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Indihar DF, Jones JJ, Ochsenbauer C, Kappes JC. Highly Sensitive Analysis of Cervical Mucosal HIV-1 Infection Using Reporter Viruses Expressing Secreted Nanoluciferase. Methods Mol Biol 2024; 2807:299-323. [PMID: 38743237 DOI: 10.1007/978-1-0716-3862-0_21] [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] [Indexed: 05/16/2024]
Abstract
Ex vivo cervical tissue explant models offer a physiologically relevant approach for studying virus-host interactions that underlie mucosal HIV-1 transmission to women. However, the utility of cervical explant tissue (CET) models has been limited for both practical and technical reasons. These include assay variation, inadequate sensitivity for assessing HIV-1 infection and replication in tissue, and constraints imposed by the requirement for using multiple replica samples of CET to test each experimental variable and assay parameter. Here, we describe an experimental approach that employs secreted nanoluciferase (sNLuc) and current HIV-1 reporter virus technologies to overcome certain limitations of earlier ex vivo CET models. This method augments application of the CET model for investigating important questions involving mucosal HIV-1 transmission.
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Affiliation(s)
- Dana F Indihar
- Division of Hematology/Oncology, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jennifer J Jones
- Division of Hematology/Oncology, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Christina Ochsenbauer
- Division of Hematology/Oncology, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John C Kappes
- Division of Hematology/Oncology, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- Birmingham VA Health Care System, Research Service, Birmingham, AL, USA.
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Fox HS, Niu M, Morsey BM, Lamberty BG, Emanuel K, Periyasamy P, Callen S, Acharya A, Kubik G, Eudy J, Guda C, Dyavar SR, Fletcher CV, Byrareddy SN, Buch S. Morphine suppresses peripheral responses and transforms brain myeloid gene expression to favor neuropathogenesis in SIV infection. Front Immunol 2022; 13:1012884. [PMID: 36466814 PMCID: PMC9709286 DOI: 10.3389/fimmu.2022.1012884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
The twin pandemics of opioid abuse and HIV infection can have devastating effects on physiological systems, including on the brain. Our previous work found that morphine increased the viral reservoir in the brains of treated SIV-infected macaques. In this study, we investigated the interaction of morphine and SIV to identify novel host-specific targets using a multimodal approach. We probed systemic parameters and performed single-cell examination of the targets for infection in the brain, microglia and macrophages. Morphine treatment created an immunosuppressive environment, blunting initial responses to infection, which persisted during antiretroviral treatment. Antiretroviral drug concentrations and penetration into the cerebrospinal fluid and brain were unchanged by morphine treatment. Interestingly, the transcriptional signature of both microglia and brain macrophages was transformed to one of a neurodegenerative phenotype. Notably, the expression of osteopontin, a pleiotropic cytokine, was significantly elevated in microglia. This was especially notable in the white matter, which is also dually affected by HIV and opioids. Increased osteopontin expression was linked to numerous HIV neuropathogenic mechanisms, including those that can maintain a viral reservoir. The opioid morphine is detrimental to SIV/HIV infection, especially in the brain.
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Affiliation(s)
- Howard S. Fox
- Departments of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, United States,*Correspondence: Howard S. Fox,
| | - Meng Niu
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Brenda M. Morsey
- Departments of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Benjamin G. Lamberty
- Departments of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Katy Emanuel
- Departments of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Palsamy Periyasamy
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Shannon Callen
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Arpan Acharya
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gregory Kubik
- The Genomics Core Facility, University of Nebraska Medical Center, Omaha, NE, United States
| | - James Eudy
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chittibabu Guda
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Shetty Ravi Dyavar
- The Antiviral Pharmacology Laboratory, University of Nebraska Medical Center, Omaha, NE, United States
| | - Courtney V. Fletcher
- The Antiviral Pharmacology Laboratory, University of Nebraska Medical Center, Omaha, NE, United States
| | - Siddappa N. Byrareddy
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Shilpa Buch
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
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Trease AJ, Niu M, Morsey B, Guda C, Byrareddy SN, Buch S, Fox HS. Antiretroviral therapy restores the homeostatic state of microglia in SIV-infected rhesus macaques. J Leukoc Biol 2022; 112:969-981. [PMID: 35686500 PMCID: PMC9796061 DOI: 10.1002/jlb.3hi0422-635r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/11/2022] [Indexed: 12/31/2022] Open
Abstract
Microglia and macrophages are essential for homeostatic maintenance and innate immune response in the brain. They are the first line of defense against infections such as HIV/SIV in the brain. However, they are susceptible to infection and function as viral reservoirs even under effective viral suppression. While current antiretroviral regimens successfully suppress viremia and improve quality of life and lifespan, neurologic complications persist and are in part attributed to activated microglia. We sought to test the hypothesis that brain microglia return to a more homeostatic-like state when viremia is suppressed by combination antiretroviral therapy. Using the SIV-rhesus macaque model, we combined single-cell RNA sequencing, bioinformatics, and pathway analysis to compare gene expression profiles of brain myeloid cells under 4 conditions: uninfected, SIV infected, SIV infected with cART suppression, and SIV encephalitis (SIVE). Our study reveals greater myeloid diversity and an elevated proinflammatory state are associated with untreated SIV infection compared with uninfected animals. The development of encephalitis and suppression of viremia both reduced myeloid diversity. However, they had converse effects on the activation state of microglia and inflammation. Notably, suggestive of a restoration of a homeostatic state in microglia, gene expression and activation of pathways related to inflammation and immune response in cART-suppressed monkeys were most similar to that in uninfected monkeys. Untreated SIV infection shared characteristics, especially in brain macrophages to SIVE, with SIVE showing dramatic inflammation. In support of our hypothesis, our study demonstrates that cART indeed restores this key component of the brain's homeostatic state. Summary: ScRNA-seq of rhesus monkey microglia reveals clusters of cells in activated states in the setting of SIV infection, which is primarily reversed by suppressing viremia with combination antiretroviral therapy.
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Affiliation(s)
- Andrew J. Trease
- Department of Neurological SciencesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Meng Niu
- Department of Genetics, Cell Biology and AnatomyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Brenda Morsey
- Department of Neurological SciencesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and AnatomyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Shilpa Buch
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Howard S. Fox
- Department of Neurological SciencesUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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Bai R, Li Z, Lv S, Hua W, Dai L, Wu H. Exploring the biological function of immune cell-related genes in human immunodeficiency virus (HIV)-1 infection based on weighted gene co-expression network analysis (WGCNA). BMC Med Genomics 2022; 15:200. [PMID: 36123690 PMCID: PMC9484082 DOI: 10.1186/s12920-022-01357-y] [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] [Accepted: 09/15/2022] [Indexed: 12/04/2022] Open
Abstract
Background Acquired immunodeficiency syndrome (AIDS) is a chronic infectious disease characterized by consistent immune dysfunction. The objective of this study is to determine whether immune cell-related genes can be used as biomarkers for the occurrence of AIDS and potential molecular mechanisms. Methods A weighted gene co-expression network analysis was performed using the GSE6740 dataset from the Gene Expression Synthesis Database to identify the Hub gene, which contained microarray data from HIV-1 positive (HIV-1+) and HIV-1 negative (HIV-1−) individuals. The HIV-1+-related differentially expressed genes were then identified using the limma package. Subsequently, the characteristic immune cell-related genes were identified as diagnostic biomarkers for HIV-1+ using the random forest model (RF), support vector machine model, and generalized linear model. Results MEdarkgreen exhibited the strongest correlation with HIV clinical features of any of these modules. As the best model for diagnosing HIV-1±, RF was used to select four critical immune cell-related genes, namely, ARRB1, DPEP2, LTBP3, and RGCC, and a nomogram model was created to predict the occurrence of HIV-1 infection based on four key immune cell-related genes. Diagnostic genes were shown to be engaged in immune-related pathways, suggesting that immunological molecules, immune cells, and immune pathways all have a role in HIV-1 infection. The CTD database was explored for prospective medications or molecular compounds that might be utilized to treat HIV-1+ patients. = Moreover, in HIV-1+ individuals, the ceRNA network revealed that ARRB1, DPEP2, LTBP3, and RGCC could be regulated by lncRNAs through the corresponding miRNAs. Ultimately, RT-PCR results from clinical blood samples demonstrated that the four diagnostic genes were significantly downregulated in HIV-1+ patients. Conclusion We screened four immune cell-related genes, ARRB1, DPEP2, LTBP3, and RGCC, which may be considered as the diagnostic markers for HIV-1/AIDS. Our findings reveal that immune related genes and pathways involved in HIV-1 pathogenesis were regulated on both genetic and epigenetic levels by constructing a ceRNA network associated with lncRNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01357-y.
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Affiliation(s)
- Ruojing Bai
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research On Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Zhen Li
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research On Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shiyun Lv
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research On Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wei Hua
- Travel Clinic, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Lili Dai
- Travel Clinic, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research On Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.
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Lo Tartaro D, Camiro-Zúñiga A, Nasi M, De Biasi S, Najera-Avila MA, Jaramillo-Jante MDR, Gibellini L, Pinti M, Neroni A, Mussini C, Soto-Ramírez LE, Calva JJ, Belaunzarán-Zamudio F, Crabtree-Ramirez B, Hernández-Leon C, Mosqueda-Gómez JL, Navarro-Álvarez S, Perez-Patrigeon S, Cossarizza A. Effective Treatment of Patients Experiencing Primary, Acute HIV Infection Decreases Exhausted/Activated CD4+ T Cells and CD8+ T Memory Stem Cells. Cells 2022; 11:cells11152307. [PMID: 35954153 PMCID: PMC9367582 DOI: 10.3390/cells11152307] [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: 06/23/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Several studies have identified main changes in T- and B-lymphocyte subsets during chronic HIV infection, but few data exist on how these subsets behave during the initial phase of HIV infection. We enrolled 22 HIV-infected patients during the acute stage of infection before the initiation of antiretroviral therapy (ART). Patients had blood samples drawn previous to ART initiation (T0), and at 2 (T1) and 12 (T2) months after ART initiation. We quantified cellular HIV-DNA content in sorted naïve and effector memory CD4 T cells and identified the main subsets of T- and B-lymphocytes using an 18-parameter flow cytometry panel. We identified correlations between the patients’ clinical and immunological data using PCA. Effective HIV treatment reduces integrated HIV DNA in effector memory T cells after 12 months (T2) of ART. The main changes in CD4+ T cells occurred at T2, with a reduction of activated memory, cytolytic and activated/exhausted stem cell memory T (TSCM) cells. Changes were present among CD8+ T cells since T1, with a reduction of several activated subsets, including activated/exhausted TSCM. At T2 a reduction of plasmablasts and exhausted B cells was also observed. A negative correlation was found between the total CD4+ T-cell count and IgM-negative plasmablasts. In patients initiating ART immediately following acute/early HIV infection, the fine analysis of T- and B-cell subsets has allowed us to identify and follow main modifications due to effective treatment, and to identify significant changes in CD4+ and CD8+ T memory stem cells.
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Affiliation(s)
- Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy; (D.L.T.); (S.D.B.); (L.G.); (A.N.)
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Antonio Camiro-Zúñiga
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
| | - Milena Nasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy
- Correspondence: (M.N.); (A.C.); Tel.: +39-059-205-5415 (M.N.); +39-059-205-5422 (A.C.)
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy; (D.L.T.); (S.D.B.); (L.G.); (A.N.)
| | - Marco A. Najera-Avila
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
| | - Maria Del Rocio Jaramillo-Jante
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy; (D.L.T.); (S.D.B.); (L.G.); (A.N.)
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Anita Neroni
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy; (D.L.T.); (S.D.B.); (L.G.); (A.N.)
| | - Cristina Mussini
- Infectious Diseases Clinics, Azienda Ospedaliero-Universitaria Policlinico di Modena, 41124 Modena, Italy;
| | - Luis E. Soto-Ramírez
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
| | - Juan J. Calva
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
| | - Francisco Belaunzarán-Zamudio
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
| | - Brenda Crabtree-Ramirez
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
| | - Christian Hernández-Leon
- Centro Ambulatorio para la Prevención y Atención del Sida e Infecciones de Transmisión Sexual (CAPASITS), Puebla 72410, Mexico;
| | - Juan L. Mosqueda-Gómez
- Centro Ambulatorio para la Prevención y Atención del Sida e Infecciones de Transmisión Sexual (CAPASITS), Leon 37320, Mexico;
| | | | - Santiago Perez-Patrigeon
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Infectious Diseases, Mexico City 14080, Mexico; (A.C.-Z.); (M.A.N.-A.); (M.D.R.J.-J.); (L.E.S.-R.); (J.J.C.); (F.B.-Z.); (B.C.-R.); (S.P.-P.)
- Division of Infectious Diseases, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy; (D.L.T.); (S.D.B.); (L.G.); (A.N.)
- National Institute for Cardiovascular Research—INRC, 40126 Bologna, Italy
- Correspondence: (M.N.); (A.C.); Tel.: +39-059-205-5415 (M.N.); +39-059-205-5422 (A.C.)
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Wang X, Mehra S, Kaushal D, Veazey RS, Xu H. Abnormal Tryptophan Metabolism in HIV and Mycobacterium tuberculosis Infection. Front Microbiol 2021; 12:666227. [PMID: 34262540 PMCID: PMC8273495 DOI: 10.3389/fmicb.2021.666227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
Host metabolism has recently gained more attention for its roles in physiological functions and pathologic conditions. Of these, metabolic tryptophan disorders generate a pattern of abnormal metabolites that are implicated in various diseases. Here, we briefly highlight the recent advances regarding abnormal tryptophan metabolism in HIV and Mycobacterium tuberculosis infection and discuss its potential impact on immune regulation, disease progression, and neurological disorders. Finally, we also discuss the potential for metabolic tryptophan interventions toward these infectious diseases.
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Affiliation(s)
- Xiaolei Wang
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
| | - Smriti Mehra
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ronald S. Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
| | - Huanbin Xu
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA, United States
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Kazer SW, Walker BD, Shalek AK. Evolution and Diversity of Immune Responses during Acute HIV Infection. Immunity 2021; 53:908-924. [PMID: 33207216 DOI: 10.1016/j.immuni.2020.10.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/03/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
Abstract
Understanding the earliest immune responses following HIV infection is critical to inform future vaccines and therapeutics. Here, we review recent prospective human studies in at-risk populations that have provided insight into immune responses during acute infection, including additional relevant data from non-human primate (NHP) studies. We discuss the timing, nature, and function of the diverse immune responses induced, the onset of immune dysfunction, and the effects of early anti-retroviral therapy administration. Treatment at onset of viremia mitigates peripheral T and B cell dysfunction, limits seroconversion, and enhances cellular antiviral immunity despite persistence of infection in lymphoid tissues. We highlight pertinent areas for future investigation, and how application of high-throughput technologies, alongside targeted NHP studies, may elucidate immune response features to target in novel preventions and cures.
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Affiliation(s)
- Samuel W Kazer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Alex K Shalek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Brief Report: CYP27B1 rs10877012 T Allele Was Linked to Non-AIDS Progression in ART-Naïve HIV-Infected Patients: A Retrospective Study. J Acquir Immune Defic Syndr 2021; 85:659-664. [PMID: 32932410 DOI: 10.1097/qai.0000000000002485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND HIV/AIDS progression is linked to vitamin D, which is regulated by several key cytochromes P450 (CYP). Single nucleotide polymorphisms (SNPs) in CYP genes influence vitamin D metabolism and serum levels. The objective of this study was to evaluate the association between CYP SNPs and the clinical AIDS progression in antiretroviral treatment (ART)-naïve HIV-infected patients. METHODS We performed a retrospective study in 661 ART-naïve HIV-infected patients who were stratified by their AIDS progression pattern [181 long-term nonprogressors (LTNPs), 332 moderate progressors, and 148 rapid progressors (RPs)]. Four CYP SNPs (CYP2R1 rs10500804, CYP2R1 rs1993116, CYP27B1 rs10877012, and CYP24A1 rs6013897) were genotyped using Agena Bioscience's MassARRAY platform. Correction for multiple testing was performed using the false discovery rate (Benjamini-Hochberg procedure). RESULTS The adjusted regression showed a significant association only for CYP27B1 rs10877012 SNP. When analyzing all HIV patients, the rs10877012 T allele was protective against AIDS progression (ordinal outcome) under the dominant [adjusted odds ratio (aOR) = 0.69; P = 0.021) and additive (aOR) = 0.75; P = 0.025] inheritance models. When analyzing LTNPs versus RPs, the rs10877012 T allele also showed a significant protective association under the dominant (aOR = 0.45; P = 0.004) and additive (aOR = 0.54; P = 0.008) inheritance models. P values remained significant after correcting by multiple comparisons only for the comparison of LTNPs versus RPs (extreme phenotypes). CONCLUSIONS The CYP27B1 rs10877012 T allele was linked to non-AIDS progression in ART-naïve HIV-infected patients. The rs10877012 SNP seems to have an impact on the clinical AIDS progression, possibly modifying vitamin D levels, which could be relevant for the pathogenesis of HIV infection.
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Singh KP, Zerbato JM, Zhao W, Braat S, Deleage C, Tennakoon GS, Mason H, Dantanarayana A, Rhodes A, Rhodes JW, Torresi J, Harman AN, Revill PA, Crane M, Estes JD, Avihingsanon A, Lewin SR, Audsley J. Intrahepatic CXCL10 is strongly associated with liver fibrosis in HIV-Hepatitis B co-infection. PLoS Pathog 2020; 16:e1008744. [PMID: 32898182 PMCID: PMC7521747 DOI: 10.1371/journal.ppat.1008744] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 09/28/2020] [Accepted: 06/25/2020] [Indexed: 12/23/2022] Open
Abstract
In HIV-hepatitis B virus (HBV) co-infection, adverse liver outcomes including liver fibrosis occur at higher frequency than in HBV-mono-infection, even following antiretroviral therapy (ART) that suppresses both HIV and HBV replication. To determine whether liver disease was associated with intrahepatic or circulating markers of inflammation or burden of HIV or HBV, liver biopsies and blood were collected from HIV-HBV co-infected individuals (n = 39) living in Bangkok, Thailand and naïve to ART. Transient elastography (TE) was performed. Intrahepatic and circulating markers of inflammation and microbial translocation were quantified by ELISA and bead arrays and HIV and HBV infection quantified by PCR. Liver fibrosis (measured by both transient elastography and liver biopsy) was statistically significantly associated with intrahepatic mRNA for CXCL10 and CXCR3 using linear and logistic regression analyses adjusted for CD4 T-cell count. There was no evidence of a relationship between liver fibrosis and circulating HBV DNA, qHBsAg, plasma HIV RNA or circulating cell-associated HIV RNA or DNA. Using immunohistochemistry of liver biopsies from this cohort, intrahepatic CXCL10 was detected in hepatocytes associated with inflammatory liver infiltrates in the portal tracts. In an in vitro model, we infected an HBV-infected hepatocyte cell line with HIV, followed by interferon-γ stimulation. HBV-infected cells lines produced significantly more CXCL10 than uninfected cells lines and this significantly increased in the presence of an increasing multiplicity of HIV infection. Conclusion: Enhanced production of CXCL10 following co-infection of hepatocytes with both HIV and HBV may contribute to accelerated liver disease in the setting of HIV-HBV co-infection.
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Affiliation(s)
- Kasha P. Singh
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Victoria, Australia
| | - Jennifer M. Zerbato
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Wei Zhao
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Sabine Braat
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire Deleage
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - G. Surekha Tennakoon
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Hugh Mason
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ashanti Dantanarayana
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ajantha Rhodes
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Jake W. Rhodes
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia
- The University of Sydney, Westmead Clinical School, Faculty of Medicine and Health, Sydney, NSW, Australia
| | - Joe Torresi
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Andrew N. Harman
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, NSW, Australia
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Megan Crane
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Jacob D. Estes
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Anchalee Avihingsanon
- Thai Red Cross AIDS Research Centre and Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sharon R. Lewin
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Victoria, Australia
| | - Jennifer Audsley
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
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10
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Nguyen S, Sada-Japp A, Petrovas C, Betts MR. Jigsaw falling into place: A review and perspective of lymphoid tissue CD8+ T cells and control of HIV. Mol Immunol 2020; 124:42-50. [PMID: 32526556 PMCID: PMC7279761 DOI: 10.1016/j.molimm.2020.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/28/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
CD8+ T cells are crucial for immunity against viral infections, including HIV. Several characteristics of CD8+ T cells, such as polyfunctionality and cytotoxicity, have been correlated with effective control of HIV. However, most of these correlates have been established in the peripheral blood. Meanwhile, HIV primarily replicates in lymphoid tissues. Therefore, it is unclear which aspects of CD8+ T cell biology are shared and which are different between blood and lymphoid tissues in the context of HIV infection. In this review, we will recapitulate the latest advancements of our knowledge on lymphoid tissue CD8+ T cells during HIV infection and discuss the insights these advancements might provide for the development of a HIV cure.
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Affiliation(s)
- Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alberto Sada-Japp
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Constantinos Petrovas
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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11
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Sannier G, Dubé M, Kaufmann DE. Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity. Front Microbiol 2020; 11:297. [PMID: 32194526 PMCID: PMC7064469 DOI: 10.3389/fmicb.2020.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
The need for definitive answers probably explains our natural tendency to seek simplicity. The reductionist “bulk” approach, in which a mean behavior is attributed to a heterogeneous cell population, fulfills this need by considerably helping the conceptualization of complex biological processes. However, the limits of this methodology are becoming increasingly clear as models seek to explain biological events occurring in vivo, where heterogeneity is the rule. Research in the HIV-1 field is no exception: the challenges encountered in the development of preventive and curative anti-HIV-1 strategies may well originate in part from inadequate assumptions built on bulk technologies, highlighting the need for new perspectives. The emergence of diverse single-cell technologies set the stage for potential breakthrough discoveries, as heterogeneous processes can now be investigated with an unprecedented depth in topics as diverse as HIV-1 tropism, dynamics of the replication cycle, latency, viral reservoirs and immune control. In this review, we summarize recent advances in the HIV-1 field made possible by single-cell technologies, and contextualize their importance.
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Affiliation(s)
- Gérémy Sannier
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Consortium for HIV/AIDS Vaccine Development (Scripps CHAVD), La Jolla, CA, United States
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12
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Jiménez-Sousa MÁ, Jiménez JL, Fernández-Rodríguez A, Bellón JM, Rodríguez C, Riera M, Portilla J, Castro Á, Muñoz-Fernández MÁ, Resino S. DBP rs16846876 and rs12512631 polymorphisms are associated with progression to AIDS naïve HIV-infected patients: a retrospective study. J Biomed Sci 2019; 26:83. [PMID: 31640710 PMCID: PMC6806573 DOI: 10.1186/s12929-019-0577-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/09/2019] [Indexed: 01/08/2023] Open
Abstract
Background Most of the circulating Vitamin D (VitD) is transported bound to vitamin D-binding protein (DBP), and several DBP single nucleotide polymorphisms (SNPs) have been related to circulating VitD concentration and disease. In this study, we evaluated the association among DBP SNPs and AIDS progression in antiretroviral treatment (ART)-naïve-HIV-infected patients. Methods We performed a retrospective study in 667 patients who were classified according to their pattern of AIDS progression (183 long-term non-progressors (LTNPs), 334 moderate progressors (MPs), and 150 rapid progressors (RPs)) and 113 healthy blood donors (HIV, HCV, and HBV negative subjects). We genotyped seven DBP SNPs (rs16846876, rs12512631, rs2070741, rs2282679, rs7041, rs1155563, rs2298849) using Agena Bioscience’s MassARRAY platform. The genetic association was evaluated by Generalized Linear Models adjusted by age at the moment of HIV diagnosis, gender, risk group, and VDR rs2228570 SNP. Multiple testing correction was performed by the false discovery rate (Benjamini and Hochberg procedure; q-value). Results All SNPs were in HWE (p > 0.05) and had similar genotypic frequencies for DBP SNPs in healthy-controls and HIV-infected patients. In unadjusted GLMs, we only found significant association with AIDS progression in rs16846876 and rs12512631 SNPs. In adjusted GLMs, DBP rs16846876 SNP showed significant association under the recessive inheritance model [LTNPs vs. RPs (adjusted odds ratio (aOR) = 3.53; q-value = 0.044) and LTNPs vs. MPs (aOR = 3.28; q-value = 0.030)] and codominant [LTNPs vs. RPs (aOR = 4.92; q-value = 0.030) and LTNPs vs. MPs (aOR = 3.15; q-value = 0.030)]. Also, we found DBP rs12512631 SNP showed significant association in the inheritance model dominant [LTNPs vs. RPs (aOR = 0.49; q-value = 0.031) and LTNPs vs. MPs (aOR = 0.6; q-value = 0.047)], additive [LTNPs vs. RPs (aOR = 0.61; q-value = 0.031)], overdominant [LTNPs vs. MPs (aOR = 0.55; q-value = 0.032)], and codominant [LTNPs vs. RPs (aOR = 0.52; q-value = 0.036) and LTNPs vs. MPs (aOR = 0.55; q-value = 0.032)]. Additionally, we found a significant association between DBP haplotypes (composed by rs16846876 and rs12512631) and AIDS progression (LTNPs vs RPs): DBP haplotype AC (aOR = 0.63; q-value = 0.028) and the DBP haplotype TT (aOR = 1.64; q-value = 0.028). Conclusions DBP rs16846876 and rs12512631 SNPs are related to the patterns of clinical AIDS progression (LTNP, MP, and RP) in ART-naïve HIV-infected patients. Our findings provide new knowledge about AIDS progression that may be relevant to understanding the pathogenesis of HIV infection.
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Affiliation(s)
- María Ángeles Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda- Pozuelo, Km 2.2, 28220, Majadahonda, Madrid, Spain.
| | - José Luis Jiménez
- Plataforma de Laboratorio, Hospital General Universitario "Gregorio Marañón", Madrid, Spain.,Fundación para la Investigación Biomédica, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda- Pozuelo, Km 2.2, 28220, Majadahonda, Madrid, Spain
| | - José María Bellón
- Fundación para la Investigación Biomédica, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Carmen Rodríguez
- Centro Sanitario Sandoval, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Melchor Riera
- Servicio de Medicina Interna-Infecciosas, Hospital Universitario "Son Espases", Palma de Mallorca, Spain
| | - Joaquín Portilla
- Servicio de Enfermedades Infecciosas, Hospital General Universitario de Alicante, Alicante, Spain
| | - Ángeles Castro
- Unidad de Enfermedades Infecciosas, Servicio de Medicina Interna, Complejo Hospitalario Universitario a Coruña (CHUAC), A Coruña, Spain
| | - María Ángeles Muñoz-Fernández
- Sección Inmunología, Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, IiSGM, and Spanish HIV HGM BioBank, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda- Pozuelo, Km 2.2, 28220, Majadahonda, Madrid, Spain.
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13
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Furler RL, Newcombe KL, Del Rio Estrada PM, Reyes-Terán G, Uittenbogaart CH, Nixon DF. Histoarchitectural Deterioration of Lymphoid Tissues in HIV-1 Infection and in Aging. AIDS Res Hum Retroviruses 2019; 35:1148-1159. [PMID: 31474115 DOI: 10.1089/aid.2019.0156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Impaired immunity is a common symptom of aging and advanced Human Immunodeficiency Virus type 1 (HIV-1) disease. In both diseases, a decline in lymphocytic function and cellularity leads to ineffective adaptive immune responses to opportunistic infections and vaccinations. Furthermore, despite sustained myeloid cellularity there is a background of chronic immune activation and a decrease in innate immune function in aging. In HIV-1 disease, myeloid cellularity is often more skewed than in normal aging, but similar chronic activation and innate immune dysfunction typically arise. Similarities between aging and HIV-1 infection have led to several investigations into HIV-1-mediated aging of the immune system. In this article, we review various studies that report alterations of leukocyte number and function during aging, and compare those alterations with those observed during progressive HIV-1 disease. We pay particular attention to changes within lymphoid tissue microenvironments and how histoarchitectural changes seen in these two diseases affect immunity. As we review various immune compartments including peripheral blood as well as primary and secondary lymphoid organs, common themes arise that help explain the decline of immunity in the elderly and in HIV-1-infected individuals with advanced disease. In both conditions, lymphoid tissues often show signs of histoarchitectural deterioration through fat accumulation and/or fibrosis. These structural changes can be attributed to a loss of communication between leukocytes and the surrounding stromal cells that produce the extracellular matrix components and growth factors necessary for cell migration, cell proliferation, and lymphoid tissue function. Despite the common general impairment of immunity in aging and HIV-1 progression, deterioration of immunity is caused by distinct mechanisms at the cellular and tissue levels in these two diseases.
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Affiliation(s)
- Robert L. Furler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Kevin L. Newcombe
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Perla M. Del Rio Estrada
- Departmento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” CDMX, Mexico DF, Mexico
| | - Gustavo Reyes-Terán
- Departmento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” CDMX, Mexico DF, Mexico
| | - Christel H. Uittenbogaart
- Department of Microbiology, Immunology and Molecular Genetics, Medicine-Pediatrics, UCLA AIDS Institute and the Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
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14
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Henrich TJ, Hsue PY, VanBrocklin H. Seeing Is Believing: Nuclear Imaging of HIV Persistence. Front Immunol 2019; 10:2077. [PMID: 31572355 PMCID: PMC6751256 DOI: 10.3389/fimmu.2019.02077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022] Open
Abstract
A major obstacle to HIV eradication is the presence of infected cells that persist despite suppressive antiretroviral therapy (ART). HIV largely resides outside of the peripheral circulation, and thus, numerous anatomical and lymphoid compartments that have the capacity to harbor HIV are inaccessible to routine sampling. As a result, there is a limited understanding of the tissue burden of HIV infection or anatomical distribution of HIV transcriptional and translational activity. Novel, non-invasive, in vivo methods are urgently needed to address this fundamental gap in knowledge. In this review, we discuss past and current nuclear imaging approaches that have been applied to HIV infection with an emphasis on current strategies to implement positron emission tomography (PET)-based imaging to directly visualize and characterize whole-body HIV burden. These imaging approaches have various limitations, such as the potential for limited PET sensitivity and specificity in the setting of ART suppression or low viral burden. However, recent advances in high-sensitivity, total-body PET imaging platforms and development of new radiotracer technologies that may enhance anatomical penetration of target-specific tracer molecules are discussed. Potential strategies to image non-viral markers of HIV tissue burden or focal immune perturbation are also addressed. Overall, emerging nuclear imaging techniques and platforms may play an important role in the development of novel therapeutic and HIV reservoir eradication strategies.
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Affiliation(s)
- Timothy J Henrich
- Division of Experimental Medicine, Department of Medicine, University of San Francisco, San Francisco, CA, United States
| | - Priscilla Y Hsue
- Division of Cardiology, Department of Medicine, University of San Francisco, San Francisco, CA, United States
| | - Henry VanBrocklin
- Radiopharmaceutical Research Program, Center for Molecular and Functional Imaging, University of San Francisco, San Francisco, CA, United States
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15
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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: 15] [Impact Index Per Article: 3.0] [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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16
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Jiménez-Sousa MA, Jiménez JL, Fernández-Rodríguez A, Brochado-Kith O, Bellón JM, Gutierrez F, Díez C, Bernal-Morell E, Viciana P, Muñoz-Fernández MA, Resino S. VDR rs2228570 Polymorphism Is Related to Non-Progression to AIDS in Antiretroviral Therapy Naïve HIV-Infected Patients. J Clin Med 2019; 8:jcm8030311. [PMID: 30841566 PMCID: PMC6463017 DOI: 10.3390/jcm8030311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/28/2022] Open
Abstract
Background: Vitamin D is a fundamental regulator of host defenses by activating genes related to innate and adaptive immunity. In this study, we analyzed the association among single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene, with clinical patterns of AIDS progression in antiretroviral treatment (ART)-naïve HIV-infected patients. Methods: We conducted a retrospective study in 667 HIV-infected patients, who were classified within three groups according to their AIDS progression pattern (183 long-term non-progressors (LTNPs), 334 moderate progressors (MPs), and 150 rapid progressors (RPs)). Five VDR SNPs (rs11568820, rs4516035, rs2228570, rs1544410, and rs7975232) were genotyped using Agena Bioscience’s MassARRAY platform. Results: Significant association results were found for rs2228570. Within all HIV patients, the presence of T allele at VDR rs2228570 SNP was protective against AIDS progression (ordinal outcome) under additive (adjusted odds ratio (aOR) = 0.75; p = 0.009), dominant (aOR = 0.69; p = 0.015), and codominant (aOR = 0.56; p = 0.017) inheritance models. In addition, the same allele was protective under additive and codominant inheritance models when we compared with LTNPs vs. RPs [aOR = 0.64 (p = 0.019) and aOR = 0.37 (p = 0.018), respectively] and when we compared MPs vs. RPs [aOR = 0.72 (p = 0.035) and aOR = 0.45 (p = 0.028), respectively]. Conclusions: The VDR rs2228570 T allele was related to a lower AIDS progression pattern in ART-naïve HIV-infected patients. These findings expand upon the knowledge about HIV pathogenesis in untreated HIV-infected patients with different clinical outcomes.
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Affiliation(s)
- María A Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
| | - José Luis Jiménez
- Plataforma de Laboratorio, Hospital General Universitario "Gregorio Marañón", 28007 Madrid, Spain.
- Fundación para la Investigación Biomédica, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), 28007 Madrid, Spain.
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
| | - Oscar Brochado-Kith
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
| | - José María Bellón
- Fundación para la Investigación Biomédica, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), 28007 Madrid, Spain.
| | - Félix Gutierrez
- Unidad de Enfermedades Infecciosas, Hospital General de Elche & Universidad Miguel Hernández, 03202 Alicante, Spain.
| | - Cristina Díez
- Servicio Microbiología, Unidad de Enfermedades Infecciosas/VIH, Hospital General Universitario Gregorio Marañon, 28007 Madrid, Spain.
| | - Enrique Bernal-Morell
- Servicio de Enfermedades Infecciosas, Hospital General Universitario Reina Sofia, 30003 Madrid, Spain.
| | - Pompeyo Viciana
- Servicio de Enfermedades Infecciosas, Hospital Virgen del Rocío, 41013 Seville, Spain.
| | - María A Muñoz-Fernández
- Sección Inmunología, Laboratorio Inmuno Biología Molecular, Hospital General Universitario Gregorio Marañón, IiSGM, and Spanish HIV HGM BioBank, 28007 Madrid, Spain.
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28007 Madrid, Spain.
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, Km 2.2, 28220 Madrid, Spain.
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