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Chattopadhyay PK. Molecular cytometry for comprehensive immune profiling. Methods Cell Biol 2024; 186:249-270. [PMID: 38705602 DOI: 10.1016/bs.mcb.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Molecular cytometry refers to a group of high-parameter technologies for single-cell analysis that share the following traits: (1) combined (multimodal) measurement of protein and transcripts, (2) medium throughput (10-100K cells), and (3) the use of oligonucleotide-tagged antibodies to detect protein expression. The platform can measure over 100 proteins and either hundreds of targeted genes or the whole transcriptome, on a cell-by-cell basis. It is currently one of the most powerful technologies available for immune monitoring. Here, we describe the technology platform (which includes CITE-Seq, REAP-Seq, and AbSeq), provide guidance for its optimization, and discuss advantages and limitations. Finally, we provide some vignettes from studies that demonstrate the application and potential insight that can be gained from molecular cytometry studies.
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Cobos Jiménez V, Geretz A, Tokarev A, Ehrenberg PK, Deletsu S, Machmach K, Mudvari P, Howard JN, Zelkoski A, Paquin-Proulx D, Del Prete GQ, Subra C, Boritz EA, Bosque A, Thomas R, Bolton DL. AP-1/c-Fos supports SIV and HIV-1 latency in CD4 T cells infected in vivo. iScience 2023; 26:108015. [PMID: 37860759 PMCID: PMC10582365 DOI: 10.1016/j.isci.2023.108015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Persistent HIV-1 reservoirs of infected CD4 T cells are a major barrier to HIV-1 cure, although the mechanisms by which they are established and maintained in vivo remain poorly characterized. To elucidate host cell gene expression patterns that govern virus gene expression, we analyzed viral RNA+ (vRNA) CD4 T cells of untreated simian immunodeficiency virus (SIV)-infected macaques by single-cell RNA sequencing. A subset of vRNA+ cells distinguished by spliced and high total vRNA (7-10% of reads) expressed diminished FOS, a component of the Activator protein 1 (AP-1) transcription factor, relative to vRNA-low and -negative cells. Conversely, FOS and JUN, another AP-1 component, were upregulated in HIV DNA+ infected cells compared to uninfected cells from people with HIV-1 on suppressive therapy. Inhibiting c-Fos in latently infected primary cells augmented reactivatable HIV-1 infection. These findings implicate AP-1 in latency establishment and maintenance and as a potential therapeutic target to limit HIV-1 reservoirs.
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Affiliation(s)
- Viviana Cobos Jiménez
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Aviva Geretz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Amanda Zelkoski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline Subra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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Tokarev A, Machmach K, Creegan M, Kim D, Eller MA, Bolton DL. Single-Cell Profiling of Latently SIV-Infected CD4 + T Cells Directly Ex Vivo to Reveal Host Factors Supporting Reservoir Persistence. Microbiol Spectr 2022; 10:e0060422. [PMID: 35510859 PMCID: PMC9241701 DOI: 10.1128/spectrum.00604-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/02/2022] [Indexed: 11/20/2022] Open
Abstract
HIV-1 cure strategies aiming to eliminate persistent infected cell reservoirs are hampered by a poor understanding of cells harboring viral DNA in vivo. We describe a novel method to identify, enumerate, and characterize in detail individual cells infected in vivo using a combination of single-cell multiplexed assays for integrated proviral DNA, quantitative viral and host gene expression, and quantitative surface protein expression without any in vitro manipulation. Latently infected CD4+ T cells, defined as harboring integrated provirus in the absence of spliced viral mRNA, were identified from macaque lymph nodes during acute, chronic, and combination antiretroviral therapy (cART)-suppressed simian immunodeficiency virus (SIV) infection. Latently infected CD4+ T cells were most abundant during acute SIV (~8% of memory CD4+ T cells) and persisted in chronic and cART-suppressed infection. Productively infected cells actively transcribing viral mRNA, by contrast, were much more labile and declined substantially between acute and chronic or cART-suppressed infection. Expression of most surface proteins and host genes was similar between latently infected cells and uninfected cells. Elevated FLIP mRNA and surface CD3 expression among latently infected cells suggest increased survival potential and capacity to respond to T cell receptor stimulation. These findings point to a large pool of latently infected CD4+ T cells established very early in acute infection and upregulated host factors that may facilitate their persistence in vivo, both of which pose potential challenges to eliminating HIV-1 reservoirs. IMPORTANCE Effective combination antiretroviral therapy controls HIV-1 infection but fails to eliminate latent viral reservoirs that give rise to viremia upon treatment interruption. Strategies to eradicate latently infected cells require a better understanding of their biology and distinguishing features to promote their elimination. Tools for studying these cells from patients are currently limited. Here, we developed a single-cell method to identify cells latently infected in vivo and to characterize these cells for expression of surface proteins and host genes without in vitro manipulation, capturing their in vivo state from SIV-infected macaques. Host factors involved in cell survival and proliferation were upregulated in latently infected cells, which were abundant in the earliest stages of acute infection. These studies provide insight into the basic biology of latently infected cells as well as potential mechanisms underlying the persistence of HIV-1/SIV reservoirs to inform development of novel HIV-1 cure strategies.
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Affiliation(s)
- Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Matthew Creegan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Dohoon Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Michael A. Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
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Mendelsohn SC, Mbandi SK, Fiore-Gartland A, Penn-Nicholson A, Musvosvi M, Mulenga H, Fisher M, Hadley K, Erasmus M, Nombida O, Tameris M, Walzl G, Naidoo K, Churchyard G, Hatherill M, Scriba TJ. Prospective multicentre head-to-head validation of host blood transcriptomic biomarkers for pulmonary tuberculosis by real-time PCR. COMMUNICATIONS MEDICINE 2022; 2:26. [PMID: 35342900 PMCID: PMC8954216 DOI: 10.1038/s43856-022-00086-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/10/2022] [Indexed: 01/31/2023] Open
Abstract
Background Sensitive point-of-care screening tests are urgently needed to identify individuals at highest risk of tuberculosis. We prospectively tested performance of host-blood transcriptomic tuberculosis signatures. Methods Adults without suspicion of tuberculosis were recruited from five endemic South African communities. Eight parsimonious host-blood transcriptomic tuberculosis signatures were measured by microfluidic RT-qPCR at enrolment. Upper respiratory swab specimens were tested with a multiplex bacterial-viral RT-qPCR panel in a subset of participants. Diagnostic and prognostic performance for microbiologically confirmed prevalent and incident pulmonary tuberculosis was tested in all participants at baseline and during active surveillance through 15 months follow-up, respectively. Results Among 20,207 HIV-uninfected and 963 HIV-infected adults screened; 2923 and 861 were enroled. There were 61 HIV-uninfected (weighted prevalence 1.1%) and 10 HIV-infected (prevalence 1.2%) tuberculosis cases at baseline. Parsimonious signature diagnostic performance was superior among symptomatic (AUCs 0.85-0.98) as compared to asymptomatic (AUCs 0.61-0.78) HIV-uninfected participants. Thereafter, 24 HIV-uninfected and 9 HIV-infected participants progressed to incident tuberculosis (1.1 and 1.0 per 100 person-years, respectively). Among HIV-uninfected individuals, prognostic performance for incident tuberculosis occurring within 6-12 months was higher relative to 15 months. 1000 HIV-uninfected participants were tested for respiratory microorganisms and 413 HIV-infected for HIV plasma viral load; 7/8 signature scores were higher (p < 0.05) in participants with viral respiratory infections or detectable HIV viraemia than those without. Conclusions Several parsimonious tuberculosis transcriptomic signatures met triage test targets among symptomatic participants, and incipient test targets within 6 months. However, the signatures were upregulated with viral infection and offered poor specificity for diagnosing sub-clinical tuberculosis.
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Affiliation(s)
- Simon C. Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Katie Hadley
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Mzwandile Erasmus
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Onke Nombida
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Michèle Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical TB Research; South African Medical Research Council Centre for TB Research; Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, 7505 Cape Town, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), 4001 Durban, South Africa
- MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - Gavin Churchyard
- The Aurum Institute, 2194 Johannesburg, South Africa
- School of Public Health, University of Witwatersrand, 2193 Johannesburg, South Africa
- Department of Medicine, Vanderbilt University, Nashville, TN 37232 USA
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa
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A Two-Part Mixed Model for Differential Expression Analysis in Single-Cell High-Throughput Gene Expression Data. Genes (Basel) 2022; 13:genes13020377. [PMID: 35205420 PMCID: PMC8872627 DOI: 10.3390/genes13020377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
The high-throughput gene expression data generated from recent single-cell RNA sequencing (scRNA-seq) and parallel single-cell reverse transcription quantitative real-time PCR (scRT-qPCR) technologies enable biologists to study the function of transcriptome at the level of individual cells. Compared with bulk RNA-seq and RT-qPCR gene expression data, single-cell data show notable distinct features, including excessive zero expression values, high variability, and clustered design. We propose to model single-cell high-throughput gene expression data using a two-part mixed model, which not only adequately accounts for the aforementioned features of single-cell expression data but also provides the flexibility of adjusting for covariates. An efficient computational algorithm, automatic differentiation, is used for estimating the model parameters. Compared with existing methods, our approach shows improved power for detecting differential expressed genes in single-cell high-throughput gene expression data.
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Sharma V, Creegan M, Tokarev A, Hsu D, Slike BM, Sacdalan C, Chan P, Spudich S, Ananworanich J, Eller MA, Krebs SJ, Vasan S, Bolton DL. Cerebrospinal fluid CD4+ T cell infection in humans and macaques during acute HIV-1 and SHIV infection. PLoS Pathog 2021; 17:e1010105. [PMID: 34874976 PMCID: PMC8683024 DOI: 10.1371/journal.ppat.1010105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 11/10/2021] [Indexed: 12/30/2022] Open
Abstract
HIV-1 replication within the central nervous system (CNS) impairs neurocognitive function and has the potential to establish persistent, compartmentalized viral reservoirs. The origins of HIV-1 detected in the CNS compartment are unknown, including whether cells within the cerebrospinal fluid (CSF) produce virus. We measured viral RNA+ cells in CSF from acutely infected macaques longitudinally and people living with early stages of acute HIV-1. Active viral transcription (spliced viral RNA) was present in CSF CD4+ T cells as early as four weeks post-SHIV infection, and among all acute HIV-1 specimens (N = 6; Fiebig III/IV). Replication-inactive CD4+ T cell infection, indicated by unspliced viral RNA in the absence of spliced viral RNA, was even more prevalent, present in CSF of >50% macaques and human CSF at ~10-fold higher frequency than productive infection. Infection levels were similar between CSF and peripheral blood (and lymph nodes in macaques), indicating comparable T cell infection across these compartments. In addition, surface markers of activation were increased on CSF T cells and monocytes and correlated with CSF soluble markers of inflammation. These studies provide direct evidence of HIV-1 replication in CD4+ T cells and broad immune activation in peripheral blood and the CNS during acute infection, likely contributing to early neuroinflammation and reservoir seeding. Thus, early initiation of antiretroviral therapy may not be able to prevent establishment of CNS viral reservoirs and sources of long-term inflammation, important targets for HIV-1 cure and therapeutic strategies. Neurological pathologies are associated with HIV-1 infection and remain common in the ongoing AIDS epidemic. Despite the advent of successful viremia suppression by anti-retroviral therapy, increased life expectancies and co-morbidities have led to higher prevalence of milder forms of neurocognitive dysfunction. How HIV-1 causes neurocognitive dysfunction is currently unclear, though it is widely believed that viral replication within the central nervous system (CNS) prior to therapy triggers these detrimental processes. The appearance of HIV-1 in the cerebrospinal fluid during the earliest stages of infection suggests that these processes may begin very early. Here, we use novel techniques to probe cells for viral infection during the first few weeks of infection in the CNS of humans and animals to determine the source of this virus. We found HIV-1 replication in T cells in the cerebrospinal fluid during this early window. In addition, infected T cells were present at similar frequencies in the CNS and other anatomic compartments, suggesting equilibration of T cell infection levels across these sites and potential for establishment of long-term reservoirs in the CNS. Our study provides new insights to the early events of viral entry and replication in the CNS with implications for subsequent viral persistence and neuronal injury.
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Affiliation(s)
- Vishakha Sharma
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Matthew Creegan
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Andrey Tokarev
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Denise Hsu
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Bonnie M. Slike
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Carlo Sacdalan
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Phillip Chan
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Serena Spudich
- Department of Neurology, Yale University, New Haven, Connecticut, United States of America
| | - Jintanat Ananworanich
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Michael A. Eller
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Shelly J. Krebs
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Sandhya Vasan
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Diane L. Bolton
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- * E-mail:
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Sharma V, Bryant C, Montero M, Creegan M, Slike B, Krebs SJ, Ratto-Kim S, Valcour V, Sithinamsuwan P, Chalermchai T, Eller MA, Bolton DL. Monocyte and CD4+ T-cell antiviral and innate responses associated with HIV-1 inflammation and cognitive impairment. AIDS 2020; 34:1289-1301. [PMID: 32598115 DOI: 10.1097/qad.0000000000002537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Mechanisms underlying immune activation and HIV-associated neurocognitive disorders (HAND) in untreated chronic infection remain unclear. The objective of this study was to identify phenotypic and transcriptional changes in blood monocytes and CD4 T cells in HIV-1-infected and uninfected individuals and elucidate processes associated with neurocognitive impairment. DESIGN A group of chronically HIV-1-infected Thai individuals (n = 19) were selected for comparison with healthy donor controls (n = 10). Infected participants were further classified as cognitively normal (n = 10) or with HAND (n = 9). Peripheral monocytes and CD4 T cells were phenotyped by flow cytometry and simultaneously isolated for multiplex qPCR-targeted gene expression profiling directly ex vivo. The frequency of HIV-1 RNA-positive cells was estimated by limiting dilution cell sorting. RESULTS Expression of genes and proteins involved in cellular activation and proinflammatory immune responses was increased in monocytes and CD4 T cells from HIV-1-infected relative to uninfected individuals. Gene expression profiles of both CD4 T cells and monocytes correlated with soluble markers of inflammation in the periphery (P < 0.05). By contrast, only modest differences in gene programs were observed between cognitively normal and HAND cases. These included increased monocyte surface CD169 protein expression relative to cognitively normal (P = 0.10), decreased surface CD163 expression relative to uninfected (P = 0.02) and cognitively normal (P = 0.06), and downregulation of EMR2 (P = 0.04) and STAT1 (P = 0.02) relative to cognitively normal. CONCLUSION Our data support a model of highly activated monocytes and CD4 T cells associated with inflammation in chronic HIV-1 infection, but impaired monocyte anti-inflammatory responses in HAND compared with cognitively normal.
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Affiliation(s)
- Vishakha Sharma
- aU.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring bHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda cThe EMMES Corporation, Rockville, Maryland dMemory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, California, USA eFaculty of Medicine, Phramongkutklao Hospital fSEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
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Pallikkuth S, Bolivar H, Fletcher MA, Babic DZ, De Armas LR, Gupta S, Termini JM, Arheart KL, Stevenson M, Tung FY, Fischl MA, Pahwa S, Stone GW. A therapeutic HIV-1 vaccine reduces markers of systemic immune activation and latent infection in patients under highly active antiretroviral therapy. Vaccine 2020; 38:4336-4345. [PMID: 32387010 DOI: 10.1016/j.vaccine.2020.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/10/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
Abstract
HIV infection is characterized by chronic immune activation and the establishment of a pool of latently infected cells. Antiretroviral therapy (ART) can suppress viral load to undetectable levels in peripheral blood by standard measure, however immune activation/chronic inflammation and latent infection persist and affect quality of life. We have now shown that a novel therapeutic HIV vaccine consisting of replication-defective HIV (HIVAX), given in the context of viral suppression under ART, can reduce both immune activation/chronic inflammation and latent infection. Immune activation, as measured by percent of CD8 + HLA-DR + CD38 + T cells, approached levels of healthy controls at week 16 following vaccination. Reduced immune activation was accompanied by a reduction in pro-inflammatory cytokines and peripheral α4β7 + plasmacytoid DC (a marker of mucosal immune activation). Levels of both HIV-1 DNA and 2-LTR circles were reduced at week 16 following vaccination, suggesting HIVAX can impact HIV-1 latency and reduce viral replication. Surprisingly, reduced immune activation/chronic inflammation was accompanied by an increase in the percent of memory CD4 + T cells expressing markers PD-1 and TIM-3. In addition, evaluation of HIV-1 Gag-specific CD4 + T cells for expression of 96 T cell related genes pre- and post-therapy revealed increased expression of a number of genes involved in the regulation of immune activation, T cell activation, and antiviral responses. Overall this study provides evidence that vaccination with HIVAX in subjects under long term antiviral suppression can reduce immune activation/chronic inflammation and latent infection (Clinicaltrials.gov, identifier NCT01428596).
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Affiliation(s)
- Suresh Pallikkuth
- Department of Microbiology and Immunology and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hector Bolivar
- Department of Medicine, Division of Infectious Diseases and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mary A Fletcher
- Department of Medicine, Division of Infectious Diseases and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dunja Z Babic
- Department of Medicine, Division of Infectious Diseases and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lesley R De Armas
- Department of Microbiology and Immunology and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sachin Gupta
- Department of Microbiology and Immunology and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - James M Termini
- Department of Microbiology and Immunology and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kristopher L Arheart
- Department of Public Health Sciences and the Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mario Stevenson
- Department of Medicine, Division of Infectious Diseases and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Margaret A Fischl
- Department of Medicine, Division of Infectious Diseases and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Savita Pahwa
- Department of Microbiology and Immunology and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Geoffrey W Stone
- Department of Microbiology and Immunology and Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL, USA
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Abstract
Mass spectrometry (MS) is an indispensable analytical technique for bioanalysis. Based on the measurement of mass/charge ratios (m/z) of ions, MS can be used for sensitive detection and accurate identification of species of interest. In traditional studies, MS is utilized to measure analytes in prepared solutions or gas-phase samples. Benefited from recent development of sampling and ionization approaches, MS has been extensively applied to the analysis of broad ranges of biological samples. We have developed a new device, the Single-probe, that can be used for in situ, real-time MS analysis of metabolites inside individual living cells. The Single-probe is a miniaturized multifunctional sampling and ionization device that is directly coupled to the mass spectrometer. With a sampling tip size smaller than 10 μm, we can insert the Single-probe tip into single cells to extract intracellular compounds, which are analyzed using MS in real-time. We have successfully used the Single-probe MS technique to detect a variety of endogenous and exogenous cellular metabolites in individual eukaryotic cells. Single cell mass spectrometry (SCMS) is a new scientific technology that has the potential to reshape approaches in biological and pharmaceutical bioanalytical research.
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Affiliation(s)
- Ning Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Wei Rao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
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10
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Piersanti RL, Santos JEP, Sheldon IM, Bromfield JJ. Lipopolysaccharide and tumor necrosis factor-alpha alter gene expression of oocytes and cumulus cells during bovine in vitro maturation. Mol Reprod Dev 2019; 86:1909-1920. [PMID: 31663199 DOI: 10.1002/mrd.23288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/08/2019] [Indexed: 12/23/2022]
Abstract
Communication between the oocyte and cumulus facilitates oocyte growth, cell cycle regulation, and metabolism. This communication is mediated by direct contact between oocytes and cumulus cells, and soluble secreted molecules. Secreted molecules involved in this process are known inflammatory mediators. Lipopolysaccharide (LPS) is detected in follicular fluid and is associated with reduced fertility, whereas accumulation of inflammatory mediators in follicular fluid, including tumor necrosis factor-α (TNF-α), is associated with female infertility. Maturation of oocytes in the presence of LPS or TNF-α reduces meiotic maturation and the capacity to develop to the blastocyst. Here we evaluated the abundance of 92 candidate genes involved immune function, epigenetic modifications, embryo development, oocyte secreted factors, apoptosis, cell cycle, and cell signaling in bovine cumulus cells or zona-free oocytes after exposure to LPS or TNF-α during in vitro maturation. We hypothesize that LPS or TNF-α will alter the abundance of transcripts in oocytes and cumulus cell in a cell type dependent manner. Exposure to LPS altered abundance of 31 transcripts in oocytes (including ACVR1V, BMP15, DNMT3A) and 12 transcripts in cumulus cells (including AREG, FGF4, PIK3IP1). Exposure to TNF-α altered 1 transcript in oocytes (IGF2) and 4 transcripts in cumulus cells (GJA1, PLD2, PTGER4, STAT1). Cumulus expansion was reduced after exposure to LPS or TNF-α. Exposing COCs to LPS had a marked effect on expression of targeted transcripts in oocytes. We propose that altered oocyte transcript abundance is associated with reduced meiotic maturation and embryo development observed in oocytes cultured in LPS or TNF-α.
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Affiliation(s)
- Rachel L Piersanti
- Department of Animal Sciences, University of Florida, Gainesville, Florida
| | - José E P Santos
- Department of Animal Sciences, University of Florida, Gainesville, Florida
| | - I Martin Sheldon
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | - John J Bromfield
- Department of Animal Sciences, University of Florida, Gainesville, Florida
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11
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Naluyima P, Lal KG, Costanzo MC, Kijak GH, Gonzalez VD, Blom K, Eller LA, Creegan M, Hong T, Kim D, Quinn TC, Björkström NK, Ljunggren HG, Serwadda D, Katabira ET, Sewankambo NK, Gray RH, Baeten JM, Michael NL, Wabwire-Mangen F, Robb ML, Bolton DL, Sandberg JK, Eller MA. Terminal Effector CD8 T Cells Defined by an IKZF2 +IL-7R - Transcriptional Signature Express FcγRIIIA, Expand in HIV Infection, and Mediate Potent HIV-Specific Antibody-Dependent Cellular Cytotoxicity. THE JOURNAL OF IMMUNOLOGY 2019; 203:2210-2221. [PMID: 31519862 PMCID: PMC6778306 DOI: 10.4049/jimmunol.1900422] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/20/2019] [Indexed: 12/23/2022]
Abstract
Chronic HIV-1 is associated with increased levels of FcγRIIIA+ CD8 T cells. FcγRIIIA+ CD8 T cells display an innate transcriptomic profile akin to NK cells. ADCC is mediated by FcγRIIIA+ CD8 T cells at levels comparable with NK cells.
HIV-1 infection expands large populations of late-stage differentiated CD8 T cells that may persist long after viral escape from TCR recognition. In this study, we investigated whether such CD8 T cell populations can perform unconventional innate-like antiviral effector functions. Chronic untreated HIV-1 infection was associated with elevated numbers of CD45RA+CD57+ terminal effector CD8 T cells expressing FcγRIIIA (CD16). The FcγRIIIA+ CD8 T cells displayed a distinctive transcriptional profile between conventional CD8 T cells and NK cells, characterized by high levels of IKZF2 and low expression of IL7R. This transcriptional profile translated into a distinct NKp80+ IL-7Rα− surface phenotype with high expression of the Helios transcription factor. Interestingly, the FcγRIIIA+ CD8 T cells mediated HIV-specific Ab-dependent cellular cytotoxicity (ADCC) activity at levels comparable with NK cells on a per cell basis. The FcγRIIIA+ CD8 T cells were highly activated in a manner that correlated positively with expansion of the CD8 T cell compartment and with plasma levels of soluble mediators of antiviral immunity and inflammation such as IP-10, TNF, IL-6, and TNFRII. The frequency of FcγRIIIA+ CD8 T cells persisted as patients initiated suppressive antiretroviral therapy, although their activation levels declined. These data indicate that terminally differentiated effector CD8 T cells acquire enhanced innate cell-like characteristics during chronic viral infection and suggest that HIV-specific ADCC is a function CD8 T cells use to target HIV-infected cells. Furthermore, as the FcγRIIIA+ CD8 T cells persist in treatment, they contribute significantly to the ADCC-capable effector cell pool in patients on antiretroviral therapy.
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Affiliation(s)
- Prossy Naluyima
- Makerere University Walter Reed Project, Kampala, Uganda.,Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kerri G Lal
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Margaret C Costanzo
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Veronica D Gonzalez
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kim Blom
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Ting Hong
- Department of Global Health, University of Washington School of Public Health, Seattle, WA 98195
| | - Dohoon Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20852.,School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - David Serwadda
- Rakai Health Sciences Program, Uganda Virus Research Institute, Entebbe, Uganda
| | - Elly T Katabira
- Faculty of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Nelson K Sewankambo
- Faculty of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ronald H Gray
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - Jared M Baeten
- Department of Global Health, University of Washington School of Public Health, Seattle, WA 98195.,Department of Medicine, University of Washington School of Public Health, Seattle, WA 98195; and.,Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98195
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | | | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Diane L Bolton
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Michael A Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910; .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
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12
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Chattopadhyay PK, Winters AF, Lomas WE, Laino AS, Woods DM. High-Parameter Single-Cell Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:411-430. [PMID: 30699035 DOI: 10.1146/annurev-anchem-061417-125927] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Thousands of transcripts and proteins confer function and discriminate cell types in the body. Using high-parameter technologies, we can now measure many of these markers at once, and multiple platforms are now capable of analysis on a cell-by-cell basis. Three high-parameter single-cell technologies have particular potential for discovering new biomarkers, revealing disease mechanisms, and increasing our fundamental understanding of cell biology. We review these three platforms (high-parameter flow cytometry, mass cytometry, and a new class of technologies called integrated molecular cytometry platforms) in this article. We describe the underlying hardware and instrumentation, the reagents involved, and the limitations and advantages of each platform. We also highlight the emerging field of high-parameter single-cell data analysis, providing an accessible overview of the data analysis process and choice of tools.
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Affiliation(s)
- Pratip K Chattopadhyay
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Aidan F Winters
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Woodrow E Lomas
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Andressa S Laino
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - David M Woods
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
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13
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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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14
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Tokarev A, Creegan M, Eller MA, Roederer M, Bolton DL. Single-cell Quantitation of mRNA and Surface Protein Expression in Simian Immunodeficiency Virus-infected CD4+ T Cells Isolated from Rhesus macaques. J Vis Exp 2018. [PMID: 30320741 DOI: 10.3791/57776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Single-cell analysis is an important tool for dissecting heterogeneous populations of cells. The identification and isolation of rare cells can be difficult. To overcome this challenge, a methodology combining indexed flow cytometry and high-throughput multiplexed quantitative polymerase chain reaction (qPCR) was developed. The objective was to identify and characterize simian immunodeficiency virus (SIV)-infected cells present within rhesus macaques. Through quantitation of surface protein by fluorescence-activated cell sorting (FACS) and mRNA by qPCR, virus-infected cells are identified by viral gene expression, which is combined with host gene and protein measurements to create a multidimensional profile. We term the approach, targeted Single-Cell Proteo-transcriptional Evaluation, or tSCEPTRE. To perform the method, viable cells are stained with fluorescent antibodies specific for surface markers used for FACS isolation of a cell subset and/or downstream phenotypic analysis. Single cells are sorted followed by immediate lysis, multiplex reverse transcription (RT), PCR pre-amplification, and high throughput qPCR of up to 96 transcripts. FACS measurements are recorded at the time of sorting and subsequently linked to the gene expression data by well position to create a combined protein and transcriptional profile. To study SIV-infected cells directly ex vivo, cells were identified by qPCR detection of multiple viral RNA species. The combination of viral transcripts and the quantity of each provide a framework for classifying cells into distinct stages of the viral life cycle (e.g., productive versus non-productive). Moreover, tSCEPTRE of SIV+ cells were compared to uninfected cells isolated from the same specimen to assess differentially expressed host genes and proteins. The analysis revealed previously unappreciated viral RNA expression heterogeneity among infected cells as well as in vivo SIV-mediated post-transcriptional gene regulation with single-cell resolution. The tSCEPTRE method is relevant for the analysis of any cell population amenable to identification by expression of surface protein marker(s), host or pathogen gene(s), or combinations thereof.
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Affiliation(s)
- Andrey Tokarev
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research
| | - Matthew Creegan
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research
| | - Michael A Eller
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research
| | | | - Diane L Bolton
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research;
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15
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Fali T, Fabre-Mersseman V, Yamamoto T, Bayard C, Papagno L, Fastenackels S, Zoorab R, Koup RA, Boddaert J, Sauce D, Appay V. Elderly human hematopoietic progenitor cells express cellular senescence markers and are more susceptible to pyroptosis. JCI Insight 2018; 3:95319. [PMID: 29997288 DOI: 10.1172/jci.insight.95319] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 05/31/2018] [Indexed: 01/24/2023] Open
Abstract
The maintenance of effective immunity over time is dependent on the capacity of hematopoietic stem cells (HSCs) to sustain the pool of immunocompetent mature cells. Decline of immune competence with old age may stem from HSC defects, including reduced self-renewal potential and impaired lymphopoiesis, as suggested in murine models. To obtain further insights into aging-related alteration of hematopoiesis, we performed a comprehensive study of blood hematopoietic progenitor cells (HPCs) from older humans. In the elderly, HPCs present active oxidative phosphorylation and are pressed to enter cell cycling. However, p53-p21 and p15 cell senescence pathways, associated with telomerase activity deficiency, strong telomere attrition, and oxidative stress, are engaged, thus limiting cell cycling. Moreover, survival of old HPCs is impacted by pyroptosis, an inflammatory form of programmed cell death. Lastly, telomerase activity deficiency and telomere length attrition of old HPCs may be passed on to progeny cells such as naive T lymphocytes, further highlighting the poor hematopoietic potential of the elderly. This pre-senescent profile is characteristic of the multiple intrinsic and extrinsic factors affecting HPCs in elderly individuals and represents a major obstacle in terms of immune reconstitution and efficacy with advanced age.
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Affiliation(s)
- Tinhinane Fali
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Véronique Fabre-Mersseman
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Takuya Yamamoto
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Laboratory of Immunosenescence, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki-City, Osaka, Japan.,Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Charles Bayard
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Laura Papagno
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Solène Fastenackels
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Rima Zoorab
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Jacques Boddaert
- AP-HP, Hôpital Pitié-Salpêtrière, Service de Gériatrie, Paris, France
| | - Delphine Sauce
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Victor Appay
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
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16
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Moysi E, Pallikkuth S, De Armas LR, Gonzalez LE, Ambrozak D, George V, Huddleston D, Pahwa R, Koup RA, Petrovas C, Pahwa S. Altered immune cell follicular dynamics in HIV infection following influenza vaccination. J Clin Invest 2018; 128:3171-3185. [PMID: 29911996 PMCID: PMC6025971 DOI: 10.1172/jci99884] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/25/2018] [Indexed: 12/29/2022] Open
Abstract
HIV infection changes the lymph node (LN) tissue architecture, potentially impairing the immunologic response to antigenic challenge. The tissue-resident immune cell dynamics in virologically suppressed HIV+ patients on combination antiretroviral therapy (cART) are not clear. We obtained LN biopsies before and 10 to 14 days after trivalent seasonal influenza immunization from healthy controls (HCs) and HIV+ volunteers on cART to investigate CD4+ T follicular helper (Tfh) and B cell dynamics by flow cytometry and quantitative imaging analysis. Prior to vaccination, compared with those in HCs, HIV+ LNs exhibited an altered follicular architecture, but harbored higher numbers of Tfh cells and increased IgG+ follicular memory B cells. Moreover, Tfh cell numbers were dependent upon preservation of the follicular dendritic cell (FDC) network and were predictive of the magnitude of the vaccine-induced IgG responses. Interestingly, postvaccination LN samples in HIV+ participants had significantly (P = 0.0179) reduced Tfh cell numbers compared with prevaccination samples, without evidence for peripheral Tfh (pTfh) cell reduction. We conclude that influenza vaccination alters the cellularity of draining LNs of HIV+ persons in conjunction with development of antigen-specific humoral responses. The underlying mechanism of Tfh cell decline warrants further investigation, as it could bear implications for the rational design of HIV vaccines.
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Affiliation(s)
- Eirini Moysi
- Tissue Analysis Core, Immunology Laboratory, Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Suresh Pallikkuth
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Lesley R. De Armas
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Louis E. Gonzalez
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - David Ambrozak
- Immunology Laboratory, VRC, NIAID, NIH, Bethesda, Maryland, USA
| | - Varghese George
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - David Huddleston
- Department of Trauma Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Rajendra Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Richard A. Koup
- Immunology Laboratory, VRC, NIAID, NIH, Bethesda, Maryland, USA
| | - Constantinos Petrovas
- Tissue Analysis Core, Immunology Laboratory, Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Savita Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
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17
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Colby DJ, Trautmann L, Pinyakorn S, Leyre L, Pagliuzza A, Kroon E, Rolland M, Takata H, Buranapraditkun S, Intasan J, Chomchey N, Muir R, Haddad EK, Tovanabutra S, Ubolyam S, Bolton DL, Fullmer BA, Gorelick RJ, Fox L, Crowell TA, Trichavaroj R, O'Connell R, Chomont N, Kim JH, Michael NL, Robb ML, Phanuphak N, Ananworanich J. Rapid HIV RNA rebound after antiretroviral treatment interruption in persons durably suppressed in Fiebig I acute HIV infection. Nat Med 2018; 24:923-926. [PMID: 29892063 PMCID: PMC6092240 DOI: 10.1038/s41591-018-0026-6] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 03/23/2018] [Indexed: 01/24/2023]
Abstract
Antiretroviral therapy during the earliest stage of acute HIV infection (Fiebig I) might minimize establishment of a latent HIV reservoir and thereby facilitate viremic control after analytical treatment interruption. We show that 8 participants, who initiated treatment during Fiebig I and were treated for a median of 2.8 years, all experienced rapid viral load rebound following analytical treatment interruption, indicating that additional strategies are required to control or eradicate HIV.
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Affiliation(s)
- Donn J Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Lydie Trautmann
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Louise Leyre
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Amélie Pagliuzza
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Eugène Kroon
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hiroshi Takata
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Supranee Buranapraditkun
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Chulalongkorn Vaccine Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jintana Intasan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Nitiya Chomchey
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Roshell Muir
- Department of Medicine, Division of Infectious Diseases & HIV Medicine at Drexel University College of Medicine, Philadelphia, PA, USA
| | - Elias K Haddad
- Department of Medicine, Division of Infectious Diseases & HIV Medicine at Drexel University College of Medicine, Philadelphia, PA, USA
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Diane L Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Brandie A Fullmer
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence Fox
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Rapee Trichavaroj
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences United States Component, Bangkok, Thailand
| | - Robert O'Connell
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences United States Component, Bangkok, Thailand
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Jerome H Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- International Vaccine Institute, Seoul, Korea
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Jintanat Ananworanich
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand.
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
- Department of Global Health, University of Amsterdam, Amsterdam, the Netherlands.
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18
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Ferrando-Martinez S, Moysi E, Pegu A, Andrews S, Nganou Makamdop K, Ambrozak D, McDermott AB, Palesch D, Paiardini M, Pavlakis GN, Brenchley JM, Douek D, Mascola JR, Petrovas C, Koup RA. Accumulation of follicular CD8+ T cells in pathogenic SIV infection. J Clin Invest 2018; 128:2089-2103. [PMID: 29664020 DOI: 10.1172/jci96207] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/06/2018] [Indexed: 01/06/2023] Open
Abstract
LN follicles constitute major reservoir sites for HIV/SIV persistence. Cure strategies could benefit from the characterization of CD8+ T cells able to access and eliminate HIV-infected cells from these areas. In this study, we provide a comprehensive analysis of the phenotype, frequency, localization, and functionality of follicular CD8+ T cells (fCD8+) in SIV-infected nonhuman primates. Although disorganization of follicles was a major factor, significant accumulation of fCD8+ cells during chronic SIV infection was also observed in intact follicles, but only in pathogenic SIV infection. In line with this, tissue inflammatory mediators were strongly associated with the accumulation of fCD8+ cells, pointing to tissue inflammation as a major factor in this process. These fCD8+ cells have cytolytic potential and can be redirected to target and kill HIV-infected cells using bispecific antibodies. Altogether, our data support the use of SIV infection to better understand the dynamics of fCD8+ cells and to develop bispecific antibodies as a strategy for virus eradication.
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Affiliation(s)
| | | | | | | | - Krystelle Nganou Makamdop
- Human Immunology Section, Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | | | | | - David Palesch
- Department of Pathology, Emory University School of Medicine and Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Mirko Paiardini
- Department of Pathology, Emory University School of Medicine and Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - George N Pavlakis
- Human Retrovirus Section, Center for Cancer Research, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Daniel Douek
- Human Immunology Section, Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
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19
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Transcriptomic signatures of NK cells suggest impaired responsiveness in HIV-1 infection and increased activity post-vaccination. Nat Commun 2018; 9:1212. [PMID: 29572470 PMCID: PMC5865158 DOI: 10.1038/s41467-018-03618-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 02/28/2018] [Indexed: 12/14/2022] Open
Abstract
Natural killer (NK) cells limit viral replication by direct recognition of infected cells, antibody-dependent cellular cytotoxicity (ADCC), and releasing cytokines. Although growing evidence supports NK cell antiviral immunity in HIV-1 infection, further knowledge of their response is necessary. Here we show that NK cells responding to models of direct cell recognition, ADCC, and cytokine activation have unique transcriptional fingerprints. Compared with healthy volunteers, individuals with chronic HIV-1 infection have higher expression of genes commonly associated with activation, and lower expression of genes associated with direct cell recognition and cytokine stimulation in their NK cells. By contrast, NK cell transcriptional profiles of individuals receiving a modified vaccinia Ankara (MVA) vectored HIV-1 vaccine show upregulation of genes associated with direct cell recognition. These findings demonstrate that targeted transcriptional profiling provides a sensitive assessment of NK cell activity, which helps understand how NK cells respond to viral infections and vaccination. Natural killer (NK) cells are important for eliminating cells under stress or infected by virus, and may have a function in anti-HIV immunity. Here the authors show that different NK-activating stimuli induce distinct transcriptional fingerprints in human NK cells that are analogous to changes caused by HIV vaccination or chronic infection.
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20
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Siqueira LG, Tribulo P, Chen Z, Denicol AC, Ortega MS, Negrón-Pérez VM, Kannampuzha-Francis J, Pohler KG, Rivera RM, Hansen PJ. Colony-stimulating factor 2 acts from days 5 to 7 of development to modify programming of the bovine conceptus at day 86 of gestation†. Biol Reprod 2018; 96:743-757. [PMID: 28379294 DOI: 10.1093/biolre/iox018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/27/2017] [Indexed: 11/13/2022] Open
Abstract
Colony-stimulating factor 2 (CSF2) is an embryokine that improves competence of the embryo to establish pregnancy and which may participate in developmental programming. We tested whether culture of bovine embryos with CSF2 alters fetal development and alleviates abnormalities associated with in vitro production (IVP) of embryos. Pregnancies were established by artificial insemination (AI), transfer of an IVP embryo (IVP), or transfer of an IVP embryo treated with 10 ng/ml CSF2 from day 5 to 7 of development (CSF2). Pregnancies were produced using X-sorted semen. Female singleton conceptuses were collected on day 86 of gestation. There were few morphological differences between groups, although IVP and CSF2 fetuses were heavier than AI fetuses. Bicarbonate concentration in allantoic fluid was lower for IVP than for AI or CSF2. Expression of 92 genes in liver, placenta, and muscle was determined. The general pattern for liver and placenta was for IVP to alter expression and for CSF2 to sometimes reverse this effect. For muscle, CSF2 affected gene expression but did not generally reverse effects of IVP. Levels of methylation for each of the three tissues at 12 loci in the promoter of insulin-like growth factor 2 (IGF2) and five in the promoter of growth factor receptor bound protein 10 were unaffected by treatment except for CSF2 effects on two CpG for IGF2 in placenta and muscle. In conclusion, CSF2 can act as a developmental programming agent but alone is not able to abolish the adverse effects of IVP on fetal characteristics.
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Affiliation(s)
- Luiz G Siqueira
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA.,Embrapa Gado de Leite, Juiz de Fora, Minas Gerais, Brazil
| | - Paula Tribulo
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Zhiyuan Chen
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Anna C Denicol
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - M Sofia Ortega
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Veronica M Negrón-Pérez
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Jasmine Kannampuzha-Francis
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Ky G Pohler
- Department of Animal Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Rocio M Rivera
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
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21
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McKain MR, Johnson MG, Uribe‐Convers S, Eaton D, Yang Y. Practical considerations for plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1038. [PMID: 29732268 PMCID: PMC5895195 DOI: 10.1002/aps3.1038] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/13/2018] [Indexed: 05/10/2023]
Abstract
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome-scale data from diverse lineages. The development of high-throughput sequencing and long-read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project-dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up-and-coming technologies that may help propel the field even further.
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Affiliation(s)
- Michael R. McKain
- Department of Biological SciencesThe University of AlabamaBox 870344TuscaloosaAlabama35487USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main Street, Box 43131LubbockTexas79409USA
| | - Simon Uribe‐Convers
- Department of Ecology and Evolutionary BiologyUniversity of Michigan830 North UniversityAnn ArborMichigan48109USA
| | - Deren Eaton
- Department of Ecology, Evolution, and Environmental BiologyColumbia University1200 Amsterdam AvenueNew YorkNew York10027USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota–Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108USA
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22
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Mpande CAM, Dintwe OB, Musvosvi M, Mabwe S, Bilek N, Hatherill M, Nemes E, Scriba TJ. Functional, Antigen-Specific Stem Cell Memory (T SCM) CD4 + T Cells Are Induced by Human Mycobacterium tuberculosis Infection. Front Immunol 2018; 9:324. [PMID: 29545791 PMCID: PMC5839236 DOI: 10.3389/fimmu.2018.00324] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/06/2018] [Indexed: 12/22/2022] Open
Abstract
Background Maintenance of long-lasting immunity is thought to depend on stem cell memory T cells (TSCM), which have superior self-renewing capacity, longevity and proliferative potential compared with central memory (TCM) or effector (TEFF) T cells. Our knowledge of TSCM derives primarily from studies of virus-specific CD8+ TSCM. We aimed to determine if infection with Mycobacterium tuberculosis (M. tb), the etiological agent of tuberculosis, generates antigen-specific CD4+ TSCM and to characterize their functional ontology. Methods We studied T cell responses to natural M. tb infection in a longitudinal adolescent cohort of recent QuantiFERON-TB Gold (QFT) converters and three cross-sectional QFT+ adult cohorts; and to bacillus Calmette-Guerin (BCG) vaccination in infants. M. tb and/or BCG-specific CD4 T cells were detected by flow cytometry using major histocompatibility complex class II tetramers bearing Ag85, CFP-10, or ESAT-6 peptides, or by intracellular cytokine staining. Transcriptomic analyses of M. tb-specific tetramer+ CD4+ TSCM (CD45RA+ CCR7+ CD27+) were performed by microfluidic qRT-PCR, and functional and phenotypic characteristics were confirmed by measuring expression of chemokine receptors, cytotoxic molecules and cytokines using flow cytometry. Results M. tb-specific TSCM were not detected in QFT-negative persons. After QFT conversion frequencies of TSCM increased to measurable levels and remained detectable thereafter, suggesting that primary M. tb infection induces TSCM cells. Gene expression (GE) profiling of tetramer+ TSCM showed that these cells were distinct from bulk CD4+ naïve T cells (TN) and shared features of bulk TSCM and M. tb-specific tetramer+ TCM and TEFF cells. These TSCM were predominantly CD95+ and CXCR3+, markers typical of CD8+ TSCM. Tetramer+ TSCM expressed significantly higher protein levels of CCR5, CCR6, CXCR3, granzyme A, granzyme K, and granulysin than bulk TN and TSCM cells. M. tb-specific TSCM were also functional, producing IL-2, IFN-γ, and TNF-α upon antigen stimulation, and their frequencies correlated positively with long-term BCG-specific CD4+ T cell proliferative potential after infant vaccination. Conclusion Human infection with M. tb induced distinct, antigen-specific CD4+ TSCM cells endowed with effector functions, including expression of cytotoxic molecules and Th1 cytokines, and displayed chemokine receptor profiles consistent with memory Th1/17 cells. Induction of CD4+ TSCM should be considered for vaccination approaches that aim to generate long-lived memory T cells against M. tb.
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Affiliation(s)
- Cheleka A. M. Mpande
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - One B. Dintwe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Simbarashe Mabwe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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23
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Moguche AO, Musvosvi M, Penn-Nicholson A, Plumlee CR, Mearns H, Geldenhuys H, Smit E, Abrahams D, Rozot V, Dintwe O, Hoff ST, Kromann I, Ruhwald M, Bang P, Larson RP, Shafiani S, Ma S, Sherman DR, Sette A, Lindestam Arlehamn CS, McKinney DM, Maecker H, Hanekom WA, Hatherill M, Andersen P, Scriba TJ, Urdahl KB. Antigen Availability Shapes T Cell Differentiation and Function during Tuberculosis. Cell Host Microbe 2018; 21:695-706.e5. [PMID: 28618268 DOI: 10.1016/j.chom.2017.05.012] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/03/2017] [Accepted: 05/30/2017] [Indexed: 01/20/2023]
Abstract
CD4 T cells are critical for protective immunity against Mycobacterium tuberculosis (Mtb), the cause of tuberculosis (TB). Yet to date, TB vaccine candidates that boost antigen-specific CD4 T cells have conferred little or no protection. Here we examined CD4 T cell responses to two leading TB vaccine antigens, ESAT-6 and Ag85B, in Mtb-infected mice and in vaccinated humans with and without underlying Mtb infection. In both species, Mtb infection drove ESAT-6-specific T cells to be more differentiated than Ag85B-specific T cells. The ability of each T cell population to control Mtb in the lungs of mice was restricted for opposite reasons: Ag85B-specific T cells were limited by reduced antigen expression during persistent infection, whereas ESAT-6-specific T cells became functionally exhausted due to chronic antigenic stimulation. Our findings suggest that different vaccination strategies will be required to optimize protection mediated by T cells recognizing antigens expressed at distinct stages of Mtb infection.
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Affiliation(s)
- Albanus O Moguche
- Center for Infectious Disease Research (CIDR), Seattle, WA 98109, USA; Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | | | - Helen Mearns
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Hennie Geldenhuys
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Erica Smit
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Deborah Abrahams
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - One Dintwe
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Søren T Hoff
- Statens Serum Institut (SSI), 2300 Copenhagen, Denmark
| | | | | | - Peter Bang
- Statens Serum Institut (SSI), 2300 Copenhagen, Denmark
| | - Ryan P Larson
- Center for Infectious Disease Research (CIDR), Seattle, WA 98109, USA
| | - Shahin Shafiani
- Center for Infectious Disease Research (CIDR), Seattle, WA 98109, USA
| | - Shuyi Ma
- Center for Infectious Disease Research (CIDR), Seattle, WA 98109, USA
| | - David R Sherman
- Center for Infectious Disease Research (CIDR), Seattle, WA 98109, USA
| | - Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla 92037, USA
| | | | - Denise M McKinney
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla 92037, USA
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Willem A Hanekom
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | | | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), University of Cape Town, Cape Town 7925, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town 7925, South Africa; Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa.
| | - Kevin B Urdahl
- Center for Infectious Disease Research (CIDR), Seattle, WA 98109, USA; Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA.
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24
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Negrón-Pérez VM, Zhang Y, Hansen PJ. Single-cell gene expression of the bovine blastocyst. Reproduction 2017; 154:627-644. [PMID: 28814615 PMCID: PMC5630521 DOI: 10.1530/rep-17-0345] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/03/2017] [Accepted: 08/16/2017] [Indexed: 12/22/2022]
Abstract
The first two differentiation events in the embryo result in three cell types - epiblast, trophectoderm (TE) and hypoblast. The purpose here was to identify molecular markers for each cell type in the bovine and evaluate the differences in gene expression among individual cells of each lineage. The cDNA from 67 individual cells of dissociated blastocysts was used to determine transcript abundance for 93 genes implicated as cell lineage markers in other species or potentially involved in developmental processes. Clustering analysis indicated that the cells belonged to two major populations (clades A and B) with two subpopulations of clade A and four of clade B. Use of lineage-specific markers from other species indicated that the two subpopulations of clade A represented epiblast and hypoblast respectively while the four subpopulations of clade B were TE. Among the genes upregulated in epiblast were AJAP1, DNMT3A, FGF4, H2AFZ, KDM2B, NANOG, POU5F1, SAV1 and SLIT2 Genes overexpressed in hypoblast included ALPL, FGFR2, FN1, GATA6, GJA1, HDAC1, MBNL3, PDGFRA and SOX17, while genes overexpressed in all four TE populations were ACTA2, CDX2, CYP11A1, GATA2, GATA3, IFNT, KRT8, RAC1 and SFN The subpopulations of TE varied among each other for multiple genes including the prototypical TE marker IFNT. New markers for each cell type in the bovine blastocyst were identified. Results also indicate heterogeneity in gene expression among TE cells. Further studies are needed to confirm whether subpopulations of TE cells represent different stages in the development of a committed TE phenotype.
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Affiliation(s)
- Verónica M. Negrón-Pérez
- Department of Animal Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Yanping Zhang
- Gene Expression and Genotyping Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Peter J. Hansen
- Department of Animal Sciences, D. H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville, Florida, USA
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25
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Cotugno N, De Armas L, Pallikkuth S, Rinaldi S, Issac B, Cagigi A, Rossi P, Palma P, Pahwa S. Perturbation of B Cell Gene Expression Persists in HIV-Infected Children Despite Effective Antiretroviral Therapy and Predicts H1N1 Response. Front Immunol 2017; 8:1083. [PMID: 28955330 PMCID: PMC5600985 DOI: 10.3389/fimmu.2017.01083] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/21/2017] [Indexed: 12/17/2022] Open
Abstract
Despite effective antiretroviral therapy (ART), HIV-infected individuals with apparently similar clinical and immunological characteristics can vary in responsiveness to vaccinations. However, molecular mechanisms responsible for such impairment, as well as biomarkers able to predict vaccine responsiveness in HIV-infected children, remain unknown. Following the hypothesis that a B cell qualitative impairment persists in HIV-infected children (HIV) despite effective ART and phenotypic B cell immune reconstitution, the aim of the current study was to investigate B cell gene expression of HIV compared to age-matched healthy controls (HCs) and to determine whether distinct gene expression patterns could predict the ability to respond to influenza vaccine. To do so, we analyzed prevaccination transcriptional levels of a 96-gene panel in equal numbers of sort-purified B cell subsets (SPBS) isolated from peripheral blood mononuclear cells using multiplexed RT-PCR. Immune responses to H1N1 antigen were determined by hemaglutination inhibition and memory B cell ELISpot assays following trivalent-inactivated influenza vaccination (TIV) for all study participants. Although there were no differences in terms of cell frequencies of SPBS between HIV and HC, the groups were distinguishable based upon gene expression analyses. Indeed, a 28-gene signature, characterized by higher expression of genes involved in the inflammatory response and immune activation was observed in activated memory B cells (CD27+CD21−) from HIV when compared to HC despite long-term viral control (>24 months). Further analysis, taking into account H1N1 responses after TIV in HIV participants, revealed that a 25-gene signature in resting memory (RM) B cells (CD27+CD21+) was able to distinguish vaccine responders from non-responders (NR). In fact, prevaccination RM B cells of responders showed a higher expression of gene sets involved in B cell adaptive immune responses (APRIL, BTK, BLIMP1) and BCR signaling (MTOR, FYN, CD86) when compared to NR. Overall, these data suggest that a perturbation at a transcriptional level in the B cell compartment persists despite stable virus control achieved through ART in HIV-infected children. Additionally, the present study demonstrates the potential utility of transcriptional evaluation of RM B cells before vaccination for identifying predictive correlates of vaccine responses in this population.
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Affiliation(s)
- Nicola Cotugno
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Rome, Italy.,Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Lesley De Armas
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Suresh Pallikkuth
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Stefano Rinaldi
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Rome, Italy.,Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Biju Issac
- Sylvester Cancer Center, Department of Biostatistics and Bioinformatics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Alberto Cagigi
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Rome, Italy.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Paolo Rossi
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Rome, Italy.,Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital-University of Rome Tor Vergata, Rome, Italy
| | - Paolo Palma
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Savita Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
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26
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Bolton DL, McGinnis K, Finak G, Chattopadhyay P, Gottardo R, Roederer M. Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells. PLoS Pathog 2017; 13:e1006445. [PMID: 28654687 PMCID: PMC5507340 DOI: 10.1371/journal.ppat.1006445] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/10/2017] [Accepted: 06/04/2017] [Indexed: 12/27/2022] Open
Abstract
CD4 T cells harboring HIV-1/SIV represent a formidable hurdle to eradicating infection, and yet their detailed phenotype remains unknown. Here we integrate two single-cell technologies, flow cytometry and highly multiplexed quantitative RT-PCR, to characterize SIV-infected CD4 T cells directly ex vivo. Within individual cells, we correlate the cellular phenotype, in terms of host protein and RNA expression, with stages of the viral life cycle defined by combinatorial expression of viral RNAs. Spliced RNA+ infected cells display multiple memory and activation phenotypes, indicating virus production by diverse CD4 T cell subsets. In most (but not all) cells, progressive infection accompanies post-transcriptional downregulation of CD4 protein, while surface MHC class I is largely retained. Interferon-stimulated genes were also commonly upregulated. Thus, we demonstrate that combined quantitation of transcriptional and post-transcriptional regulation at the single-cell level informs in vivo mechanisms of viral replication and immune evasion. HIV-1, and its simian counterpart, SIV, infect and kill CD4 T cells, resulting in their massive depletion that ultimately leads to AIDS in the absence of antiretroviral therapy. With effective therapy, these cells are largely preserved, but a subset harbors latent virus that can persist for decades and reemerge upon therapy interruption, preventing HIV-1 cure. To prevent or eliminate productive cellular infection, there is tremendous demand to identify host factors expressed by these cells in vivo, which may serve as unique biomarkers or drug targets. Here we provide the first detailed combined transcriptomic and protein expression profile of SIV-infected cells directly ex vivo using novel single-cell technologies. Our survey of activation markers, interferon-stimulated genes, and viral restriction factors identified multiple host genes differentially expressed by SIV-infected cells and will inform future therapeutic strategies.
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Affiliation(s)
- Diane L. Bolton
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Kathleen McGinnis
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Greg Finak
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pratip Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
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27
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Phetsouphanh C, Xu Y, Munier ML, Zaunders JJ, Kelleher AD. Single-cell profiling of lineage determining transcription factors in antigen-specific CD4 + T cells reveals unexpected complexity in recall responses during immune reconstitution. Immunol Cell Biol 2017; 95:640-646. [PMID: 28485382 PMCID: PMC5550558 DOI: 10.1038/icb.2017.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/29/2017] [Accepted: 03/29/2017] [Indexed: 02/06/2023]
Abstract
Recent studies of protein and gene expression at the single-cell level have revealed that the memory T-cell compartment is more heterogeneous than previously acknowledged. Identifying different T helper subsets involved in memory responses at the single-cell level is thus necessary to understand the level of heterogeneity within this population. Antigen-specific CD4+ T cells were measured using the CD25/OX40 assay together with a qualitative multiplex single-cell RT-PCR assay. Transcription profiles and subset proportions within the antigen-specific CD4+ T-cell population were dissected. Cytomegalovirus (CMV)-specific CD4+ T-cell responses skewed toward a Th1 response, whereas Tetanus toxoid responses skewed toward a Th2 type response. Fluctuations in CD4+ T-cell subsets were observed within the HIV-Gag-specific response during ongoing antiretroviral therapy. Strong effector responses (Th1) were observed in early treatment, however with ongoing therapy this effector response significantly decreased in combination with an increase in Tregs and circulating Tfh-like BCL-6+ memory cells. The apparent increase in Tcm in peripheral blood after a several weeks of antiretroviral therapy may be due to Tfh-like cell egress from germinal centers into the periphery.
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Affiliation(s)
- Chansavath Phetsouphanh
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Kensington, New South Wales, Australia
| | - Yin Xu
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Kensington, New South Wales, Australia
| | - Mee Ling Munier
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Kensington, New South Wales, Australia
| | - John J Zaunders
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Kensington, New South Wales, Australia.,Centre for Applied Medical Research, St Vicent's Hospital, Sydney, Australia
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Kensington, New South Wales, Australia.,Centre for Applied Medical Research, St Vicent's Hospital, Sydney, Australia
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28
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Strbo N, Romero L, Alcaide M, Fischl M. Isolation and Flow Cytometric Analysis of Human Endocervical Gamma Delta T Cells. J Vis Exp 2017. [PMID: 28287518 DOI: 10.3791/55038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The female reproductive tract (FRT) mucosal immune system serves as the first line of defense. Better knowledge of the genital mucosa is therefore essential for understanding pathogenicity of different pathogens including HIV. Gamma delta (GD) T cells are the prototype of 'unconventional' T cells and represent a relatively small subset of T cells defined by their expression of heterodimeric T-cell receptors (TCRs) composed of gamma and delta chains. This sets them apart from the classical and much better known CD4+ helper T cells and CD8+ cytotoxic T cells that are defined by alpha-beta TCRs. GD T cells often show tissue-specific localization and are enriched in epithelium. GD T cells orchestrate immune responses in inflammation, tumor surveillance, infectious disease, and autoimmunity. Here, we present a method to reproducibly isolate and analyze human endocervical intraepithelial GD T lymphocytes. We have used endocervical cytobrush samples from women participating in the Women's Interagency HIV Infection Study (WIHS). Knowledge about GD T cells interactions during conditions in which there is an insult to the vaginal mucosal could be applied to any clinical study in which mucosal vulnerability is addressed, including the development of vaginal microbicides.In addition, knowledge about mucosal GD T cell responses has potential for application of GD T cell-based immune therapy in treating infectious diseases.
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Affiliation(s)
- Natasa Strbo
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami;
| | - Laura Romero
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami
| | - Maria Alcaide
- Division of Infectious Diseases, Miller School of Medicine, University of Miami
| | - Margaret Fischl
- Division of Infectious Diseases, Miller School of Medicine, University of Miami
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29
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de Armas LR, Cotugno N, Pallikkuth S, Pan L, Rinaldi S, Sanchez MC, Gonzalez L, Cagigi A, Rossi P, Palma P, Pahwa S. Induction of IL21 in Peripheral T Follicular Helper Cells Is an Indicator of Influenza Vaccine Response in a Previously Vaccinated HIV-Infected Pediatric Cohort. THE JOURNAL OF IMMUNOLOGY 2017; 198:1995-2005. [PMID: 28130496 DOI: 10.4049/jimmunol.1601425] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/22/2016] [Indexed: 12/27/2022]
Abstract
HIV-infected patients of all ages frequently underperform in response to seasonal influenza vaccination, despite virologic control of HIV. The molecular mechanisms governing this impairment, as well as predictive biomarkers for responsiveness, remain unknown. This study was performed in samples obtained prevaccination (T0) from HIV-infected children who received the 2012-2013 seasonal influenza vaccine. Response status was determined based on established criterion for hemagglutination inhibition titer; participants with a hemagglutination titer ≥1:40 plus a ≥4-fold increase over T0 at 3 wk postvaccination were designated as responders. All children had a history of prior influenza vaccinations. At T0, the frequencies of CD4 T cell subsets, including peripheral T follicular helper (pTfh) cells, which provide help to B cells for developing into Ab-secreting cells, were similar between responders and nonresponders. However, in response to in vitro stimulation with influenza A/California/7/2009 (H1N1) Ag, differential gene expression related to pTfh cell function was observed by Fluidigm high-density RT-PCR between responders and nonresponders. In responders, H1N1 stimulation at T0 also resulted in CXCR5 induction (mRNA and protein) in CD4 T cells and IL21 gene induction in pTfh cells that were strongly associated with H1N1-specific B cell responses postvaccination. In contrast, CD4 T cells of nonresponders exhibited increased expression of IL2 and STAT5 genes, which are known to antagonize peripheral Tfh cell function. These results suggest that the quality of pTfh cells at the time of immunization is important for influenza vaccine responses and provide a rationale for targeted, ex vivo Ag-driven molecular profiling of purified immune cells to detect predictive biomarkers of the vaccine response.
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Affiliation(s)
- Lesley R de Armas
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL 33136.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136; and
| | - Nicola Cotugno
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Suresh Pallikkuth
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL 33136.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136; and
| | - Li Pan
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL 33136.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136; and
| | - Stefano Rinaldi
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL 33136.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136; and
| | - M Celeste Sanchez
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL 33136.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136; and
| | - Louis Gonzalez
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL 33136.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136; and
| | - Alberto Cagigi
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Paolo Rossi
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Paolo Palma
- Research Unit in Congenital and Perinatal Infection, Immune and Infectious Diseases Division, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Savita Pahwa
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL 33136; .,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136; and
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30
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Highly Multiplexed, Single Cell Transcriptomic Analysis of T-Cells by Microfluidic PCR. Methods Mol Biol 2016. [PMID: 27787802 DOI: 10.1007/978-1-4939-6548-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recently, technologies have been developed to measure expression of 96 (or more) mRNA transcripts at once from a single cell. Here we describe methods and important considerations for use of Fluidigm's BioMark platform for multiplexed single cell gene expression. We describe how to qualify primer/probes, select genes to examine in 96-parameter panels, perform the reverse transcription/cDNA synthesis step, and operate the instrument. In addition, we describe data analysis considerations. This technology has enormous value for characterizing the heterogeneity of T-cells, thereby providing a useful tool for immune monitoring.
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31
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Mahnke YD, Fletez-Brant K, Sereti I, Roederer M. Reconstitution of Peripheral T Cells by Tissue-Derived CCR4+ Central Memory Cells Following HIV-1 Antiretroviral Therapy. Pathog Immun 2016; 1:260-290. [PMID: 27819062 PMCID: PMC5093337 DOI: 10.20411/pai.v1i2.129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: Highly active antiretroviral therapy induces clinical benefits to HIV-1 infected individuals, which can be striking in those with progressive disease. Improved survival and decreased incidence of opportunistic infections go hand in hand with a suppression of the plasma viral load, an increase in peripheral CD4+ T-cell counts, as well as a reduction in the activation status of both CD4+ and CD8+ T cells. Methods: We investigated T-cell dynamics during ART by polychromatic flow cytometry in total as well as in HIV-1-specific CD4+ and CD8+ T cells in patients with advanced disease. We also measured gene expression by single cell transcriptomics to assess functional state. Results: The cytokine pattern of HIV-specific CD8+ T cells was not altered after ART, though their magnitude decreased significantly as the plasma viral load was suppressed to undetectable levels. Importantly, while CD4+ T cell numbers increased substantially during the first year, the population did not normalize: the increases were largely due to expansion of mucosal-derived CCR4+ CD4+ TCM; transcriptomic analysis revealed that these are not classical Th2-type cells. Conclusion: The apparent long-term normalization of CD4+ T-cell numbers following ART does not comprise a normal balance of functionally distinct cells, but results in a dramatic Th2 shift of the reconstituting immune system.
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Affiliation(s)
- Yolanda D Mahnke
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Kipper Fletez-Brant
- Immunology Core Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD
| | - Irini Sereti
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
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32
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Siqueira LGB, Hansen PJ. Sex differences in response of the bovine embryo to colony-stimulating factor 2. Reproduction 2016; 152:645-654. [PMID: 27601717 PMCID: PMC5097130 DOI: 10.1530/rep-16-0336] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/05/2016] [Indexed: 01/09/2023]
Abstract
We tested whether gene expression of the bovine morula is modified by CSF2 in a sex-dependent manner and if sex determines the effect of CSF2 on competence of embryos to become blastocysts. Embryos were produced in vitro using X- or Y-sorted semen and treated at Day 5 of culture with 10 ng/mL bovine CSF2 or control. In experiment 1, morulae were collected at Day 6 and biological replicates (n = 8) were evaluated for transcript abundance of 90 genes by RT-qPCR using the Fluidigm Delta Gene assay. Expression of more than one-third (33 of 90) of genes examined was affected by sex. The effect of CSF2 on gene expression was modified by sex (P < 0.05) for five genes (DDX3Y/DDX3X-like, NANOG, MYF6, POU5F1 and RIPK3) and tended (P < 0.10) to be modified by sex for five other genes (DAPK1, HOXA5, PPP2R3A, PTEN and TNFSF8). In experiment 2, embryos were treated at Day 5 with control or CSF2 and blastocysts were collected at Day 7 for immunolabeling to determine the number of inner cell mass (ICM) and trophectoderm (TE) cells. CSF2 increased the percent of putative zygotes that became blastocysts for females, but did not affect the development of males. There was no effect of CSF2 or interaction of CSF2 with sex on the total number of blastomeres in blastocysts or in the number of inner cell mass or trophectoderm cells. In conclusion, CSF2 exerted divergent responses on gene expression and development of female and male embryos. These results are evidence of sexually dimorphic responses of the preimplantation embryo to this embryokine.
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Affiliation(s)
- Luiz G B Siqueira
- Department of Animal SciencesD.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida, USA.,Embrapa Gado de LeiteJuiz de Fora, MG, Brazil
| | - Peter J Hansen
- Department of Animal SciencesD.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida, USA
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33
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Suliman S, Geldenhuys H, Johnson JL, Hughes JE, Smit E, Murphy M, Toefy A, Lerumo L, Hopley C, Pienaar B, Chheng P, Nemes E, Hoft DF, Hanekom WA, Boom WH, Hatherill M, Scriba TJ. Bacillus Calmette-Guérin (BCG) Revaccination of Adults with Latent Mycobacterium tuberculosis Infection Induces Long-Lived BCG-Reactive NK Cell Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2016; 197:1100-1110. [PMID: 27412415 PMCID: PMC4976036 DOI: 10.4049/jimmunol.1501996] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 06/07/2016] [Indexed: 01/14/2023]
Abstract
One third of the global population is estimated to be latently infected with Mycobacterium tuberculosis We performed a phase I randomized controlled trial of isoniazid preventive therapy (IPT) before revaccination with bacillus Calmette-Guérin (BCG) in healthy, tuberculin skin test-positive (≥15-mm induration), HIV-negative South African adults. We hypothesized that preclearance of latent bacilli with IPT modulates BCG immunogenicity following revaccination. Frequencies and coexpression of IFN-γ, TNF-α, IL-2, IL-17, and/or IL-22 in CD4 T cells and IFN-γ-expressing CD8 T, γδ T, CD3(+)CD56(+) NKT-like, and NK cells in response to BCG were measured using whole blood intracellular cytokine staining and flow cytometry. We analyzed 72 participants who were revaccinated with BCG after IPT (n = 33) or without prior IPT (n = 39). IPT had little effect on frequencies or cytokine coexpression patterns of M. tuberculosis- or BCG-specific responses. Revaccination transiently boosted BCG-specific Th1 cytokine-expressing CD4, CD8, and γδ T cells. Despite high frequencies of IFN-γ-expressing BCG-reactive CD3(+)CD56(+) NKT-like cells and CD3(-)CD56(dim) and CD3(-)CD56(hi) NK cells at baseline, BCG revaccination boosted these responses, which remained elevated up to 1 y after revaccination. Such BCG-reactive memory NK cells were induced by BCG vaccination in infants, whereas in vitro IFN-γ expression by NK cells upon BCG stimulation was dependent on IL-12 and IL-18. Our data suggest that isoniazid preclearance of M. tuberculosis bacilli has little effect on the magnitude, persistence, or functional attributes of lymphocyte responses boosted by BCG revaccination. Our study highlights the surprising durability of BCG-boosted memory NKT-like and NK cells expressing antimycobacterial effector molecules, which may be novel targets for tuberculosis vaccines.
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Affiliation(s)
- Sara Suliman
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Hennie Geldenhuys
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - John L. Johnson
- Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH, U.S.A
| | - Jane E. Hughes
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Erica Smit
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Melissa Murphy
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Asma Toefy
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lesedi Lerumo
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Christiaan Hopley
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Bernadette Pienaar
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Phalkun Chheng
- Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH, U.S.A
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Daniel F. Hoft
- Division of Immunobiology, Departments of Internal Medicine and Molecular Biology, Saint Louis University Medical Center, and Center for Vaccine Development, Saint Louis, MO, USA
| | - Willem A. Hanekom
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - W. Henry Boom
- Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, OH, U.S.A
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa,Corresponding Author
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34
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Vaccari M, Gordon SN, Fourati S, Schifanella L, Liyanage NPM, Cameron M, Keele BF, Shen X, Tomaras GD, Billings E, Rao M, Chung AW, Dowell KG, Bailey-Kellogg C, Brown EP, Ackerman ME, Vargas-Inchaustegui DA, Whitney S, Doster MN, Binello N, Pegu P, Montefiori DC, Foulds K, Quinn DS, Donaldson M, Liang F, Loré K, Roederer M, Koup RA, McDermott A, Ma ZM, Miller CJ, Phan TB, Forthal DN, Blackburn M, Caccuri F, Bissa M, Ferrari G, Kalyanaraman V, Ferrari MG, Thompson D, Robert-Guroff M, Ratto-Kim S, Kim JH, Michael NL, Phogat S, Barnett SW, Tartaglia J, Venzon D, Stablein DM, Alter G, Sekaly RP, Franchini G. Adjuvant-dependent innate and adaptive immune signatures of risk of SIVmac251 acquisition. Nat Med 2016; 22:762-70. [PMID: 27239761 PMCID: PMC5916782 DOI: 10.1038/nm.4105] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/05/2016] [Indexed: 12/24/2022]
Abstract
A recombinant vaccine containing Aventis Pasteur's canarypox vector (ALVAC)-HIV and gp120 alum decreased the risk of HIV acquisition in the RV144 vaccine trial. The substitution of alum with the more immunogenic MF59 adjuvant is under consideration for the next efficacy human trial. We found here that an ALVAC-simian immunodeficiency virus (SIV) and gp120 alum (ALVAC-SIV + gp120) equivalent vaccine, but not an ALVAC-SIV + gp120 MF59 vaccine, was efficacious in delaying the onset of SIVmac251 in rhesus macaques, despite the higher immunogenicity of the latter adjuvant. Vaccine efficacy was associated with alum-induced, but not with MF59-induced, envelope (Env)-dependent mucosal innate lymphoid cells (ILCs) that produce interleukin (IL)-17, as well as with mucosal IgG to the gp120 variable region 2 (V2) and the expression of 12 genes, ten of which are part of the RAS pathway. The association between RAS activation and vaccine efficacy was also observed in an independent efficacious SIV-vaccine approach. Whether RAS activation, mucosal ILCs and antibodies to V2 are also important hallmarks of HIV-vaccine efficacy in humans will require further studies.
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Affiliation(s)
- Monica Vaccari
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Shari N Gordon
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Slim Fourati
- Department of Pathology, Case Western Reserve, Cleveland, Ohio, USA
| | - Luca Schifanella
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
- Department of Biomedical and Clinical Sciences, 'L. Sacco' Hospital, University of Milan, Italy
| | - Namal P M Liyanage
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Mark Cameron
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Durham, North Carolina, USA
| | | | - Erik Billings
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mangala Rao
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Amy W Chung
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
| | - Karen G Dowell
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
| | | | - Eric P Brown
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | | | | | - Melvin N Doster
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Nicolo Binello
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Poonam Pegu
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Kathryn Foulds
- Vaccine Research Center, US National Institutes of Health, Bethesda, Maryland, USA
| | - David S Quinn
- Vaccine Research Center, US National Institutes of Health, Bethesda, Maryland, USA
| | - Mitzi Donaldson
- Vaccine Research Center, US National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Mario Roederer
- Vaccine Research Center, US National Institutes of Health, Bethesda, Maryland, USA
| | - Richard A Koup
- Vaccine Research Center, US National Institutes of Health, Bethesda, Maryland, USA
| | - Adrian McDermott
- Vaccine Research Center, US National Institutes of Health, Bethesda, Maryland, USA
| | - Zhong-Min Ma
- California National Primate Research Center, University of California, Davis, California, USA
| | - Christopher J Miller
- California National Primate Research Center, University of California, Davis, California, USA
| | - Tran B Phan
- University of California, Irvine School of Medicine, Irvine, California, USA
| | - Donald N Forthal
- University of California, Irvine School of Medicine, Irvine, California, USA
| | - Matthew Blackburn
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Francesca Caccuri
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Massimiliano Bissa
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Durham, North Carolina, USA
| | | | | | - DeVon Thompson
- Advanced Bioscience Laboratories, Rockville, Maryland, USA
| | - Marjorie Robert-Guroff
- Immune Biology of Retroviral Infection Section, National Cancer Institute, Bethesda, Maryland, USA
| | - Silvia Ratto-Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jerome H Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | - David Venzon
- Biostatistics and Data Management Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
| | | | - Genoveffa Franchini
- Animal Models and Vaccine Section, National Cancer Institute, Bethesda, Maryland, USA
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35
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Pan N, Rao W, Standke SJ, Yang Z. Using Dicationic Ion-Pairing Compounds To Enhance the Single Cell Mass Spectrometry Analysis Using the Single-Probe: A Microscale Sampling and Ionization Device. Anal Chem 2016; 88:6812-9. [PMID: 27239862 DOI: 10.1021/acs.analchem.6b01284] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A unique mass spectrometry (MS) method has been developed to determine the negatively charged species in live single cells using the positive ionization mode. The method utilizes dicationic ion-pairing compounds through the miniaturized multifunctional device, the single-probe, for reactive MS analysis of live single cells under ambient conditions. In this study, two dicationic reagents, 1,5-pentanediyl-bis(1-butylpyrrolidinium) difluoride (C5(bpyr)2F2) and 1,3-propanediyl-bis(tripropylphosphonium) difluoride (C3(triprp)2F2), were added in the solvent and introduced into single cells to extract cellular contents for real-time MS analysis. The negatively charged (1- charged) cell metabolites, which form stable ion-pairs (1+ charged) with dicationic compounds (2+ charged), were detected in positive ionization mode with a greatly improved sensitivity. We have tentatively assigned 192 and 70 negatively charged common metabolites as adducts with (C5(bpyr)2F2) and (C3(triprp)2F2), respectively, in three separate SCMS experiments in the positive ion mode. The total number of tentatively assigned metabolites is 285 for C5(bpyr)2F2 and 143 for C3(triprp)2F2. In addition, the selectivity of dicationic compounds in the complex formation allows for the discrimination of overlapped ion peaks with low abundances. Tandem (MS/MS) analyses at the single cell level were conducted for selected adduct ions for molecular identification. The utilization of the dicationic compounds in the single-probe MS technique provides an effective approach to the detection of a broad range of metabolites at the single cell level.
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Affiliation(s)
- Ning Pan
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Wei Rao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Shawna J Standke
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
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36
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Lissina A, Ambrozak DR, Boswell KL, Yang W, Boritz E, Wakabayashi Y, Iglesias MC, Hashimoto M, Takiguchi M, Haddad E, Douek DC, Zhu J, Koup RA, Yamamoto T, Appay V. Fine-tuning of CD8(+) T-cell effector functions by targeting the 2B4-CD48 interaction. Immunol Cell Biol 2016; 94:583-92. [PMID: 26860368 DOI: 10.1038/icb.2016.17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 01/08/2016] [Accepted: 01/24/2016] [Indexed: 12/22/2022]
Abstract
Polyfunctionality and cytotoxic activity dictate CD8(+) T-cell efficacy in the eradication of infected and malignant cells. The induction of these effector functions depends on the specific interaction between the T-cell receptor (TCR) and its cognate peptide-MHC class I complex, in addition to signals provided by co-stimulatory or co-inhibitory receptors, which can further regulate these functions. Among these receptors, the role of 2B4 is contested, as it has been described as either co-stimulatory or co-inhibitory in modulating T-cell functions. We therefore combined functional, transcriptional and epigenetic approaches to further characterize the impact of disrupting the interaction of 2B4 with its ligand CD48, on the activity of human effector CD8(+) T-cell clones. In this setting, we show that the 2B4-CD48 axis is involved in the fine-tuning of CD8(+) T-cell effector function upon antigenic stimulation. Blocking this interaction resulted in reduced CD8(+) T-cell clone-mediated cytolytic activity, together with a subtle drop in the expression of genes involved in effector function regulation. Our results also imply a variable contribution of the 2B4-CD48 interaction to the modulation of CD8(+) T-cell functional properties, potentially linked to intrinsic levels of T-bet expression and TCR avidity. The present study thus provides further insights into the role of the 2B4-CD48 interaction in the fine regulation of CD8(+) T-cell effector function upon antigenic stimulation.
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Affiliation(s)
- Anna Lissina
- Sorbonne Universités, UPMC Univ Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,INSERM U1135, CIMI-Paris, Paris, France
| | - David R Ambrozak
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kristin L Boswell
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wenjing Yang
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Eli Boritz
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Yoshiyuki Wakabayashi
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Maria C Iglesias
- Sorbonne Universités, UPMC Univ Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,INSERM U1135, CIMI-Paris, Paris, France
| | - Masao Hashimoto
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | - Elias Haddad
- Vaccine and Gene Therapy Institute of Florida, Lucie, FL, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Takuya Yamamoto
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Victor Appay
- Sorbonne Universités, UPMC Univ Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,INSERM U1135, CIMI-Paris, Paris, France
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37
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Uribe-Convers S, Settles ML, Tank DC. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One 2016; 11:e0148203. [PMID: 26828929 PMCID: PMC4734709 DOI: 10.1371/journal.pone.0148203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/14/2016] [Indexed: 11/30/2022] Open
Abstract
Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500bp for 349 samples.
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Affiliation(s)
- Simon Uribe-Convers
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | - Matthew L. Settles
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - David C. Tank
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
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38
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Burel JG, Apte SH, Doolan DL. Systems Approaches towards Molecular Profiling of Human Immunity. Trends Immunol 2016; 37:53-67. [DOI: 10.1016/j.it.2015.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 12/12/2022]
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Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity. Oncotarget 2015; 6:1302-14. [PMID: 25514598 PMCID: PMC4359234 DOI: 10.18632/oncotarget.2744] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022] Open
Abstract
A lack of cell surface markers for the specific identification, isolation and subsequent analysis of living prostate tumor cells hampers progress in the field. Specific characterization of tumor cells and their microenvironment in a multi-parameter molecular assay could significantly improve prognostic accuracy for the heterogeneous prostate tumor tissue. Novel functionalized gold-nano particles allow fluorescence-based detection of absolute mRNA expression levels in living cells by fluorescent activated flow cytometry (FACS). We use of this technique to separate prostate tumor and benign cells in human prostate needle biopsies based on the expression levels of the tumor marker alpha-methylacyl-CoA racemase (AMACR). We combined RNA and protein detection of living cells by FACS to gate for epithelial cell adhesion molecule (EPCAM) positive tumor and benign cells, EPCAM/CD45 double negative mesenchymal cells and CD45 positive infiltrating lymphocytes. EPCAM positive epithelial cells were further sub-gated into AMACR high and low expressing cells. Two hundred cells from each population and several biopsies from the same patient were analyzed using a multiplexed gene expression profile to generate a cell type resolved profile of the specimen. This technique provides the basis for the clinical evaluation of cell type resolved gene expression profiles as pre-therapeutic prognostic markers for prostate cancer.
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40
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Walsh MT, Hsiao AP, Lee HS, Liu Z, Huang X. Capture and enumeration of mRNA transcripts from single cells using a microfluidic device. LAB ON A CHIP 2015; 15:2968-2980. [PMID: 26040942 DOI: 10.1039/c5lc00445d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Accurate measurement of RNA transcripts from single cells will enable the precise classification of cell types and characterization of the heterogeneity in cell populations that play key roles in normal cellular physiology and diseases. As a step towards this end, we have developed a microfluidic device and methods for automatic hydrodynamic capture of single mammalian cells and subsequent immobilization and digital counting of polyadenylated mRNA molecules released from the individual cells. Using single-molecule fluorescence imaging, we have demonstrated that polyadenylated mRNA molecules from single HeLa cells can be captured within minutes by hybridization to polydeoxyribothymidine oligonucleotides covalently attached on the glass surface in the device. The total mRNA molecule counts in the individual HeLa cells are found to vary significantly from one another. Our technology opens up the possibility of direct digital enumeration of RNA transcripts from single cells with single-molecule sensitivity using a single integrated microfluidic device.
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Affiliation(s)
- Matthew T Walsh
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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41
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Cotugno N, De Armas L, Pallikkuth S, Rossi P, Palma P, Pahwa S. Paediatric HIV infection in the ‘omics era: defining transcriptional signatures of viral control and vaccine responses. J Virus Erad 2015. [DOI: 10.1016/s2055-6640(20)30507-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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42
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Cotugno N, De Armas L, Pallikkuth S, Rossi P, Palma P, Pahwa S. Paediatric HIV infection in the 'omics era: defining transcriptional signatures of viral control and vaccine responses. J Virus Erad 2015; 1:153-158. [PMID: 26807446 PMCID: PMC4721557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Modern technologies and their increased accessibility have shifted 'benchtop' medical research to the larger dimension of 'omics. The huge amount of data derived from gene expression and sequencing experiments has propelled physicians, basic scientists and bioinformaticians towards a common goal to transform 'big data' into predictive constructs that are readily available and will offer clinical utility. Although most of the studies available in the literature have been performed on healthy subjects and in peripheral blood mononuclear cells (PBMC), which are a heterogenous and extremely variable pool of cells, scientists are now trying to address mechanistic questions in purified cell subsets in pathological conditions. In the field of HIV, few attempts have been made to comprehensively evaluate gene-expression profiles of infected patients with different disease status. With the view of discovering a path towards remission or viral eradication, perinatally HIV-infected children represent a unique model. In fact the well-defined time of infection and the resulting opportunity to start early treatment, thereby generating a smaller size of viral reservoir and a more intact immune system, allow for investigation of therapeutic strategies to defeat the virus. In this scenario, 'transcriptomic' or gene expression technologies and supporting bioinformatics applications need to be strategically integrated to provide novel information about immune correlates of virus control following treatment interruption. Here we review modern techniques for gene expression analysis and discuss the best transcriptomic strategies applicable to the field of functional cure in paediatric HIV infection.
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Affiliation(s)
- Nicola Cotugno
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy,Department of Systems Medicine,
University of Rome,‘Tor Vergata’,
Italy
| | - Lesley De Armas
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA
| | - Suresh Pallikkuth
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA
| | - Paolo Rossi
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy,Department of Systems Medicine,
University of Rome,‘Tor Vergata’,
Italy
| | - Paolo Palma
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy
| | - Savita Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA,Corresponding author: Savita Pahwa,
Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami1580 NW 10th Avenue,
Miami,
FL33136,
USA
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43
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Chattopadhyay PK, Roederer M. A mine is a terrible thing to waste: high content, single cell technologies for comprehensive immune analysis. Am J Transplant 2015; 15:1155-61. [PMID: 25708158 DOI: 10.1111/ajt.13193] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 01/25/2023]
Abstract
In recent years, an incredible variety of single cell technologies have become available to analyze immune responses. These technologies include polychromatic flow cytometry, mass cytometry, highly multiplexed single cell qPCR, RNA sequencing, microtools, and high-resolution imaging. In this article, we review these platforms, describing their power and limitations for comprehensive analysis of the immune system. We relate the properties of these technologies to the various cellular states relevant to an immune response, in order to address which technologies are most appropriate for which settings.
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Affiliation(s)
- P K Chattopadhyay
- Vaccine Research Center, National Institutes of Health, Bethesda, MD
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44
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Herderschee J, Fenwick C, Pantaleo G, Roger T, Calandra T. Emerging single-cell technologies in immunology. J Leukoc Biol 2015; 98:23-32. [PMID: 25908734 DOI: 10.1189/jlb.6ru0115-020r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/26/2015] [Indexed: 12/14/2022] Open
Abstract
During evolution, the immune system has diversified to protect the host from the extremely wide array of possible pathogens. Until recently, immune responses were dissected by use of global approaches and bulk tools, averaging responses across samples and potentially missing particular contributions of individual cells. This is a strongly limiting factor, considering that initial immune responses are likely to be triggered by a restricted number of cells at the vanguard of host defenses. The development of novel, single-cell technologies is a major innovation offering great promise for basic and translational immunology with the potential to overcome some of the limitations of traditional research tools, such as polychromatic flow cytometry or microscopy-based methods. At the transcriptional level, much progress has been made in the fields of microfluidics and single-cell RNA sequencing. At the protein level, mass cytometry already allows the analysis of twice as many parameters as flow cytometry. In this review, we explore the basis and outcome of immune-cell diversity, how genetically identical cells become functionally different, and the consequences for the exploration of host-immune defense responses. We will highlight the advantages, trade-offs, and potential pitfalls of emerging, single-cell-based technologies and how they provide unprecedented detail of immune responses.
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Affiliation(s)
- Jacobus Herderschee
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Craig Fenwick
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Thierry Roger
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Thierry Calandra
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
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45
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Dodson MV, Du M, Wang S, Bergen WG, Fernyhough-Culver M, Basu U, Poulos SP, Hausman GJ. Adipose depots differ in cellularity, adipokines produced, gene expression, and cell systems. Adipocyte 2014; 3:236-41. [PMID: 26317047 PMCID: PMC4550680 DOI: 10.4161/adip.28321] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/20/2014] [Accepted: 02/21/2014] [Indexed: 12/28/2022] Open
Abstract
The race to manage the health concerns related to excess fat deposition has spawned a proliferation of clinical and basic research efforts to understand variables including dietary uptake, metabolism, and lipid deposition by adipocytes. A full appreciation of these variables must also include a depot-specific understanding of content and location in order to elucidate mechanisms governing cellular development and regulation of fat deposition. Because adipose tissue depots contain various cell types, differences in the cellularity among and within adipose depots are presently being documented to ascertain functional differences. This has led to the possibility of there being, within any one adipose depot, cellular distinctions that essentially result in adipose depots within depots. The papers comprising this issue will underscore numerous differences in cellularity (development, histogenesis, growth, metabolic function, regulation) of different adipose depots. Such information is useful in deciphering adipose depot involvement both in normal physiology and in pathology. Obesity, diabetes, metabolic syndrome, carcass composition of meat animals, performance of elite athletes, physiology/pathophysiology of aging, and numerous other diseases might be altered with a greater understanding of adipose depots and the cells that comprise them-including stem cells-during initial development and subsequent periods of normal/abnormal growth into senescence. Once thought to be dormant and innocuous, the adipocyte is emerging as a dynamic and influential cell and research will continue to identify complex physiologic regulation of processes involved in adipose depot physiology.
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Affiliation(s)
- Michael V Dodson
- Department of Animal Sciences; Washington State University; Pullman, WA USA
| | - Min Du
- Department of Animal Sciences; Washington State University; Pullman, WA USA
| | - Songbo Wang
- Department of Animal Sciences; Washington State University; Pullman, WA USA
- College of Animal Science; South China Agricultural University; Guangzhou, PR China
| | - Werner G Bergen
- Program in Cellular and Molecular Biosciences/Department of Animal Sciences; Auburn University; Auburn, AL USA
| | | | | | | | - Gary J Hausman
- Department of Animal and Dairy Science; University of Georgia; Athens, GA USA
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46
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Jena B, Moyes JS, Huls H, Cooper LJN. Driving CAR-based T-cell therapy to success. Curr Hematol Malig Rep 2014; 9:50-6. [PMID: 24488441 DOI: 10.1007/s11899-013-0197-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
T cells that have been genetically modified, activated, and propagated ex vivo can be infused to control tumor progression in patients who are refractory to conventional treatments. Early-phase clinical trials demonstrate that the tumor-associated antigen (TAA) CD19 can be therapeutically engaged through the enforced expression of a chimeric antigen receptor (CAR) on clinical-grade T cells. Advances in vector design, the architecture of the CAR molecule especially as associated with T-cell co-stimulatory pathways, and understanding of the tumor microenvironment, play significant roles in the successful treatment of medically fragile patients. However, some recipients of CAR(+) T cells demonstrate incomplete responses. Understanding the potential for treatment failure provides a pathway to improve the potency of adoptive transfer of CAR(+) T cells. High throughput single-cell analyses to understand the complexity of the inoculum coupled with animal models may provide insight into the therapeutic potential of genetically modified T cells. This review focuses on recent advances regarding the human application of CD19-specific CAR(+) T cells and explores how their success for hematologic cancers can provide a framework for investigational treatment of solid tumor malignancies.
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Affiliation(s)
- Bipulendu Jena
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Pediatrics (Unit #907), 1515 Holcombe Blvd., Houston, TX, 77030, USA
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47
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Pan N, Rao W, Kothapalli NR, Liu R, Burgett AWG, Yang Z. The single-probe: a miniaturized multifunctional device for single cell mass spectrometry analysis. Anal Chem 2014; 86:9376-80. [PMID: 25222919 DOI: 10.1021/ac5029038] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new mass spectrometry (MS) technology, the Single-probe MS, capable of real-time, in situ metabolomic analysis of individual living cells. The Single-probe is a miniaturized multifunctional sampling and ionization device that is directly coupled to the mass spectrometer. With a sampling tip smaller than individual eukaryotic cells (<10 μm), the Single-probe can be inserted into single cells to sample the intracellular compounds for real-time MS analysis. We have used the Single-probe to detect several cellular metabolites and the anticancer small molecules paclitaxel, doxorubicin, and OSW-1 in individual cervical cancer cells (HeLa). Single cell mass spectrometry (SCMS) is an emerging scientific technology that could reshape the analytical science of many research disciplines, and the Single-probe MS technology is a novel method for SCMS that, through its accessible fabrication protocols, can be broadly applied to different research areas.
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Affiliation(s)
- Ning Pan
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
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48
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McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A, Webster P, Beechem J, Gottardo R. Modeling bi-modality improves characterization of cell cycle on gene expression in single cells. PLoS Comput Biol 2014; 10:e1003696. [PMID: 25032992 PMCID: PMC4102402 DOI: 10.1371/journal.pcbi.1003696] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/14/2014] [Indexed: 01/02/2023] Open
Abstract
Advances in high-throughput, single cell gene expression are allowing interrogation of cell heterogeneity. However, there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level. We assess the effect of cell cycle phase on gene expression in single cells by measuring 333 genes in 930 cells across three phases and three cell lines. We determine each cell's phase non-invasively without chemical arrest and use it as a covariate in tests of differential expression. We observe bi-modal gene expression, a previously-described phenomenon, wherein the expression of otherwise abundant genes is either strongly positive, or undetectable within individual cells. This bi-modality is likely both biologically and technically driven. Irrespective of its source, we show that it should be modeled to draw accurate inferences from single cell expression experiments. To this end, we propose a semi-continuous modeling framework based on the generalized linear model, and use it to characterize genes with consistent cell cycle effects across three cell lines. Our new computational framework improves the detection of previously characterized cell-cycle genes compared to approaches that do not account for the bi-modality of single-cell data. We use our semi-continuous modelling framework to estimate single cell gene co-expression networks. These networks suggest that in addition to having phase-dependent shifts in expression (when averaged over many cells), some, but not all, canonical cell cycle genes tend to be co-expressed in groups in single cells. We estimate the amount of single cell expression variability attributable to the cell cycle. We find that the cell cycle explains only 5%–17% of expression variability, suggesting that the cell cycle will not tend to be a large nuisance factor in analysis of the single cell transcriptome. Recent technological advances have enabled the measurement of gene expression in individual cells, revealing that there is substantial variability in expression, even within a homogeneous cell population. In this paper, we develop new analytical methods that account for the intrinsic, stochastic nature of single cell expression in order to characterize the effect of cell cycle on gene expression at the single-cell level. Applying these methods to populations of asynchronously cycling cells, we are able to identify large numbers of genes with cell cycle-associated expression patterns. By measuring and adjusting for cellular-level factors, we are able to derive estimates of co-expressing gene networks that more closely reflect cellular-level processes as opposed to sample-level processes. We find that cell cycle phase only accounts for a modest amount of the overall variability of gene expression within an individual cell. The analytical methods demonstrated in this paper are universally applicable to single cell expression data and represent a promising tool to the scientific community.
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Affiliation(s)
- Andrew McDavid
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lucas Dennis
- NanoString Technologies, Seattle, Washington, United States of America
| | - Patrick Danaher
- NanoString Technologies, Seattle, Washington, United States of America
| | - Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Krouse
- NanoString Technologies, Seattle, Washington, United States of America
| | - Alice Wang
- BD Biosciences, San Jose, California, United States of America
| | - Philippa Webster
- NanoString Technologies, Seattle, Washington, United States of America
| | - Joseph Beechem
- NanoString Technologies, Seattle, Washington, United States of America
| | - Raphael Gottardo
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Lim B, Reddy V, Hu X, Kim K, Jadhav M, Abedini-Nassab R, Noh YW, Lim YT, Yellen BB, Kim C. Magnetophoretic circuits for digital control of single particles and cells. Nat Commun 2014; 5:3846. [DOI: 10.1038/ncomms4846] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 04/09/2014] [Indexed: 11/09/2022] Open
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Adalsteinsson VA, Tahirova N, Tallapragada N, Yao X, Campion L, Angelini A, Douce TB, Huang C, Bowman B, Williamson CA, Kwon DS, Wittrup KD, Love JC. Single cells from human primary colorectal tumors exhibit polyfunctional heterogeneity in secretions of ELR+ CXC chemokines. Integr Biol (Camb) 2014; 5:1272-81. [PMID: 23995780 DOI: 10.1039/c3ib40059j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer is an inflammatory disease of tissue that is largely influenced by the interactions between multiple cell types, secreted factors, and signal transduction pathways. While single-cell sequencing continues to refine our understanding of the clonotypic heterogeneity within tumors, the complex interplay between genetic variations and non-genetic factors ultimately affects therapeutic outcome. Much has been learned through bulk studies of secreted factors in the tumor microenvironment, but the secretory behavior of single cells has been largely uncharacterized. Here we directly profiled the secretions of ELR+ CXC chemokines from thousands of single colorectal tumor and stromal cells, using an array of subnanoliter wells and a technique called microengraving to characterize both the rates of secretion of several factors at once and the numbers of cells secreting each chemokine. The ELR+ CXC chemokines are highly redundant, pro-angiogenic cytokines that signal via the CXCR1 and CXCR2 receptors, influencing tumor growth and progression. We find that human primary colorectal tumor and stromal cells exhibit polyfunctional heterogeneity in the combinations and magnitudes of secretions for these chemokines. In cell lines, we observe similar variance: phenotypes observed in bulk can be largely absent among the majority of single cells, and discordances exist between secretory states measured and gene expression for these chemokines among single cells. Together, these measures suggest secretory states among tumor cells are complex and can evolve dynamically. Most importantly, this study reveals new insight into the intratumoral phenotypic heterogeneity of human primary tumors.
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Affiliation(s)
- Viktor A Adalsteinsson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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