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Adams SK, Ducharme GE, Loveday EK. All the single cells: if you like it then you should put some virus on it. J Virol 2024; 98:e0127323. [PMID: 38904395 DOI: 10.1128/jvi.01273-23] [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] [Indexed: 06/22/2024] Open
Abstract
Across a rich 70-year history, single-cell virology has revealed the impact of host and pathogen heterogeneity during virus infections. Recent technological innovations have enabled higher-resolution analyses of cellular and viral heterogeneity. Furthermore, single-cell analysis has revealed extreme phenotypes and provided additional insights into host-pathogen dynamics. Using a single-cell approach to explore fundamental virology questions, contemporary researchers have contributed to a revival of interest in single-cell virology with increased insights and enthusiasm.
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Affiliation(s)
- Sophia K Adams
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Grace E Ducharme
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Emma K Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
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2
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Acchioni C, Sandini S, Acchioni M, Sgarbanti M. Co-Infections and Superinfections between HIV-1 and Other Human Viruses at the Cellular Level. Pathogens 2024; 13:349. [PMID: 38787201 PMCID: PMC11124504 DOI: 10.3390/pathogens13050349] [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: 03/16/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Co-infection or superinfection of the host by two or more virus species is a common event, potentially leading to viral interference, viral synergy, or neutral interaction. The simultaneous presence of two or more viruses, even distantly related, within the same cell depends upon viral tropism, i.e., the entry of viruses via receptors present on the same cell type. Subsequently, productive infection depends on the ability of these viruses to replicate efficiently in the same cellular environment. HIV-1 initially targets CCR5-expressing tissue memory CD4+ T cells, and in the absence of early cART initiation, a co-receptor switch may occur, leading to the infection of naïve and memory CXCR4-expressing CD4+ T cells. HIV-1 infection of macrophages at the G1 stage of their cell cycle also occurs in vivo, broadening the possible occurrence of co-infections between HIV-1 and other viruses at the cellular level. Moreover, HIV-1-infected DCs can transfer the virus to CD4+ T cells via trans-infection. This review focuses on the description of reported co-infections within the same cell between HIV-1 and other human pathogenic, non-pathogenic, or low-pathogenic viruses, including HIV-2, HTLV, HSV, HHV-6/-7, GBV-C, Dengue, and Ebola viruses, also discussing the possible reciprocal interactions in terms of virus replication and virus pseudotyping.
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Affiliation(s)
| | | | | | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (C.A.); (S.S.); (M.A.)
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3
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Moar P, Premeaux TA, Atkins A, Ndhlovu LC. The latent HIV reservoir: current advances in genetic sequencing approaches. mBio 2023; 14:e0134423. [PMID: 37811964 PMCID: PMC10653892 DOI: 10.1128/mbio.01344-23] [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] [Indexed: 10/10/2023] Open
Abstract
Multiple cellular HIV reservoirs in diverse anatomical sites can undergo clonal expansion and persist for years despite suppressive antiretroviral therapy, posing a major barrier toward an HIV cure. Commonly adopted assays to assess HIV reservoir size mainly consist of PCR-based measures of cell-associated total proviral DNA, intact proviruses and transcriptionally competent provirus (viral RNA), flow cytometry and microscopy-based methods to measure translationally competent provirus (viral protein), and quantitative viral outgrowth assay, the gold standard to measure replication-competent provirus; yet no assay alone can provide a comprehensive view of the total HIV reservoir or its dynamics. Furthermore, the detection of extant provirus by these measures does not preclude defects affecting replication competence. An accurate measure of the latent reservoir is essential for evaluating the efficacy of HIV cure strategies. Recent approaches have been developed, which generate proviral sequence data to create a more detailed profile of the latent reservoir. These sequencing approaches are valuable tools to understand the complex multicellular processes in a diverse range of tissues and cell types and have provided insights into the mechanisms of HIV establishment and persistence. These advancements over previous sequencing methods have allowed multiplexing and new assays have emerged, which can document transcriptional activity, chromosome accessibility, and in-depth cellular phenotypes harboring latent HIV, enabling the characterization of rare infected cells across restrictive sites such as the brain. In this manuscript, we provide a review of HIV sequencing-based assays adopted to address challenges in quantifying and characterizing the latent HIV reservoir.
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Affiliation(s)
- Preeti Moar
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Thomas A. Premeaux
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Andrew Atkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York City, New York, USA
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4
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Kulkarni S, Endsley JJ, Lai Z, Bradley T, Sharan R. Single-Cell Transcriptomics of Mtb/HIV Co-Infection. Cells 2023; 12:2295. [PMID: 37759517 PMCID: PMC10529032 DOI: 10.3390/cells12182295] [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: 05/31/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) co-infection continues to pose a significant healthcare burden. HIV co-infection during TB predisposes the host to the reactivation of latent TB infection (LTBI), worsening disease conditions and mortality. There is a lack of biomarkers of LTBI reactivation and/or immune-related transcriptional signatures to distinguish active TB from LTBI and predict TB reactivation upon HIV co-infection. Characterizing individual cells using next-generation sequencing-based technologies has facilitated novel biological discoveries about infectious diseases, including TB and HIV pathogenesis. Compared to the more conventional sequencing techniques that provide a bulk assessment, single-cell RNA sequencing (scRNA-seq) can reveal complex and new cell types and identify more high-resolution cellular heterogeneity. This review will summarize the progress made in defining the immune atlas of TB and HIV infections using scRNA-seq, including host-pathogen interactions, heterogeneity in HIV pathogenesis, and the animal models employed to model disease. This review will also address the tools needed to bridge the gap between disease outcomes in single infection vs. co-infection. Finally, it will elaborate on the translational benefits of single-cell sequencing in TB/HIV diagnosis in humans.
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Affiliation(s)
- Smita Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Janice J. Endsley
- Departments of Microbiology & Immunology and Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, The University of Texas Health San Antonio, San Antonio, TX 78229, USA;
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA;
- Departments of Pediatrics and Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO 66160, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, MO 64108, USA
| | - Riti Sharan
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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5
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Cortés‐Llanos B, Jain V, Cooper‐Volkheimer A, Browne EP, Murdoch DM, Allbritton NL. Automated microarray platform for single-cell sorting and collection of lymphocytes following HIV reactivation. Bioeng Transl Med 2023; 8:e10551. [PMID: 37693052 PMCID: PMC10487311 DOI: 10.1002/btm2.10551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 09/12/2023] Open
Abstract
A promising strategy to cure HIV-infected individuals is to use latency reversing agents (LRAs) to reactivate latent viruses, followed by host clearance of infected reservoir cells. However, reactivation of latent proviruses within infected cells is heterogeneous and often incomplete. This fact limits strategies to cure HIV which may require complete elimination of viable virus from all cellular reservoirs. For this reason, understanding the mechanism(s) of reactivation of HIV within cellular reservoirs is critical to achieve therapeutic success. Methodologies enabling temporal tracking of single cells as they reactivate followed by sorting and molecular analysis of those cells are urgently needed. To this end, microraft arrays were adapted to image T-lymphocytes expressing mCherry under the control of the HIV long terminal repeat (LTR) promoter, in response to the application of LRAs (prostratin, iBET151, and SAHA). In response to prostratin, iBET151, and SAHA, 30.5%, 11.2%, and 12.1% percentage of cells, respectively. The arrays enabled large numbers of single cells (>25,000) to be imaged over time. mCherry fluorescence quantification identified cell subpopulations with differing reactivation kinetics. Significant heterogeneity was observed at the single-cell level between different LRAs in terms of time to reactivation, rate of mCherry fluorescence increase upon reactivation, and peak fluorescence attained. In response to prostratin, subpopulations of T lymphocytes with slow and fast reactivation kinetics were identified. Single T-lymphocytes that were either fast or slow reactivators were sorted, and single-cell RNA-sequencing was performed. Different genes associated with inflammation, immune activation, and cellular and viral transcription factors were found.
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Affiliation(s)
- Belén Cortés‐Llanos
- Department of BioengineeringUniversity of WashingtonWashingtonUSA
- Department of MedicineDuke UniversityNorth CarolinaUSA
| | - Vaibhav Jain
- Department of Molecular PhysiologyDuke UniversityNorth CarolinaUSA
| | | | - Edward P. Browne
- Department of MedicineUniversity of North CarolinaNorth CarolinaUSA
- Department of Microbiology and ImmunologyUniversity of North CarolinaNorth CarolinaUSA
- UNC HIV Cure CenterUniversity of North CarolinaNorth CarolinaUSA
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6
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Cortés-Llanos B, Jain V, Volkheimer A, Browne EP, Murdoch DM, Allbritton NL. Automated microarray for single-cell sorting and collection of lymphocytes following HIV reactivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526757. [PMID: 36778314 PMCID: PMC9915582 DOI: 10.1101/2023.02.02.526757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A promising strategy to cure HIV infected individuals is to use latency reversing agents (LRAs) to reactivate latent viruses, followed by host clearance of infected reservoir cells. However, reactivation of latent proviruses within infected cells is heterogeneous and often incomplete. This fact limits strategies to cure HIV which may require complete elimination of viable virus from all cellular reservoirs. For this reason, understanding the mechanism(s) of reactivation of HIV within cellular reservoirs is critical to achieve therapeutic success. Methodologies enabling temporal tracking of single cells as they reactivate followed by sorting and molecular analysis of those cells are urgently needed. To this end, microraft arrays were adapted to image T-lymphocytes expressing mCherry under the control of the HIV long terminal repeat (LTR) promoter, in response to the application of various LRAs (prostratin, iBET151, and SAHA). In response to prostratin, iBET151, and SAHA, 30.5 %, 11.2 %, and 12.1 % percentage of cells respectively, reactivated similar to that observed in other experimental systems. The arrays enabled large numbers of single cells (>25,000) to be imaged over time. mCherry fluorescence quantification identified cell subpopulations with differing reactivation kinetics. Significant heterogeneity was observed at the single cell level between different LRAs in terms of time to reactivation, rate of mCherry fluorescence increase upon reactivation, and peak fluorescence attained. In response to prostratin, subpopulations of T lymphocytes with slow and fast reactivation kinetics were identified. Single T-lymphocytes that were either fast or slow reactivators were sorted, and single-cell RNA-sequencing was performed. Different genes associated with inflammation, immune activation, and cellular and viral transcription factors were found. These results advance our conceptual understanding of HIV reactivation dynamics at the single-cell level toward a cure for HIV.
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Single-Cell Imaging Shows That the Transcriptional State of the HIV-1 Provirus and Its Reactivation Potential Depend on the Integration Site. mBio 2022; 13:e0000722. [PMID: 35708287 PMCID: PMC9426465 DOI: 10.1128/mbio.00007-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Current antiretroviral treatment fails to cure HIV-1 infection since latent provirus resides in long-lived cellular reservoirs, rebounding whenever therapy is discontinued. The molecular mechanisms underlying HIV-1 latency are complex where the possible link between integration and transcription is poorly understood. HIV-1 integration is targeted toward active chromatin by the direct interaction with a host protein, lens epithelium-derived growth factor (LEDGF/p75). LEDGINs are small-molecule inhibitors of the LEDGF/p75-integrase (IN) interaction that effectively inhibit and retarget HIV-1 integration out of preferred integration sites, resulting in residual provirus that is more latent. Here, we describe a single-cell branched DNA imaging method for simultaneous detection of viral DNA and RNA. We investigated how treatment with LEDGINs affects the location, transcription, and reactivation of HIV-1 in both cell lines and primary cells. This approach demonstrated that LEDGIN-mediated retargeting hampered the baseline transcriptional state and the transcriptional reactivation of the provirus, evidenced by the reduction in viral RNA expression per residual copy. Moreover, treatment of primary cells with LEDGINs induced an enrichment of provirus in deep latency. These results corroborate the impact of integration site selection for the HIV-1 transcriptional state and support block-and-lock functional cure strategies in which the latent reservoir is permanently silenced after retargeting.
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8
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Global transcriptomic characterization of T cells in individuals with chronic HIV-1 infection. Cell Discov 2022; 8:29. [PMID: 35351857 PMCID: PMC8964811 DOI: 10.1038/s41421-021-00367-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
To obtain a comprehensive scenario of T cell profiles and synergistic immune responses, we performed single-cell RNA sequencing (scRNA-seq) on the peripheral T cells of 14 individuals with chronic human immunodeficiency virus 1 (HIV-1) infection, including nine treatment-naive (TP) and eight antiretroviral therapy (ART) participants (of whom three were paired with TP cases), and compared the results with four healthy donors (HD). Through analyzing the transcriptional profiles of CD4+ and CD8+ T cells, coupled with assembled T cell receptor sequences, we observed the significant loss of naive T cells, prolonged inflammation, and increased response to interferon-α in TP individuals, which could be partially restored by ART. Interestingly, we revealed that CD4+ and CD8+ Effector-GNLY clusters were expanded in TP cases, and persistently increased in ART individuals where they were typically correlated with poor immune restoration. This transcriptional dataset enables a deeper understanding of the pathogenesis of HIV-1 infection and is also a rich resource for developing novel immune targeted therapeutic strategies.
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9
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Lau CY, Adan MA, Maldarelli F. Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. Viruses 2021; 13:2512. [PMID: 34960781 PMCID: PMC8708047 DOI: 10.3390/v13122512] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antiretroviral therapy (ART) effectively reduces cycles of viral replication but does not target proviral populations in cells that persist for prolonged periods and that can undergo clonal expansion. Consequently, chronic human immunodeficiency virus (HIV) infection is sustained during ART by a reservoir of long-lived latently infected cells and their progeny. This proviral landscape undergoes change over time on ART. One of the forces driving change in the landscape is the clonal expansion of infected CD4 T cells, which presents a key obstacle to HIV eradication. Potential mechanisms of clonal expansion include general immune activation, antigenic stimulation, homeostatic proliferation, and provirus-driven clonal expansion, each of which likely contributes in varying, and largely unmeasured, amounts to maintaining the reservoir. The role of clinical events, such as infections or neoplasms, in driving these mechanisms remains uncertain, but characterizing these forces may shed light on approaches to effectively eradicate HIV. A limited number of individuals have been cured of HIV infection in the setting of bone marrow transplant; information from these and other studies may identify the means to eradicate or control the virus without ART. In this review, we describe the mechanisms of HIV-1 persistence and clonal expansion, along with the attempts to modify these factors as part of reservoir reduction and cure strategies.
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Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
- Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
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10
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Emerging Single-cell Approaches to Understand HIV in the Central Nervous System. Curr HIV/AIDS Rep 2021; 19:113-120. [PMID: 34822063 PMCID: PMC8613726 DOI: 10.1007/s11904-021-00586-7] [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] [Accepted: 10/05/2021] [Indexed: 11/23/2022]
Abstract
Purpose of Review This review highlights emerging single-cell sequencing methods relevant to translational studies of HIV in the central nervous system (CNS), summarizes limited single-cell studies of HIV in the CNS, and discusses opportunities for future HIV translational CNS studies. Recent Findings Innovative methods utilizing single-cell technologies have advanced the study of genomes, proteomes, transcriptomes, and epigenomes at an enhanced resolution and depth. Single-cell analyses of central nervous system tissue, including autopsy brain and CSF cells, may shed light on CNS perturbations in people living with HIV. New strategies can distinguish distinct molecular identifies of rare infected cells at single-cell level, suggesting an opportunity to uncloak the molecular identity of hidden HIV in the CNS reservoir. Summary Adoption of multimodal “omics” analyses to translational HIV studies and tissue compartments beyond blood will be critical to advancing our understanding of viral establishment, persistence, and eradication.
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11
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Freen-van Heeren JJ. Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses. BIOTECH 2021; 10:21. [PMID: 35822795 PMCID: PMC9245478 DOI: 10.3390/biotech10040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2.
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12
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de Armas LR, Gavegnano C, Pallikkuth S, Rinaldi S, Pan L, Battivelli E, Verdin E, Younis RT, Pahwa R, Williams SL, Schinazi RF, Pahwa S. The Effect of JAK1/2 Inhibitors on HIV Reservoir Using Primary Lymphoid Cell Model of HIV Latency. Front Immunol 2021; 12:720697. [PMID: 34531866 PMCID: PMC8438319 DOI: 10.3389/fimmu.2021.720697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/13/2021] [Indexed: 01/10/2023] Open
Abstract
HIV eradication is hindered by the existence of latent HIV reservoirs in CD4+ T cells. Therapeutic strategies targeting latent cells are required to achieve a functional cure, however the study of latently infected cells from HIV infected persons is extremely challenging due to the lack of biomarkers that uniquely characterize them. In this study, the dual reporter virus HIVGKO was used to investigate latency establishment and maintenance in lymphoid-derived CD4+ T cells. Single cell technologies to evaluate protein expression, host gene expression, and HIV transcript expression were integrated to identify and analyze latently infected cells. FDA-approved, JAK1/2 inhibitors were tested in this system as a potential therapeutic strategy to target the latent reservoir. Latent and productively infected tonsillar CD4+ T cells displayed similar activation profiles as measured by expression of CD69, CD25, and HLADR, however latent cells showed higher CXCR5 expression 3 days post-infection. Single cell analysis revealed a small set of genes, including HIST1-related genes and the inflammatory cytokine, IL32, that were upregulated in latent compared to uninfected and productively infected cells suggesting a role for these molecular pathways in persistent HIV infection. In vitro treatment of HIV-infected CD4+ T cells with physiological concentrations of JAK1/2 inhibitors, ruxolitinib and baricitinib, used in clinical settings to target inflammation, reduced latent and productive infection events when added 24 hr after infection and blocked HIV reactivation from latent cells. Our methods using an established model of HIV latency and lymphoid-derived cells shed light on the biology of latency in a crucial anatomical site for HIV persistence and provides key insights about repurposing baricitinib or ruxolitinib to target the HIV reservoir.
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Affiliation(s)
- Lesley R de Armas
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Christina Gavegnano
- Department of Pathology and Experimental Medicine, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, United States.,Department of Pharmacology and Chemical Biology, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, United States.,Center for AIDS Research, Department of Pediatrics, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, United States
| | - Suresh Pallikkuth
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Stefano Rinaldi
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Li Pan
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Emilie Battivelli
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, United States.,Department of Medicine, University of California San Francisco, San Francisco, CA, United States.,Buck Institute for Research on Aging, Novato, CA, United States
| | - Eric Verdin
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, United States.,Department of Medicine, University of California San Francisco, San Francisco, CA, United States.,Buck Institute for Research on Aging, Novato, CA, United States
| | - Ramzi T Younis
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Rajendra Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Siôn L Williams
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Department of Pediatrics, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, United States
| | - Savita Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
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13
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Combined single-cell transcriptional, translational, and genomic profiling reveals HIV-1 reservoir diversity. Cell Rep 2021; 36:109643. [PMID: 34469719 DOI: 10.1016/j.celrep.2021.109643] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022] Open
Abstract
Although understanding the diversity of HIV-1 reservoirs is key to achieving a cure, their study at the single-cell level in primary samples remains challenging. We combine flow cytometric multiplexed fluorescent in situ RNA hybridization for different viral genes with HIV-1 p24 protein detection, cell phenotyping, and downstream near-full-length single-cell vDNA sequencing. Stimulation-induced viral RNA-positive (vRNA+) cells from viremic and antiretroviral-therapy (ART)-suppressed individuals differ in their ability to produce p24. In participants on ART, latency-reversing agents (LRAs) induce a wide variety of viral gene transcription and translation patterns with LRA class-specific differences in reactivation potency. Reactivated proviruses, including in p24+ cells, are mostly defective. Although LRAs efficiently induce transcription in all memory cell subsets, we observe induction of translation mostly in effector memory cells, rather than in the long-lived central memory pool. We identify HIV-1 clones with diverse transcriptional and translational patterns between individual cells, and this finding suggests that cell-intrinsic factors influence reservoir persistence and heterogeneity.
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14
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Zou D, Qi J, Wu W, Xu D, Tu Y, Liu T, Zhang J, Li X, Lu F, He L. Applications of Single-Cell Sequencing in Dermatology. Med Sci Monit 2021; 27:e931862. [PMID: 34011922 PMCID: PMC8147034 DOI: 10.12659/msm.931862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Single-cell sequencing (SCS) is a promising new technique used to assess the genomics, transcriptomics, epigenetics, and other multi-omics at the single-cell level. In addition to elucidating the immune microenvironment and revealing the pathomechanisms of disease and drug resistance, SCS can profile the actual state of an individual cell and identify a novel cell type and differentiation trajectories, which cannot be achieved by bulk tissue sequencing technique. SCS technique serves as powerful tools to explore more meaningful biomarkers of diagnosis, prognosis, and new therapeutic targets in clinical practice. The SCS technique has been widely applied in the field of dermatology. In this review, we summarize the advances of SCS in dermatology.
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Affiliation(s)
- Dandan Zou
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Jue Qi
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Wenjuan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Dan Xu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Ying Tu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Tongyun Liu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Juan Zhang
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
| | - Xing Li
- Department of Dermatology, People's Hospital of Chuxiong Yi Autonomous Prefecture, Chuxiong, Yunnan, China (mainland)
| | - Fengyan Lu
- Qujing Affiliated Hospital of Kunming Medical University and Department of Dermatology, The First People's Hospital of Qujing, Qujing, Yunnan, China (mainland)
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China (mainland)
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15
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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: 24] [Impact Index Per Article: 8.0] [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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16
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Veenhuis RT, Abreu CM, Shirk EN, Gama L, Clements JE. HIV replication and latency in monocytes and macrophages. Semin Immunol 2021; 51:101472. [PMID: 33648815 PMCID: PMC10171083 DOI: 10.1016/j.smim.2021.101472] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 12/13/2022]
Abstract
The relevance of monocyte and macrophage reservoirs in virally suppressed people with HIV (vsPWH) has previously been debatable. Macrophages were assumed to have a moderate life span and lack self-renewing potential. However, recent studies have challenged this dogma and now suggest an important role of these cell as long-lived HIV reservoirs. Lentiviruses have a long-documented association with macrophages and abundant evidence exists that macrophages are important target cells for HIV in vivo. A critical understanding of HIV infection, replication, and latency in macrophages is needed in order to determine the appropriate method of measuring and eliminating this cellular reservoir. This review provides a brief discussion of the biology and acute and chronic infection of monocytes and macrophages, with a more substantial focus on replication, latency and measurement of the reservoir in cells of myeloid origin.
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Affiliation(s)
- Rebecca T Veenhuis
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Celina M Abreu
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Erin N Shirk
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lucio Gama
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Vaccine Research Center, NIAID, NIH, Bethesda, MD, United States
| | - Janice E Clements
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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17
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Sulen A, Islam S, Wolff ASB, Oftedal BE. The prospects of single-cell analysis in autoimmunity. Scand J Immunol 2020; 92:e12964. [PMID: 32869859 DOI: 10.1111/sji.12964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 12/29/2022]
Abstract
In the last decade, there has been a tremendous development of technologies focused on analysing various molecular attributes in single cells, with an ever-increasing number of parameters becoming available at the DNA, RNA and protein levels. Much of this progress has involved cells in suspension, but also in situ analysis of tissues has taken great leaps. Paralleling the development in the laboratory, and because of increasing complexity, the analysis of single-cell data is also constantly being updated with new algorithms and analysis platforms. Our immune system shares this complexity, and immunologists have therefore been in the forefront of this technological development. These technologies clearly open new avenues for immunology research, maybe particularly within autoimmunity where the interaction between the faulty immune system and the thymus or the target organ is important. However, the technologies currently available can seem overwhelming and daunting. The aim of this review is to remedy this by giving a balanced overview of the prospects of using single-cell analysis in basal and clinical autoimmunity research, with an emphasis on endocrine autoimmunity.
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Affiliation(s)
- André Sulen
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Shahinul Islam
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette S B Wolff
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bergithe E Oftedal
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
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