, knowledge about tropism is critical for illness diagnosis and regimen prescription. To improve tropism prediction accuracy, we developed two novel methods, the extreme gradient boosting based XGBpred and the hidden Markov model based HMMpred. Both XGBpred and HMMpred achieved higher specificities (72.56% and 72.09%) than the state-of-the-art methods Geno2pheno (61.6%) and G2p_str (68.60%) in a 10-fold cross validation test at the same sensitivity of 93.73%. Moreover, XGBpred had more outstanding performances (with AUCs 0.9483, 0.9464) than HMMpred (0.8829, 0.8774) on the Hivcopred and Newdb (created in this work) datasets containing larger proportions of hard-to-predict dual tropic samples in the X4-using tropic samples. Therefore, we recommend the use of our novel method XGBpred to predict tropism. The two methods and datasets are available via http://spg.med.tsinghua.edu.cn:23334/XGBpred/. In addition, our models identified that positions 5, 11, 13, 18, 22, 24, and 25 were correlated with HIV-1 tropism.
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15
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DeLeon O, Hodis H, O’Malley Y, Johnson J, Salimi H, Zhai Y, Winter E, Remec C, Eichelberger N, Van Cleave B, Puliadi R, Harrington RD, Stapleton JT, Haim H. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model. PLoS Biol 2017; 15:e2001549. [PMID: 28384158 PMCID: PMC5383018 DOI: 10.1371/journal.pbio.2001549] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 01/08/2023] Open
Abstract
The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties of variants expected to appear in the future. HIV-1 is the causative agent of the global AIDS pandemic. The envelope glycoproteins (Envs) of HIV-1 constitute a primary target for antibody-based vaccines. However, the diversity of Envs in the population limits the potential efficacy of this approach. Accurate estimates of the range of variants that currently infect patients and those expected to appear in the future will likely contribute to the design of population-targeted immunogens. We found that different properties (features) of Env have different propensities for small “fluctuations” in their values among viruses that infect patients at any given time point. This propensity of each feature for in-host variance, which we designate “volatility”, is conserved among patients. We apply this parameter to model the evolution of features (in patients and population) as a diffusion process driven by their “diffusion coefficients” (volatilities). Using volatilities measured from a few patient samples from the 1980s, we accurately predict properties of viruses that evolved in the population over the course of 30 years. The diffusion-based model described here efficiently captures evolution of phenotypes in biological systems controlled by a dominant random component.
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Affiliation(s)
- Orlando DeLeon
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hagit Hodis
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yunxia O’Malley
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jacklyn Johnson
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hamid Salimi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yinjie Zhai
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Elizabeth Winter
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Claire Remec
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Noah Eichelberger
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Brandon Van Cleave
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramya Puliadi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert D. Harrington
- Center for AIDS Research (CFAR) at the University of Washington, Seattle, Washington, United States of America
| | - Jack T. Stapleton
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Veterans Affairs Medical Center, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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16
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Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use. Sci Rep 2017; 7:42215. [PMID: 28186189 PMCID: PMC5301480 DOI: 10.1038/srep42215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/06/2017] [Indexed: 01/31/2023] Open
Abstract
The coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing (NGS), but not all of these new technologies have been fully validated for use in clinical practice. The Illumina NGS technology is used in many laboratories but its ability to predict HIV-1 tropism has not been evaluated while the 454 GS-Junior (Roche) is used for routine diagnosis. The genotypic prediction of HIV-1 tropism is based on sequencing the V3 region and interpreting the results with an appropriate algorithm. We compared the performances of the MiSeq (Illumina) and 454 GS-Junior (Roche) systems with a reference phenotypic assay. We used clinical samples for the NGS tropism predictions and assessed their ability to quantify CXCR4-using variants. The data show that the Illumina platform can be used to detect minor CXCR4-using variants in clinical practice but technical optimization are needed to improve quantification.
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17
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Rossi FW, Prevete N, Rivellese F, Lobasso A, Napolitano F, Granata F, Selleri C, de Paulis A. HIV-1 Nef promotes migration and chemokine synthesis of human basophils and mast cells through the interaction with CXCR4. Clin Mol Allergy 2016; 14:15. [PMID: 27822141 PMCID: PMC5088669 DOI: 10.1186/s12948-016-0052-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/25/2016] [Indexed: 01/03/2023] Open
Abstract
Background The Nef protein can be detected in plasma of HIV-1-infected patients and plays a role in the pathogenesis of HIV-1. Nef produced during the early stages of infection is fundamental in creating the ideal environment for viral replication, e.g. by reducing the ability of infected cells to induce an immune response. Aim Based on previous experience showing that both Tat and gp41 of HIV-1 are potent chemotactic factors for basophils and mast cells, and gp120 is a powerful stimulus for the release of histamine and cytokines (IL-4 and IL-13) from basophils, in this study we aimed to verify if the HIV Nef protein can exert some effects on basophils and mast cells purified from healthy volunteers through the interaction with the CXCL12 receptor, CXCR4. Methods Basophils purified from peripheral blood cells of 30 healthy volunteers and mast cells obtained from lung tissue of ten healthy volunteers were tested by flow cytometric analysis, chemotaxis and chemokine production by ELISA assays. Results Nef is a potent chemoattractant for basophils and lung mast cells obtained from healthy, HIV-1 and HIV-2 seronegative individuals. Incubation of basophils and mast cells with Nef induces the release of chemokines (CXCL8/IL-8 and CCL3/MIP-1α). The chemotactic activity of Nef on basophils and mast cells is mediated by the interaction with CXCR4 receptors, being blocked by preincubation of FcεRI+ cells with an anti-CXCR4 Ab. Stimulation with Nef or CXCL12/SDF-1α, a CXCR4 ligand, desensitizes basophils to a subsequent challenge with an autologous or heterologous stimulus. Conclusions These results indicate that Nef, a HIV-1-encoded α-chemokine homolog protein, plays a direct role in basophils and mast cell recruitment and activation at sites of HIV-1 replication, by promoting directional migration of human FcεRI+ cells and the release of chemokines from these cells. Together with our previous results, these data suggest that FcεRI+ cells contribute to the dysregulation of the immune system in HIV-1 infection.
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Affiliation(s)
- Francesca Wanda Rossi
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Nella Prevete
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Felice Rivellese
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy ; Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Antonio Lobasso
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Filomena Napolitano
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Francescopaolo Granata
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Carmine Selleri
- Hematology Branch, Department of Medicine, University of Salerno, Salerno, Italy
| | - Amato de Paulis
- Department of Translational Medical Sciences and Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
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18
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Identification of apolipoprotein using feature selection technique. Sci Rep 2016; 6:30441. [PMID: 27443605 PMCID: PMC4957217 DOI: 10.1038/srep30441] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/01/2016] [Indexed: 12/16/2022] Open
Abstract
Apolipoprotein is a kind of protein which can transport the lipids through the lymphatic and circulatory systems. The abnormal expression level of apolipoprotein always causes angiocardiopathy. Thus, correct recognition of apolipoprotein from proteomic data is very crucial to the comprehension of cardiovascular system and drug design. This study is to develop a computational model to predict apolipoproteins. In the model, the apolipoproteins and non-apolipoproteins were collected to form benchmark dataset. On the basis of the dataset, we extracted the g-gap dipeptide composition information from residue sequences to formulate protein samples. To exclude redundant information or noise, the analysis of various (ANOVA)-based feature selection technique was proposed to find out the best feature subset. The support vector machine (SVM) was selected as discrimination algorithm. Results show that 96.2% of sensitivity and 99.3% of specificity were achieved in five-fold cross-validation. These findings open new perspectives to improve apolipoproteins prediction by considering the specific dipeptides. We expect that these findings will help to improve drug development in anti-angiocardiopathy disease.
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