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Rauch DA, Ramos PV, Khanfar M, Harding J, Joseph A, Griffith O, Griffith M, Ratner L. Single-Cell Transcriptomic Analysis of Kaposi Sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592010. [PMID: 38746135 PMCID: PMC11092626 DOI: 10.1101/2024.05.01.592010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Kaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of "spindle cells", vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined skin and blood samples from twelve subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a proliferative fraction of lymphatic endothelial cells, and the second represented an angiogenic population of vascular endothelial tip cells. Both infected clusters contained cells expressing lytic and latent KSHV genes. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive tumor cells was found to be in the 6% range in HIV-associated KS, correlated inversely with tumor-infiltrating immune cells, and was reduced in biopsies from HIV-negative individuals. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors were identified in subjects treated with antiretroviral therapy alone, or immunotherapy. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers. Author Summary Kaposi sarcoma (KS) is a malignancy caused by the KS-associated herpesvirus (KSHV) that causes skin lesions, and may also be found in lymph nodes, lungs, gastrointestinal tract, and other organs in immunosuppressed individuals more commonly than immunocompetent subjects. The current study examined gene expression in single cells from the tumor and blood of these subjects, and identified the characteristics of the complex mixtures of cells in the tumor. This method also identified differences in KSHV gene expression in different cell types and associated cellular genes expressed in KSHV infected cells. In addition, changes in the cellular composition could be elucidated with therapeutic interventions.
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Brandt L, Angelino P, Martinez R, Cristinelli S, Ciuffi A. Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro through Cell Activation Dynamics. Cells 2023; 12:2689. [PMID: 38067117 PMCID: PMC10706042 DOI: 10.3390/cells12232689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.
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Affiliation(s)
- Ludivine Brandt
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Paolo Angelino
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
- Translational Data Science (TDS)-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
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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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Znaidia M, de Souza-Angelo Y, Létoffé S, Staropoli I, Grzelak L, Ghigo JM, Schwartz O, Casartelli N. Exposure to Secreted Bacterial Factors Promotes HIV-1 Replication in CD4 + T Cells. Microbiol Spectr 2023; 11:e0431322. [PMID: 36853052 PMCID: PMC10100953 DOI: 10.1128/spectrum.04313-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
Microbial translocation is associated with systemic immune activation in HIV-1 disease. Circulating T cells can encounter microbial products in the bloodstream and lymph nodes, where viral replication takes place. The mechanisms by which bacteria contribute to HIV-associated pathogenesis are not completely deciphered. Here, we examined how bacteria may impact T cell function and viral replication. We established cocultures between a panel of live bacteria and uninfected or HIV-1-infected activated peripheral blood CD4-positive (CD4+) T cells. We show that some bacteria, such as Escherichia coli and Acinetobacter baumannii, sustain lymphocyte activation and enhance HIV-1 replication. Bacteria secrete soluble factors that upregulate CD25 and ICAM-1 cell surface levels and activate NF-κB nuclear translocation. Our data also demonstrate that CD25 polarizes at the virological synapse, suggesting a previously unappreciated role of CD25 during viral replication. These findings highlight how interactions between bacterial factors and T cells may promote T cell activation and HIV-1 replication. IMPORTANCE People living with HIV suffer from chronic immune activation despite effective antiretroviral therapy. Early after infection, HIV-1 actively replicates in the gut, causing the breakage of the intestinal epithelial barrier and microbial translocation. Microbial translocation and chronic immune activation have been proven linked; however, gaps in our knowledge on how bacteria contribute to the development of HIV-related diseases remain. Whether T cells in the peripheral blood react to bacterial products and how this affects viral replication are unknown. We show that some bacteria enriched in people living with HIV activate T cells and favor HIV-1's spread. Bacteria release soluble factors that cause the overexpression of cellular molecules related to their activation state. T cells overexpressing these molecules also replicate HIV-1 more efficiently. These results help us learn more about how HIV-1, T cells, and bacteria interact with each other, as well as the mechanisms behind chronic immune activation.
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Affiliation(s)
- M. Znaidia
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - Y. de Souza-Angelo
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - S. Létoffé
- Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - I. Staropoli
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - L. Grzelak
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
| | - J. M. Ghigo
- Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, Paris, France
| | - O. Schwartz
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
- Vaccine Research Institute, Créteil, France
| | - N. Casartelli
- Institut Pasteur, Université Paris-Cité, UMR CNRS 3569, Virus and Immunity Unit, Paris, France
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Identification of CD98 as a Novel Biomarker for HIV-1 Permissiveness and Latent Infection. mBio 2022; 13:e0249622. [PMID: 36214569 PMCID: PMC9765422 DOI: 10.1128/mbio.02496-22] [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] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) can integrate viral DNA into host cell chromosomes to establish a long-term stable latent reservoir, which is a major obstacle to cure HIV-1 infection. The characteristics of the HIV-1 latent reservoir have not been fully understood. Here, we identified 126 upregulated plasma membrane proteins in HIV-1 latently infected cells by a label-free liquid chromatography-tandem mass spectrometry analysis. The higher levels of CD98 expression in multiple HIV-1 latently infected cell lines and primary CD4+ T cells compared to uninfected cells were further confirmed by quantitative reverse transcription PCR (RT-qPCR) and flow cytometry analyses. In addition, CD98high CD4+ T cells displayed hyper-permissiveness to HIV-1 infection and possessed distinct immune phenotypic profiles associated with Th17 and peripheral follicular T helper (pTFH) characteristics. Notably, the CD98high resting memory CD4+ T cells harbored significantly higher cell-associated viral RNA and intact provirus than CD98low counterparts in HIV-1-infected individuals receiving combined antiretroviral therapy. Furthermore, CD98high CD4+ T cells exhibited a robust proliferative capacity and significantly contributed to the clonal expansion of the HIV-1 latent reservoir. Our study demonstrates that CD98 can be used as a novel biomarker of HIV-1 latently infected cells to indicate the effect of various strategies to reduce the viral reservoir. IMPORTANCE Identification of cellular biomarkers is the crucial challenge to eradicate the HIV-1 latent reservoir. In our study, we identified CD98 as a novel plasma membrane biomarker for HIV-1 permissiveness and latent infection. Importantly, CD98high CD4+ T cells exhibited a hyper-permissiveness to HIV-1 infection and significantly contributed to the clonal expansion of the HIV-1 latent reservoir. CD98 could be targeted to develop therapeutic strategies to reduce the HIV-1 latent reservoir in further research.
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Pollara J, Khanal S, Edwards RW, Hora B, Ferrari G, Haynes BF, Bradley T. Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy. BMC Immunol 2022; 23:48. [PMID: 36175869 PMCID: PMC9520965 DOI: 10.1186/s12865-022-00523-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/21/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cellular immune responses are phenotypically and functionally perturbed during HIV-1 infection, with the majority of function restored upon antiretroviral therapy (ART). Despite ART, residual inflammation remains that can lead to HIV-related co-morbidities and mortality, indicating that ART does not fully restore normal immune cell function. Thus, understanding the dynamics of the immune cell landscape during HIV-1 infection and ART is critical to defining cellular dysfunction that occurs during HIV-1 infection and imprints during therapy. RESULTS Here, we have applied single-cell transcriptome sequencing of peripheral blood immune cells from chronic untreated HIV-1 individuals, HIV-1-infected individuals receiving ART and HIV-1 negative individuals. We also applied single-cell transcriptome sequencing to a primary cell model of early HIV-1 infection using CD4+ T cells from healthy donors. We described changes in the transcriptome at high resolution that occurred during HIV-1 infection, and perturbations that remained during ART. We also determined transcriptional differences among T cells expressing HIV-1 transcripts that identified key regulators of HIV-1 infection that may serve as targets for future therapies to block HIV-1 infection. CONCLUSIONS This work identified key molecular pathways that are altered in immune cells during chronic HIV-1 infection that could remain despite therapy. We also identified key genes that are upregulated during early HIV-1 infection that provide insights on the mechanism of HIV-1 infection and could be targets for future therapy.
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Affiliation(s)
- Justin Pollara
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - R Whitney Edwards
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Barton F Haynes
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Immunology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Pediatrics, University of Missouri at Kansas City School of Medicine, Kansas City, MO, 64108, USA.
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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7
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Eid J, Socol M, Naillon A, Feuillard J, Ciandrini L, Margeat E, Charlot B, Mougel M. Viro-fluidics: Real-time analysis of virus production kinetics at the single-cell level. BIOPHYSICAL REPORTS 2022; 2:100068. [PMID: 36425325 PMCID: PMC9680794 DOI: 10.1016/j.bpr.2022.100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Real-time visualization and quantification of viruses released by a cell are crucial to further decipher infection processes. Kinetics studies at the single-cell level will circumvent the limitations of bulk assays with asynchronous virus replication. We have implemented a "viro-fluidic" method, which combines microfluidics and virology at single-cell and single-virus resolutions. As an experimental model, we used standard cell lines producing fluorescent HIV-like particles (VLPs). First, to scale the strategy to the single-cell level, we validated a sensitive flow virometry system to detect VLPs in low concentration samples (≥104 VLPs/mL). Then, this system was coupled to a single-cell trapping device to monitor in real-time the VLPs released, one at a time, from single cells under cell culture conditions. Our results revealed an average production rate of 50 VLPs/h/cell similar to the rate estimated for the same cells grown in population. Thus, the virus-producing capacities of the trapped cells were preserved and its real-time monitoring was accurate. Moreover, single-cell analysis revealed a release of VLPs with stochastic bursts with typical time intervals of few minutes, revealing the existence of limiting step(s) in the virus biogenesis process. Our tools can be applied to other pathogens or to extracellular vesicles to elucidate the dissemination mechanisms of these biological nanoparticles.
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Affiliation(s)
- Joëlle Eid
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Marius Socol
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Antoine Naillon
- Université Grenoble Alpes, CNRS, Grenoble INP, 3SR, Grenoble, France
| | - Jérôme Feuillard
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Luca Ciandrini
- CBS, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Emmanuel Margeat
- CBS, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Benoit Charlot
- IES, Université de Montpellier, CNRS, Montpellier, France
| | - Marylène Mougel
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
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Boateng AT, Abaidoo-Myles A, Bonney EY, Kyei GB. Isoform selective versus non-selective histone deacetylase inhibitors in HIV latency reversal. AIDS Res Hum Retroviruses 2022; 38:615-621. [PMID: 35778852 PMCID: PMC9419941 DOI: 10.1089/aid.2021.0195] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV remains incurable due to the persistence of a latent viral reservoir found in HIV infected cells, primarily resting memory CD4+ T cells. Depletion of this reservoir may be the only way to end this deadly epidemic. In latency, the integrated proviral DNA of HIV is transcriptionally silenced partly due to the activity of histone deacetylases (HDACs). One strategy proposed to overcome this challenge, is the use of HDAC inhibitors as latency reversal agents to induce viral expression (shock) under the cover of antiretroviral therapy (ART). It is hoped that this will lead to elimination of the reservoir by immunologic and viral cytopathic (kill). However, there are 18 isoforms of HDACs leading to varying selectivity for HDAC inhibitors. Here we review HDAC inhibitors with emphasis on their selectivity for HIV latency reversal.
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Affiliation(s)
| | - Araba Abaidoo-Myles
- University of Ghana College of Health Sciences, 108322, Accra, Greater Accra, Ghana;
| | - Evelyn Yayra Bonney
- University of Ghana College of Health Sciences, 108322, Accra, Greater Accra, Ghana;
| | - George B Kyei
- University of Ghana College of Health Sciences, 108322, Virology, Off Akilakpa Sawyerr Road, Accra, Ghana;
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Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV)-associated primary effusion lymphomas (PEL) are traditionally viewed as homogenous regarding viral transcription and lineage of origin, but so far this contention has not been explored at the single-cell level. Single-cell RNA sequencing of latently infected PEL supports the existence of multiple subpopulations even within a single cell line. At most 1% of the cells showed evidence of near-complete lytic transcription. The majority of cells only expressed the canonical viral latent transcripts: those originating from the latency locus, the viral interferon regulatory factor locus, and the viral lncRNA nut-1/Pan/T1.1; however, a significant fraction of cells showed various degrees of more permissive transcription, and some showed no evidence of KSHV transcripts whatsoever. Levels of viral interleukin-6 (IL-6)/K2 mRNA emerged as the most distinguishing feature to subset KSHV-infected PEL. One newly uncovered phenotype is the existence of BCBL-1 cells that readily adhered to fibronectin and that displayed mesenchymal lineage-like characteristics. IMPORTANCE Latency is the defining characteristic of the Herpesviridae and central to the tumorigenesis phenotype of Kaposi's sarcoma-associated herpesvirus (KSHV). KSHV-driven primary effusion lymphomas (PEL) rapidly develop resistance to therapy, suggesting tumor instability and plasticity. At any given time, a fraction of PEL cells spontaneously reactivate KSHV, suggesting transcriptional heterogeneity even within a clonal cell line under optimal growth conditions. This study employed single-cell mRNA sequencing to explore the within-population variability of KSHV transcription and how it relates to host cell transcription. Individual clonal PEL cells exhibited differing patterns of viral transcription. Most cells showed the canonical pattern of KSHV latency (LANA, vCyc, vFLIP, Kaposin, and vIRFs), but a significant fraction evidenced extended viral gene transcription, including of the viral IL-6 homolog, open reading frame K2. This study suggests new targets of intervention for PEL. It establishes a conceptual framework to design KSHV cure studies analogous to those for HIV.
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Richardson ZA, Deleage C, Tutuka CSA, Walkiewicz M, Del Río-Estrada PM, Pascoe RD, Evans VA, Reyesteran G, Gonzales M, Roberts-Thomson S, González-Navarro M, Torres-Ruiz F, Estes JD, Lewin SR, Cameron PU. Multiparameter immunohistochemistry analysis of HIV DNA, RNA and immune checkpoints in lymph node tissue. J Immunol Methods 2022; 501:113198. [PMID: 34863818 PMCID: PMC9036546 DOI: 10.1016/j.jim.2021.113198] [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: 05/23/2021] [Revised: 09/02/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022]
Abstract
The main barrier to a cure for HIV is the persistence of long-lived and proliferating latently infected CD4+ T-cells despite antiretroviral therapy (ART). Latency is well characterized in multiple CD4+ T-cell subsets, however, the contribution of regulatory T-cells (Tregs) expressing FoxP3 as well as immune checkpoints (ICs) PD-1 and CTLA-4 as targets for productive and latent HIV infection in people living with HIV on suppressive ART is less well defined. We used multiplex detection of HIV DNA and RNA with immunohistochemistry (mIHC) on formalin-fixed paraffin embedded (FFPE) cells to simultaneously detect HIV RNA and DNA and cellular markers. HIV DNA and RNA were detected by in situ hybridization (ISH) (RNA/DNAscope) and IHC was used to detect cellular markers (CD4, PD-1, FoxP3, and CTLA-4) by incorporating the tyramide system amplification (TSA) system. We evaluated latently infected cell lines, a primary cell model of HIV latency and excisional lymph node (LN) biopsies collected from people living with HIV (PLWH) on and off ART. We clearly detected infected cells that coexpressed HIV RNA and DNA (active replication) and DNA only (latently infected cells) in combination with IHC markers in the in vitro infection model as well as LN tissue from PLWH both on and off ART. Combining ISH targeting HIV RNA and DNA with IHC provides a platform to detect and quantify HIV persistence within cells identified by multiple markers in tissue samples from PLWH on ART or to study HIV latency.
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Affiliation(s)
- Zuwena A Richardson
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Claire Deleage
- Frederick National Laboratories for Cancer Research, MD, Frederick, United States of America
| | - Candani S A Tutuka
- Olivia Newton John Cancer Centre Research Institute, Austin Hospital, Heidelberg, Australia; La Trobe School of Cancer Medicine, La Trobe University, Melbourne, Australia
| | - Marzena Walkiewicz
- Olivia Newton John Cancer Centre Research Institute, Austin Hospital, Heidelberg, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Perla M Del Río-Estrada
- Centro de Investigación en Enfermdades Infecciosas, Instituto Nacional de Enfermedades Respiratoriras, Mexico City, Mexico
| | - Rachel D Pascoe
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Vanessa A Evans
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Gustavo Reyesteran
- Centro de Investigación en Enfermdades Infecciosas, Instituto Nacional de Enfermedades Respiratoriras, Mexico City, Mexico
| | - Michael Gonzales
- Pathology Department, The Royal Melbourne Hospital, Melbourne, Australia
| | | | - Mauricio González-Navarro
- Centro de Investigación en Enfermdades Infecciosas, Instituto Nacional de Enfermedades Respiratoriras, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermdades Infecciosas, Instituto Nacional de Enfermedades Respiratoriras, Mexico City, Mexico
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health Science University, Portland, Oregon, USA
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia; Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia; Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia; La Trobe School of Cancer Medicine, La Trobe University, Melbourne, Australia; Launceston General Hospital, Tasmania, Launceston, Australia.
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Zhang Y, Xing X, Long B, Cao Y, Hu S, Li X, Yu Y, Tian D, Sui B, Luo Z, Liu W, Lv L, Wu Q, Dai J, Zhou M, Han H, Fu ZF, Gong H, Bai F, Zhao L. A spatial and cellular distribution of rabies virus infection in the mouse brain revealed by fMOST and single-cell RNA sequencing. Clin Transl Med 2022; 12:e700. [PMID: 35051311 PMCID: PMC8776042 DOI: 10.1002/ctm2.700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Neurotropic virus infection can cause serious damage to the central nervous system (CNS) in both humans and animals. The complexity of the CNS poses unique challenges to investigate the infection of these viruses in the brain using traditional techniques. METHODS In this study, we explore the use of fluorescence micro-optical sectioning tomography (fMOST) and single-cell RNA sequencing (scRNA-seq) to map the spatial and cellular distribution of a representative neurotropic virus, rabies virus (RABV), in the whole brain. Mice were inoculated with a lethal dose of a recombinant RABV encoding enhanced green fluorescent protein (EGFP) under different infection routes, and a three-dimensional (3D) view of RABV distribution in the whole mouse brain was obtained using fMOST. Meanwhile, we pinpointed the cellular distribution of RABV by utilizing scRNA-seq. RESULTS Our fMOST data provided the 3D view of a neurotropic virus in the whole mouse brain, which indicated that the spatial distribution of RABV in the brain was influenced by the infection route. Interestingly, we provided evidence that RABV could infect multiple nuclei related to fear independent of different infection routes. More surprisingly, our scRNA-seq data revealed that besides neurons RABV could infect macrophages and the infiltrating macrophages played at least three different antiviral roles during RABV infection. CONCLUSION This study draws a comprehensively spatial and cellular map of typical neurotropic virus infection in the mouse brain, providing a novel and insightful strategy to investigate the pathogenesis of RABV and other neurotropic viruses.
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12
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Izumida M, Kakoki K, Hayashi H, Matsuyama T, Kubo Y. Rab3a, a small GTP-binding protein, is required for the stabilization of the murine leukaemia virus Gag protein. Small GTPases 2022; 13:162-182. [PMID: 34180342 PMCID: PMC9707528 DOI: 10.1080/21541248.2021.1939631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We recently identified a CD63-interacting protein to understand the role of CD63 in virion production of the human immunodeficiency virus type 1, and we have found that Rab3a forms a complex with CD63. In this study, we analysed the effect of Rab3a on virion production of the murine leukaemia virus (MLV), which is another member of the retrovirus family. We found that Rab3a silencing induced lysosomal degradation of the MLV Gag protein, and recovery of the Rab3a expression restored the level of the Gag protein through a complex formation of MLV Gag and Rab3a, indicating that Rab3a is required for MLV Gag protein expression. In contrast, CD63 silencing decreased the infectivity of released virions but had no effect on virion production, indicating that CD63 facilitates the infectivity of released MLV particles. Although Rab3a induced CD63 degradation in uninfected cells, the complex of MLV Gag and Rab3a suppressed the Rab3a-mediated CD63 degradation in MLV-infected cells. Finally, we found that the MLV Gag protein interacts with Rab3a to stabilize its own protein and CD63 that facilitates the infectivity of released MLV particles. Considering the involvement of Rab3a in lysosome trafficking to the plasma membrane, it may also induce cell surface transport of the MLV Gag protein.
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Affiliation(s)
- Mai Izumida
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan,Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Katsura Kakoki
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Japan Association for Development of Community Medicine, Urology Department, Omura Municipal Hospital, Nagasaki, Japan
| | - Hideki Hayashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Medical University Research Administrator, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Toshifumi Matsuyama
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Department of Cancer Stem Cell, Institute of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yoshinao Kubo
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan,Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,CONTACT Yoshinao Kubo Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki852-8523, Japan
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13
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Huang W, Wang D, Yao YF. Understanding the pathogenesis of infectious diseases by single-cell RNA sequencing. MICROBIAL CELL 2021; 8:208-222. [PMID: 34527720 PMCID: PMC8404151 DOI: 10.15698/mic2021.09.759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022]
Abstract
Infections are highly orchestrated and dynamic processes, which involve both pathogen and host. Transcriptional profiling at the single-cell level enables the analysis of cell diversity, heterogeneity of the immune response, and detailed molecular mechanisms underlying infectious diseases caused by bacteria, viruses, fungi, and parasites. Herein, we highlight recent remarkable advances in single-cell RNA sequencing (scRNA-seq) technologies and their applications in the investigation of host-pathogen interactions, current challenges and potential prospects for disease treatment are discussed as well. We propose that with the aid of scRNA-seq, the mechanism of infectious diseases will be further revealed thus inspiring the development of novel interventions and therapies.
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Affiliation(s)
- Wanqiu Huang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
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14
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Brandt L, Cristinelli S, Ciuffi A. Single-Cell Analysis Reveals Heterogeneity of Virus Infection, Pathogenicity, and Host Responses: HIV as a Pioneering Example. Annu Rev Virol 2021; 7:333-350. [PMID: 32991268 DOI: 10.1146/annurev-virology-021820-102458] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
While analyses of cell populations provide averaged information about viral infections, single-cell analyses offer individual consideration, thereby revealing a broad spectrum of diversity as well as identifying extreme phenotypes that can be exploited to further understand the complex virus-host interplay. Single-cell technologies applied in the context of human immunodeficiency virus (HIV) infection proved to be valuable tools to help uncover specific biomarkers as well as novel candidate players in virus-host interactions. This review aims at providing an updated overview of single-cell analyses in the field of HIV and acquired knowledge on HIV infection, latency, and host response. Although HIV is a pioneering example, similar single-cell approaches have proven to be valuable for elucidating the behavior and virus-host interplay in a range of other viruses.
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Affiliation(s)
- Ludivine Brandt
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
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15
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Modeling poliovirus replication dynamics from live time-lapse single-cell imaging data. Sci Rep 2021; 11:9622. [PMID: 33953215 PMCID: PMC8100109 DOI: 10.1038/s41598-021-87694-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 03/15/2021] [Indexed: 02/03/2023] Open
Abstract
Viruses experience selective pressure on the timing and order of events during infection to maximize the number of viable offspring they produce. Additionally, they may experience variability in cellular environments encountered, as individual eukaryotic cells can display variation in gene expression among cells. This leads to a dynamic phenotypic landscape that viruses must face to replicate. To examine replication dynamics displayed by viruses faced with this variable landscape, we have developed a method for fitting a stochastic mechanistic model of viral infection to time-lapse imaging data from high-throughput single-cell poliovirus infection experiments. The model's mechanistic parameters provide estimates of several aspects associated with the virus's intracellular dynamics. We examine distributions of parameter estimates and assess their variability to gain insight into the root causes of variability in viral growth dynamics. We also fit our model to experiments performed under various drug treatments and examine which parameters differ under these conditions. We find that parameters associated with translation and early stage viral replication processes are essential for the model to capture experimentally observed dynamics. In aggregate, our results suggest that differences in viral growth data generated under different treatments can largely be captured by steps that occur early in the replication process.
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16
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Aso H, Nagaoka S, Kawakami E, Ito J, Islam S, Tan BJY, Nakaoka S, Ashizaki K, Shiroguchi K, Suzuki Y, Satou Y, Koyanagi Y, Sato K. Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In Vivo. Cell Rep 2021; 32:107887. [PMID: 32668246 DOI: 10.1016/j.celrep.2020.107887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
For eradication of HIV-1 infection, it is important to elucidate the detailed features and heterogeneity of HIV-1-infected cells in vivo. To reveal multiple characteristics of HIV-1-producing cells in vivo, we use a hematopoietic-stem-cell-transplanted humanized mouse model infected with GFP-encoding replication-competent HIV-1. We perform multiomics experiments using recently developed technology to identify the features of HIV-1-infected cells. Genome-wide HIV-1 integration-site analysis reveals that productive HIV-1 infection tends to occur in cells with viral integration into transcriptionally active genomic regions. Bulk transcriptome analysis reveals that a high level of viral mRNA is transcribed in HIV-1-infected cells. Moreover, single-cell transcriptome analysis shows the heterogeneity of HIV-1-infected cells, including CXCL13high cells and a subpopulation with low expression of interferon-stimulated genes, which can contribute to efficient viral spread in vivo. Our findings describe multiple characteristics of HIV-1-producing cells in vivo, which could provide clues for the development of an HIV-1 cure.
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Affiliation(s)
- Hirofumi Aso
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Shumpei Nagaoka
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Eiryo Kawakami
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan; Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba 2608670, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Saiful Islam
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Benjy Jek Yang Tan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 0600810, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Koichi Ashizaki
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan
| | - Katsuyuki Shiroguchi
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 5650874, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 2300045, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 2778561, Japan
| | - Yorifumi Satou
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan.
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17
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Zielinski JM, Luke JJ, Guglietta S, Krieg C. High Throughput Multi-Omics Approaches for Clinical Trial Evaluation and Drug Discovery. Front Immunol 2021; 12:590742. [PMID: 33868223 PMCID: PMC8044891 DOI: 10.3389/fimmu.2021.590742] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
High throughput single cell multi-omics platforms, such as mass cytometry (cytometry by time-of-flight; CyTOF), high dimensional imaging (>6 marker; Hyperion, MIBIscope, CODEX, MACSima) and the recently evolved genomic cytometry (Citeseq or REAPseq) have enabled unprecedented insights into many biological and clinical questions, such as hematopoiesis, transplantation, cancer, and autoimmunity. In synergy with constantly adapting new single-cell analysis approaches and subsequent accumulating big data collections from these platforms, whole atlases of cell types and cellular and sub-cellular interaction networks are created. These atlases build an ideal scientific discovery environment for reference and data mining approaches, which often times reveals new cellular disease networks. In this review we will discuss how combinations and fusions of different -omic workflows on a single cell level can be used to examine cellular phenotypes, immune effector functions, and even dynamic changes, such as metabolomic state of different cells in a sample or even in a defined tissue location. We will touch on how pre-print platforms help in optimization and reproducibility of workflows, as well as community outreach. We will also shortly discuss how leveraging single cell multi-omic approaches can be used to accelerate cellular biomarker discovery during clinical trials to predict response to therapy, follow responsive cell types, and define novel druggable target pathways. Single cell proteome approaches already have changed how we explore cellular mechanism in disease and during therapy. Current challenges in the field are how we share these disruptive technologies to the scientific communities while still including new approaches, such as genomic cytometry and single cell metabolomics.
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Affiliation(s)
- Jessica M Zielinski
- Hollings Cancer Center, Medical University of South Carolina (MUSC), Charleston, SC, United States
| | - Jason J Luke
- Hillman Cancer Center, Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Silvia Guglietta
- Hollings Cancer Center, Medical University of South Carolina (MUSC), Charleston, SC, United States
| | - Carsten Krieg
- Hollings Cancer Center, Medical University of South Carolina (MUSC), Charleston, SC, United States
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18
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Fromentin R, Chomont N. HIV persistence in subsets of CD4+ T cells: 50 shades of reservoirs. Semin Immunol 2021; 51:101438. [PMID: 33272901 PMCID: PMC8164644 DOI: 10.1016/j.smim.2020.101438] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/19/2020] [Indexed: 12/16/2022]
Abstract
Antiretroviral therapy controls HIV replication but does not eliminate the virus from the infected host. The persistence of a small pool of cells harboring integrated and replication-competent HIV genomes impedes viral eradication efforts. The HIV reservoir was originally described as a relatively homogeneous pool of resting memory CD4+ T cells. Over the past 20 years, the identification of multiple cellular subsets of CD4+ T cells endowed with distinct biological properties shed new lights on the heterogeneity of HIV reservoirs. It is now clear that HIV persists in a large variety of CD4+ T cells, which contribute to HIV persistence through different mechanisms. In this review, we summarize recent findings indicating that specific biological features of well-characterized subsets of CD4+ T cells individually contribute to the persistence of HIV. These include an increased sensitivity to HIV infection, specific tissue locations, enhanced survival and heightened capacity to proliferate. We also discuss the relative abilities of these cellular reservoirs to contribute to viral rebound upon ART interruption. Together, these findings reveal that the HIV reservoir is not homogeneous and should be viewed as a mosaic of multiple cell types that all contribute to HIV persistence through different mechanisms.
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Affiliation(s)
- Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada.
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19
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Single-cell RNA-seq reveals CD16 - monocytes as key regulators of human monocyte transcriptional response to Toxoplasma. Sci Rep 2020; 10:21047. [PMID: 33273621 PMCID: PMC7713135 DOI: 10.1038/s41598-020-78250-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Monocytes are among the major myeloid cells that respond to Toxoplasma, a ubiquitous foodborne that infects ≥ 1 billion people worldwide, in human peripheral blood. As such, a molecular understanding of human monocyte-Toxoplasma interactions can expedite the development of novel human toxoplasmosis control strategies. Current molecular studies on monocyte-Toxoplasma interactions are based on average cell or parasite responses across bulk cell populations. Although informative, population-level averages of monocyte responses to Toxoplasma have sometimes produced contradictory results, such as whether CCL2 or IL12 define effective monocyte responses to the parasite. Here, we used single-cell dual RNA sequencing (scDual-Seq) to comprehensively define, for the first time, the monocyte and parasite transcriptional responses that underpin human monocyte-Toxoplasma encounters at the single cell level. We report extreme transcriptional variability between individual monocytes. Furthermore, we report that Toxoplasma-exposed and unexposed monocytes are transcriptionally distinguished by a reactive subset of CD14+CD16- monocytes. Functional cytokine assays on sorted monocyte populations show that the infection-distinguishing monocytes secrete high levels of chemokines, such as CCL2 and CXCL5. These findings uncover the Toxoplasma-induced monocyte transcriptional heterogeneity and shed new light on the cell populations that largely define cytokine and chemokine secretion in human monocytes exposed to Toxoplasma.
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20
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Wang S, Zhang Q, Hui H, Agrawal K, Karris MAY, Rana TM. An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics. Emerg Microbes Infect 2020; 9:2333-2347. [PMID: 32954948 PMCID: PMC7646563 DOI: 10.1080/22221751.2020.1826361] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023]
Abstract
Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters, and three of these (exhausted CD4+ and CD8+ T cells and interferon-responsive CD8+ T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8+ T cell population expressing KLRG1, TIGIT, and T-betdimEomeshi markers. Ex-vivo antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8+ T cells demonstrating the contribution of KLRG1+ population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.
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Affiliation(s)
- Shaobo Wang
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- UCSD Center for AIDS Research, University of California San Diego, La Jolla, CA, USA
| | - Qiong Zhang
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- UCSD Center for AIDS Research, University of California San Diego, La Jolla, CA, USA
| | - Hui Hui
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- Department of Biology, Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
| | - Kriti Agrawal
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- Department of Biology, Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
| | - Maile Ann Young Karris
- Department of Medicine, Division of Infectious Diseases, University of California San Diego, La Jolla, CA, USA
| | - Tariq M. Rana
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- UCSD Center for AIDS Research, University of California San Diego, La Jolla, CA, USA
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21
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Tamalet C, Devaux C, Dubourg G, Colson P. Resistance to human immunodeficiency virus infection: a rare but neglected state. Ann N Y Acad Sci 2020; 1485:22-42. [PMID: 33009659 DOI: 10.1111/nyas.14452] [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: 04/15/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022]
Abstract
The natural history of human immunodeficiency virus (HIV) infection is well understood. In most individuals sexually exposed to HIV, the risk of becoming infected depends on the viral load and on sexual practices and gender. However, a low percentage of individuals who practice frequent unprotected sexual intercourse with HIV-infected partners remain uninfected. Although the systematic study of these individuals has made it possible to identify HIV resistance factors including protective genetic patterns, such epidemiological situations remain paradoxical and not fully understood. In vitro experiments have demonstrated that peripheral blood mononuclear cells (PBMCs) from HIV-free, unexposed blood donors are not equally susceptible to HIV infection; in addition, PBMCs from highly exposed seronegative individuals are generally resistant to infection by primary HIV clinical isolates. We review the literature on permissiveness of PBMCs from healthy blood donors and uninfected hyperexposed individuals to sustained infection and replication of HIV-1 in vitro. In addition, we focus on recent evidence indicating that the gut microbiota may either contribute to natural resistance to or delay replication of HIV infected individuals.
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Affiliation(s)
- Catherine Tamalet
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Gregory Dubourg
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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22
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Lyu J, Miao T, Dong J, Cao R, Li Y, Chen Q. Reflection on lower rates of COVID-19 in children: Does childhood immunizations offer unexpected protection? Med Hypotheses 2020; 143:109842. [PMID: 32425304 PMCID: PMC7227545 DOI: 10.1016/j.mehy.2020.109842] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/25/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023]
Abstract
The incidence of COVID-19 in children and teenagers is only about 2% in China. Children had mild symptoms and hardly infected other children or adults. It is worth considering that children are the most vulnerable to respiratory pathogens, but fatal SARS-like virus had not caused severe cases among them. According to the pathological studies of COVID-19 and SARS, a sharp decrease in T lymphocytes leads to the breakdown of the immune system. The cellular immune system of children differs from that of adults may be the keystone of atypical clinical manifestations or even covert infection. The frequent childhood vaccinations and repeated pathogens infections might be resulting in trained immunity of innate immune cells, immune fitness of adaptive immune cells or cross-protection of antibodies in the children. Therefore, due to lack of specific vaccine, some vaccines for tuberculosis, influenza and pneumonia may have certain application potential for the front-line health workers in the prevention and control of COVID-19. However, for high-risk susceptible populations, such as the elderly with basic diseases such as hypertension and diabetes, it is necessary to explore the remedial effect of the planned immune process on their immunity to achieve the trained immunity or immune fitness, so as to improve their own antiviral ability.
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Affiliation(s)
- Jinglu Lyu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | - Tianyu Miao
- Department of Pulmonary and Critical Care Medicine, Vascular Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Jiajia Dong
- Department of Pulmonary and Critical Care Medicine, Vascular Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Ranran Cao
- Sichuan Provincial Centers for Disease Control and Prevention, Chengdu, Sichuan 610041, China
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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23
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Singh R. Single-Cell Sequencing in Human Genital Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:203-220. [PMID: 32949402 DOI: 10.1007/978-981-15-4494-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Human genital infections are one of the most concerning issues worldwide and can be categorized into sexually transmitted, urinary tract and vaginal infections. These infections, if left untreated, can disseminate to the other parts of the body and cause more complicated illnesses such as pelvic inflammatory disease, urethritis, and anogenital cancers. The effective treatment against these infections is further complicated by the emergence of antimicrobial resistance in the genital infection causing pathogens. Furthermore, the development and applications of single-cell sequencing technologies have open new possibilities to study the drug resistant clones, cell to cell variations, the discovery of acquired drug resistance mutations, transcriptional diversity of a pathogen across different infection stages, to identify rare cell types and investigate different cellular states of genital infection causing pathogens, and to develop novel therapeutical strategies. In this chapter, I will provide a complete review of the applications of single-cell sequencing in human genital infections before discussing their limitations and challenges.
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Affiliation(s)
- Reema Singh
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada. .,Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK, Canada.
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24
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Noé A, Cargill TN, Nielsen CM, Russell AJC, Barnes E. The Application of Single-Cell RNA Sequencing in Vaccinology. J Immunol Res 2020; 2020:8624963. [PMID: 32802896 PMCID: PMC7411487 DOI: 10.1155/2020/8624963] [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: 03/20/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA sequencing allows highly detailed profiling of cellular immune responses from limited-volume samples, advancing prospects of a new era of systems immunology. The power of single-cell RNA sequencing offers various opportunities to decipher the immune response to infectious diseases and vaccines. Here, we describe the potential uses of single-cell RNA sequencing methods in prophylactic vaccine development, concentrating on infectious diseases including COVID-19. Using examples from several diseases, we review how single-cell RNA sequencing has been used to evaluate the immunological response to different vaccine platforms and regimens. By highlighting published and unpublished single-cell RNA sequencing studies relevant to vaccinology, we discuss some general considerations how the field could be enriched with the widespread adoption of this technology.
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MESH Headings
- Animals
- Betacoronavirus/immunology
- COVID-19
- Cell Line
- Clinical Trials as Topic
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Disease Models, Animal
- Drug Evaluation, Preclinical
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Immunity, Cellular/genetics
- Immunity, Innate/genetics
- Immunogenicity, Vaccine
- Pandemics/prevention & control
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- RNA, Viral/isolation & purification
- RNA-Seq/methods
- SARS-CoV-2
- Single-Cell Analysis
- Vaccinology/methods
- Viral Vaccines/administration & dosage
- Viral Vaccines/immunology
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Affiliation(s)
- Andrés Noé
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Tamsin N. Cargill
- Peter Medawar Building for Pathogen Research and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Carolyn M. Nielsen
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | | | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
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25
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León-Rivera R, Morsey B, Niu M, Fox HS, Berman JW. Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities. mBio 2020; 11:e01037-20. [PMID: 32723919 PMCID: PMC7387797 DOI: 10.1128/mbio.01037-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/22/2020] [Indexed: 12/31/2022] Open
Abstract
HIV reservoirs persist despite successful antiretroviral therapy (ART) and are a major obstacle to the eradication and cure of HIV. The mature monocyte subset, CD14+CD16+, contributes to viral reservoirs and HIV-associated comorbidities. Only a subset of monocytes harbors HIV (HIV+), while the rest remain uninfected, exposed cells (HIVexp). We developed an innovative single cell RNA sequencing (scRNAseq) pipeline that detects HIV and host transcripts simultaneously, enabling us to examine differences between HIV+ and HIVexp mature monocytes. Using this, we characterized uninfected, HIV+, and HIVexp primary human mature monocytes with and without ART. We showed that HIV+ mature monocytes do not form their own cluster separately from HIVexp but can be distinguished by significant differential gene expression. We found that ART decreased levels of unspliced HIV transcripts potentially by modulating host transcriptional regulators shown to decrease viral infection and replication. We also identified and characterized mature monocyte subpopulations differentially impacted by HIV and ART. We identified genes dysregulated by ART in HIVexp monocytes compared to their uninfected counterpart and, of interest, the junctional protein ALCAM, suggesting that ART impacts monocyte functions. Our data provide a novel method for simultaneous detection of HIV and host transcripts. We identify potential targets, such as those genes whose expression is increased in HIV+ mature monocytes compared to HIVexp, to block their entry into tissues, preventing establishment/replenishment of HIV reservoirs even with ART, thereby reducing and/or eliminating viral burden and HIV-associated comorbidities. Our data also highlight the heterogeneity of mature monocyte subsets and their potential contributions to HIV pathogenesis in the ART era.IMPORTANCE HIV enters tissues early after infection, leading to establishment and persistence of HIV reservoirs despite antiretroviral therapy (ART). Viral reservoirs are a major obstacle to the eradication and cure of HIV. CD14+CD16+ (mature) monocytes may contribute to establishment and reseeding of reservoirs. A subset of monocytes, consisting mainly of CD14+CD16+ cells, harbors HIV (HIV+), while the rest remain uninfected, exposed cells (HIVexp). It is important to identify cells harboring virus to eliminate reservoirs. Using an innovative single-cell RNA sequencing (scRNAseq) pipeline to detect HIV and host transcripts simultaneously, we characterized HIV+ and HIVexp primary human mature monocytes with and without ART. HIV+ mature monocytes are not a unique subpopulation but rather can be distinguished from HIVexp by differential gene expression. We characterized mature monocyte subpopulations differently impacted by HIV and ART, highlighting their potential contributions to HIV-associated comorbidities. Our data propose therapeutic targets to block HIV+ monocyte entry into tissues, preventing establishment and replenishment of reservoirs even with ART.
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Affiliation(s)
- Rosiris León-Rivera
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Brenda Morsey
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Meng Niu
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Howard S Fox
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan W Berman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
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26
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Liu W, He H, Zheng SY. Microfluidics in Single-Cell Virology: Technologies and Applications. Trends Biotechnol 2020; 38:1360-1372. [PMID: 32430227 DOI: 10.1016/j.tibtech.2020.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
Abstract
Microfluidics has proven to be a powerful tool for probing biology at the single-cell level. However, it is only in the past 5 years that single-cell microfluidics has been used in the field of virology. An array of strategies based on microwells, microvalves, and droplets is now available for tracking viral infection dynamics, identifying cell subpopulations with particular phenotypes, as well as high-throughput screening. The insights into the virus-host interactions gained at the single-cell level are unprecedented and usually inaccessible by population-based experiments. Therefore, single-cell microfluidics, which opens new avenues for mechanism elucidation and development of antiviral therapeutics, would be a valuable tool for the study of viral pathogenesis.
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Affiliation(s)
- Wu Liu
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Hongzhang He
- Captis Diagnostics Inc., Pittsburgh, PA 15213, USA
| | - Si-Yang Zheng
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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27
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Hsiao F, Frouard J, Gramatica A, Xie G, Telwatte S, Lee GQ, Roychoudhury P, Schwarzer R, Luo X, Yukl SA, Lee S, Hoh R, Deeks SG, Jones RB, Cavrois M, Greene WC, Roan NR. Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection. PLoS Pathog 2020; 16:e1008450. [PMID: 32353080 PMCID: PMC7192375 DOI: 10.1371/journal.ppat.1008450] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
The primary reservoir for HIV is within memory CD4+ T cells residing within tissues, yet the features that make some of these cells more susceptible than others to infection by HIV is not well understood. Recent studies demonstrated that CCR5-tropic HIV-1 efficiently enters tissue-derived memory CD4+ T cells expressing CD127, the alpha chain of the IL7 receptor, but rarely completes the replication cycle. We now demonstrate that the inability of HIV to replicate in these CD127-expressing cells is not due to post-entry restriction by SAMHD1. Rather, relative to other memory T cell subsets, these cells are highly prone to undergoing latent infection with HIV, as revealed by the high levels of integrated HIV DNA in these cells. Host gene expression profiling revealed that CD127-expressing memory CD4+ T cells are phenotypically distinct from other tissue memory CD4+ T cells, and are defined by a quiescent state with diminished NFκB, NFAT, and Ox40 signaling. However, latently-infected CD127+ cells harbored unspliced HIV transcripts and stimulation of these cells with anti-CD3/CD28 reversed latency. These findings identify a novel subset of memory CD4+ T cells found in tissue and not in blood that are preferentially targeted for latent infection by HIV, and may serve as an important reservoir to target for HIV eradication efforts.
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Affiliation(s)
- Feng Hsiao
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
- Department of Urology, University of California, San Francisco, California, United States of America
| | - Julie Frouard
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
- Department of Urology, University of California, San Francisco, California, United States of America
| | - Andrea Gramatica
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
| | - Guorui Xie
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
- Department of Urology, University of California, San Francisco, California, United States of America
| | - Sushama Telwatte
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco, California, United States of America
| | - Guinevere Q. Lee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Roland Schwarzer
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
| | - Xiaoyu Luo
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
| | - Steven A. Yukl
- San Francisco Veterans Affairs (VA) Medical Center and University of California, San Francisco, California, United States of America
| | - Sulggi Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, California, United States of America
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - R. Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
| | - Marielle Cavrois
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
| | - Warner C. Greene
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
- Departments of Medicine and Departments of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Nadia R. Roan
- Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
- Department of Urology, University of California, San Francisco, California, United States of America
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28
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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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29
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Shnayder M, Nachshon A, Rozman B, Bernshtein B, Lavi M, Fein N, Poole E, Avdic S, Blyth E, Gottlieb D, Abendroth A, Slobedman B, Sinclair J, Stern-Ginossar N, Schwartz M. Single cell analysis reveals human cytomegalovirus drives latently infected cells towards an anergic-like monocyte state. eLife 2020; 9:e52168. [PMID: 31967545 PMCID: PMC7039680 DOI: 10.7554/elife.52168] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/21/2020] [Indexed: 12/25/2022] Open
Abstract
Human cytomegalovirus (HCMV) causes a lifelong infection through establishment of latency. Although reactivation from latency can cause life-threatening disease, our molecular understanding of HCMV latency is incomplete. Here we use single cell RNA-seq analysis to characterize latency in monocytes and hematopoietic stem and progenitor cells (HSPCs). In monocytes, we identify host cell surface markers that enable enrichment of latent cells harboring higher viral transcript levels, which can reactivate more efficiently, and are characterized by reduced intrinsic immune response that is important for viral gene expression. Significantly, in latent HSPCs, viral transcripts could be detected only in monocyte progenitors and were also associated with reduced immune-response. Overall, our work indicates that regardless of the developmental stage in which HCMV infects, HCMV drives hematopoietic cells towards a weaker immune-responsive monocyte state and that this anergic-like state is crucial for the virus ability to express its transcripts and to eventually reactivate.
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Affiliation(s)
- Miri Shnayder
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Batsheva Rozman
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Biana Bernshtein
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Michael Lavi
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Noam Fein
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Emma Poole
- Department of Medicine, Addenbrooke's Hospital, University of CambridgeCambridgeUnited Kingdom
| | - Selmir Avdic
- Sydney Cellular Therapies Laboratory, WestmeadSydneyAustralia
| | - Emily Blyth
- Sydney Cellular Therapies Laboratory, WestmeadSydneyAustralia
- Blood and Bone Marrow Transplant Unit, Westmead HospitalSydneyAustralia
| | - David Gottlieb
- Sydney Cellular Therapies Laboratory, WestmeadSydneyAustralia
- Blood and Bone Marrow Transplant Unit, Westmead HospitalSydneyAustralia
| | - Allison Abendroth
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, Charles Perkins Centre, University of SydneySydneyAustralia
| | - Barry Slobedman
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, Charles Perkins Centre, University of SydneySydneyAustralia
| | - John Sinclair
- Department of Medicine, Addenbrooke's Hospital, University of CambridgeCambridgeUnited Kingdom
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
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30
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Immunology Driven by Large-Scale Single-Cell Sequencing. Trends Immunol 2019; 40:1011-1021. [DOI: 10.1016/j.it.2019.09.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 12/28/2022]
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31
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Wyler E, Franke V, Menegatti J, Kocks C, Boltengagen A, Praktiknjo S, Walch-Rückheim B, Bosse J, Rajewsky N, Grässer F, Akalin A, Landthaler M. Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program. Nat Commun 2019; 10:4878. [PMID: 31653857 PMCID: PMC6814756 DOI: 10.1038/s41467-019-12894-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Herpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantify the transcriptome of single human primary fibroblasts during the first hours of lytic infection with HSV-1. By applying a generalizable analysis scheme, we define a precise temporal order of early viral gene expression and propose a set-wise emergence of viral genes. We identify host cell genes and pathways relevant for infection by combining three different computational approaches: gene and pathway overdispersion analysis, prediction of cell-state transition probabilities, as well as future cell states. One transcriptional program, which correlates with increased resistance to infection, implicates the transcription factor NRF2. Consequently, Bardoxolone methyl and Sulforaphane, two known NRF2 agonists, impair virus production, suggesting that NRF2 activation restricts viral infection. Our study provides insights into early stages of HSV-1 infection and serves as a general blueprint for the investigation of heterogeneous cell states in virus infection.
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Affiliation(s)
- Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Vedran Franke
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Jennifer Menegatti
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse Haus, 4766421, Homburg/Saar, Germany
| | - Christine Kocks
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Anastasiya Boltengagen
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Samantha Praktiknjo
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Barbara Walch-Rückheim
- Institute of Virology and Center of Human und Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Jens Bosse
- Heinrich Pette Institute (HPI), Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Friedrich Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse Haus, 4766421, Homburg/Saar, Germany
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
- IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany.
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32
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Csősz É, Tóth F, Mahdi M, Tsaprailis G, Emri M, Tőzsér J. Analysis of networks of host proteins in the early time points following HIV transduction. BMC Bioinformatics 2019; 20:398. [PMID: 31315557 PMCID: PMC6637640 DOI: 10.1186/s12859-019-2990-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background Utilization of quantitative proteomics data on the network level is still a challenge in proteomics data analysis. Currently existing models use sophisticated, sometimes hard to implement analysis techniques. Our aim was to generate a relatively simple strategy for quantitative proteomics data analysis in order to utilize as much of the data generated in a proteomics experiment as possible. Results In this study, we applied label-free proteomics, and generated a network model utilizing both qualitative, and quantitative data, in order to examine the early host response to Human Immunodeficiency Virus type 1 (HIV-1). A weighted network model was generated based on the amount of proteins measured by mass spectrometry, and analysis of weighted networks and functional sub-networks revealed upregulation of proteins involved in translation, transcription, and DNA condensation in the early phase of the viral life-cycle. Conclusion A relatively simple strategy for network analysis was created and applied to examine the effect of HIV-1 on host cellular proteome. We believe that our model may prove beneficial in creating algorithms, allowing for both quantitative and qualitative studies of proteome change in various biological and pathological processes by quantitative mass spectrometry. Electronic supplementary material The online version of this article (10.1186/s12859-019-2990-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary.
| | - Ferenc Tóth
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary
| | - Mohamed Mahdi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary
| | - George Tsaprailis
- Arizona Research Labs, University of Arizona, PO Box 210066, Administration Building, Room 601, Tucson, AZ, 85721-0066, USA.,The Scripps Research Institute, 132 Scripps Way, Jupiter, FL, 33458, USA
| | - Miklós Emri
- Department of Medical Imaging, Division of Nuclear Medicine and Translational Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98., Debrecen, 4032, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary. .,Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary.
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33
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van den Esker MH, Koets AP. Application of Transcriptomics to Enhance Early Diagnostics of Mycobacterial Infections, with an Emphasis on Mycobacterium avium ssp. paratuberculosis. Vet Sci 2019; 6:vetsci6030059. [PMID: 31247942 PMCID: PMC6789504 DOI: 10.3390/vetsci6030059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/14/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022] Open
Abstract
Mycobacteria cause a wide variety of disease in human and animals. Species that infect ruminants include M. bovis and M. avium ssp. paratuberculosis (MAP). MAP is the causative agent of Johne’s disease in ruminants, which is a chronic granulomatous enteric infection that leads to severe economic losses worldwide. Characteristic of MAP infection is the long, latent phase in which intermittent shedding can take place, while diagnostic tests are unable to reliably detect an infection in this stage. This leads to unnoticed dissemination within herds and the presence of many undetected, silent carriers, which makes the eradication of Johne’s disease difficult. To improve the control of MAP infection, research is aimed at improving early diagnosis. Transcriptomic approaches can be applied to characterize host-pathogen interactions during infection, and to develop novel biomarkers using transcriptional profiles. Studies have focused on the identification of specific RNAs that are expressed in different infection stages, which will assist in the development and clinical implementation of early diagnostic tests.
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Affiliation(s)
- Marielle H van den Esker
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, 8200 AB Lelystad, The Netherlands
| | - Ad P Koets
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, 8200 AB Lelystad, The Netherlands.
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3508 TD Utrecht, The Netherlands.
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Abstract
Current primary cell models for HIV latency correlate poorly with the reactivation behavior of patient cells. We have developed a new model, called QUECEL, which generates a large and homogenous population of latently infected CD4+ memory cells. By purifying HIV-infected cells and inducing cell quiescence with a defined cocktail of cytokines, we have eliminated the largest problems with previous primary cell models of HIV latency: variable infection levels, ill-defined polarization states, and inefficient shutdown of cellular transcription. Latency reversal in the QUECEL model by a wide range of agents correlates strongly with RNA induction in patient samples. This scalable and highly reproducible model of HIV latency will permit detailed analysis of cellular mechanisms controlling HIV latency and reactivation. The latent HIV reservoir is generated following HIV infection of activated effector CD4 T cells, which then transition to a memory phenotype. Here, we describe an ex vivo method, called QUECEL (quiescent effector cell latency), that mimics this process efficiently and allows production of large numbers of latently infected CD4+ T cells. Naïve CD4+ T cells were polarized into the four major T cell subsets (Th1, Th2, Th17, and Treg) and subsequently infected with a single-round reporter virus which expressed GFP/CD8a. The infected cells were purified and coerced into quiescence using a defined cocktail of cytokines, including tumor growth factor beta, interleukin-10 (IL-10), and IL-8, producing a homogeneous population of latently infected cells. Flow cytometry and transcriptome sequencing (RNA-Seq) demonstrated that the cells maintained the correct polarization phenotypes and had withdrawn from the cell cycle. Key pathways and gene sets enriched during transition from quiescence to reactivation include E2F targets, G2M checkpoint, estrogen response late gene expression, and c-myc targets. Reactivation of HIV by latency-reversing agents (LRAs) closely mimics RNA induction profiles seen in cells from well-suppressed HIV patient samples using the envelope detection of in vitro transcription sequencing (EDITS) assay. Since homogeneous populations of latently infected cells can be recovered, the QUECEL model has an excellent signal-to-noise ratio and has been extremely consistent and reproducible in numerous experiments performed during the last 4 years. The ease, efficiency, and accuracy of the mimicking of physiological conditions make the QUECEL model a robust and reproducible tool to study the molecular mechanisms underlying HIV latency.
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35
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Abner E, Jordan A. HIV "shock and kill" therapy: In need of revision. Antiviral Res 2019; 166:19-34. [PMID: 30914265 DOI: 10.1016/j.antiviral.2019.03.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/08/2019] [Accepted: 03/17/2019] [Indexed: 01/05/2023]
Abstract
The implementation of antiretroviral therapy 23 years ago has rendered HIV infection clinically manageable. However, the disease remains incurable, since it establishes latent proviral reservoirs, which in turn can stochastically begin reproducing viral particles throughout the patient's lifetime. Viral latency itself depends in large part on the silencing environment of the infected host cell, which can be chemically manipulated. "Shock and kill" therapy intends to reverse proviral quiescence by inducing transcription with pharmaceuticals and allowing a combination of antiretroviral therapy, host immune clearance and HIV-cytolysis to remove latently infected cells, leading to a complete cure. Over 160 compounds functioning as latency-reversing agents (LRAs) have been identified to date, but none of the candidates has yet led to a promising functional cure. Furthermore, fundamental bioinformatic and clinical research from the past decade has highlighted the complexity and highly heterogeneous nature of the proviral reservoirs, shedding doubt on the "shock and kill" concept. Alternative therapies such as the HIV transcription-inhibiting "block and lock" strategy are therefore being considered. In this review we describe the variety of existing classes of LRAs, discuss their current drawbacks and highlight the potential for combinatorial "shocktail" therapies for potent proviral reactivation. We also suggest investigating LRAs with lesser-known mechanisms of action, and examine the feasibility of "block and lock" therapy.
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Affiliation(s)
- Erik Abner
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain.
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Ye C, Zhou Q, Hong Y, Li QQ. Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution. RNA Biol 2019; 16:785-797. [PMID: 30810468 DOI: 10.1080/15476286.2019.1586139] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Alternative polyadenylation (APA) has been discovered to play regulatory roles in the development of many cancer cells through preferential addition of a poly(A) tail at specific sites of pre-mRNA. A recent study found that APA was involved in the mediation of acute myeloid leukaemia (AML). However, unlike gene expression heterogeneity, little attention has been directed toward variations in single-cell APA for different cell types during AML development. Here, we used single-cell RNA-seq data of a massive population of 16,843 bone marrow mononuclear cells (BMMCs) from healthy and AML patient samples to investigate dynamic APA usage in different cell types. Abnormalities of APA dynamics in the BMMCs from AML patient samples were uncovered compared to the stable APA dynamics in samples from healthy individuals, as well as lower APA diversity between eight cell types in AML patients. Genes with APA dynamics specific to the AML samples were significantly enriched in cellular signal transduction pathways that contribute to AML development. Moreover, many leukaemic cell marker genes such as NF-κB, GATA2 and IAP-Family genes exhibited APA dynamics that specifically affected abnormal proliferation and differentiation of leukemic BMMCs. Additionally, mature erythroid cells displayed greater APA dynamics and global 3' UTR shortening compared with other cell types. Our results revealed extensive involvement of APA regulation in leukemia development and erythropoiesis at the single-cell level, providing a high-resolution atlas to navigate cellular mRNA processing landscapes of differentiated cells in AML.
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Affiliation(s)
- Congting Ye
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China
| | - Qian Zhou
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China.,b Graduate College of Biomedical Sciences , Western University of Health Sciences , Pomona , CA , USA
| | - Yiling Hong
- c College of Veterinary Medicine , Western University of Health Sciences , Pomona , CA , USA
| | - Qingshun Quinn Li
- a Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems , College of the Environment and Ecology, Xiamen University , Xiamen , Fujian , China.,b Graduate College of Biomedical Sciences , Western University of Health Sciences , Pomona , CA , USA
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Chattopadhyay PK, Roederer M, Bolton DL. A deadly dance: the choreography of host-pathogen interactions, as revealed by single-cell technologies. Nat Commun 2018; 9:4638. [PMID: 30401874 PMCID: PMC6219517 DOI: 10.1038/s41467-018-06214-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 01/07/2023] Open
Abstract
Pathogens have numerous mechanisms by which they replicate within a host, who in turn responds by developing innate and adaptive immune countermeasures to limit disease. The advent of high-content single-cell technologies has facilitated a greater understanding of the properties of host cells harboring infection, the host's pathogen-specific immune responses, and the mechanisms pathogens have evolved to escape host control. Here we review these advances and argue for greater inclusion of higher resolution single-cell technologies into approaches for defining immune evasion mechanisms by pathogens.
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Affiliation(s)
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, 20892, MD, USA
| | - Diane L Bolton
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research, Silver Spring, 20910, MD, USA.
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Microfluidics: an Untapped Resource in Viral Diagnostics and Viral Cell Biology. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0105-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Cristinelli S, Ciuffi A. The use of single-cell RNA-Seq to understand virus-host interactions. Curr Opin Virol 2018; 29:39-50. [PMID: 29558678 DOI: 10.1016/j.coviro.2018.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Single-cell analyses allow uncovering cellular heterogeneity, not only per se, but also in response to viral infection. Similarly, single cell transcriptome analyses (scRNA-Seq) can highlight specific signatures, identifying cell subsets with particular phenotypes, which are relevant in the understanding of virus-host interactions.
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Affiliation(s)
- Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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