1
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Larragoite ET, Nell RA, Martins LJ, Barrows LR, Planelles V, Spivak AM. Histone deacetylase inhibition reduces deleterious cytokine release induced by ingenol stimulation. Biochem Pharmacol 2022; 195:114844. [PMID: 34801521 PMCID: PMC8712404 DOI: 10.1016/j.bcp.2021.114844] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 01/03/2023]
Abstract
Latency reversing agents (LRAs), such as protein kinase C (PKC) agonists, constitute a promising strategy for exposing and eliminating the HIV-1 latent reservoir. PKC agonists activate NF-κB and induce deleterious pro-inflammatory cytokine production. Adjuvant pharmacological agents, such as ruxolitinib, a JAK inhibitor, have previously been combined with LRAs to reduce deleterious pro-inflammatory cytokine secretion without inhibiting HIV-1 reactivation in vitro. Histone deacetylase inhibitors (HDACi) are known to dampen pro-inflammatory cytokine secretion in the context of other diseases and synergize with LRAs to reactivate latent HIV-1. This study investigates whether a panel of epigenetic modifiers, including HDACi, could dampen PKC-induced pro-inflammatory cytokine secretion during latency reversal. We screened an epigenetic modifier library for compounds that reduced intracellular IL-6 production induced by the PKC agonist Ingenol-3,20-dibenzoate. We further tested the most promising epigenetic inhibitor class, HDACi, for their ability to reduce pro-inflammatory cytokines and reactivate latent HIV-1 ex vivo. We identified nine epigenetic modulators that reduced PKC-induced intracellular IL-6. In cells from aviremic individuals living with HIV-1, the HDAC1-3 inhibitor, suberohydroxamic acid (SBHA), reduced secretion of pro-inflammatory cytokines TNF-α, IL-5, IL-2r, and IL-17 but did not significantly reactivate latent HIV-1 when combined with Ingenol-3,20-dibenzoate. Combining SBHA and Ingenol-3,20-dibenzoate reduces deleterious cytokine production during latency reversal but does not induce significant viral reactivation in aviremic donor PBMCs. The ability of SBHA to reduce PKC-induced pro-inflammatory cytokines when combined with Ingenol-3,20-dibenzoate suggests SBHA can be used to reduced PKC induced pro-inflammatory cytokines but not to achieve latency reversal in the context of HIV-1.
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Affiliation(s)
- Erin T. Larragoite
- Department of Pathology, University of Utah, Salt Lake City, United States
| | - Racheal A. Nell
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, United States
| | - Laura J. Martins
- Department of Pathology, University of Utah, Salt Lake City, United States
| | - Louis R. Barrows
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, United States
| | - Vicente Planelles
- Department of Pathology, University of Utah, Salt Lake City, United States
| | - Adam M. Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, United States, Corresponding Author: Adam M. Spivak, 50 North Medical Drive, Division of Infectious Diseases, Room 4B319, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, Phone: 801-587-1964, Fax: 801-585-3377,
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2
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Redecke V, Tawaratsumida K, Larragoite ET, Williams ESCP, Planelles V, Spivak AM, Hirayama L, Elgort M, Swenson S, Smith R, Worthen B, Zimmerman R, Slev P, Cahoon B, Astill M, Häcker H. A rapid and affordable point of care test for antibodies against SARS-CoV-2 based on hemagglutination and artificial intelligence interpretation. Sci Rep 2021; 11:24507. [PMID: 34969960 PMCID: PMC8718524 DOI: 10.1038/s41598-021-04298-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Diagnostic tests that detect antibodies (AB) against SARS-CoV-2 for evaluation of seroprevalence and guidance of health care measures are important tools for managing the COVID-19 pandemic. Current tests have certain limitations with regard to turnaround time, costs and availability, particularly in point-of-care (POC) settings. We established a hemagglutination-based AB test that is based on bi-specific proteins which contain a dromedary-derived antibody (nanobody) binding red blood cells (RBD) and a SARS-CoV-2-derived antigen, such as the receptor-binding domain of the Spike protein (Spike-RBD). While the nanobody mediates swift binding to RBC, the antigen moiety directs instantaneous, visually apparent hemagglutination in the presence of SARS-CoV-2-specific AB generated in COVID-19 patients or vaccinated individuals. Method comparison studies with assays cleared by emergency use authorization demonstrate high specificity and sensitivity. To further increase objectivity of test interpretation, we developed an image analysis tool based on digital image acquisition (via a cell phone) and a machine learning algorithm based on defined sample-training and -validation datasets. Preliminary data, including a small clinical study, provides proof of principle for test performance in a POC setting. Together, the data support the interpretation that this AB test format, which we refer to as 'NanoSpot.ai', is suitable for POC testing, can be manufactured at very low costs and, based on its generic mode of action, can likely be adapted to a variety of other pathogens.
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Affiliation(s)
- Vanessa Redecke
- Laboratory of Innate Immunity and Signal Transduction, Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kazuki Tawaratsumida
- Laboratory of Innate Immunity and Signal Transduction, Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Erin T Larragoite
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Elizabeth S C P Williams
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Adam M Spivak
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Lincoln Hirayama
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA
| | - Marc Elgort
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA
| | | | | | | | | | - Patricia Slev
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA
| | | | - Mark Astill
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA
| | - Hans Häcker
- Laboratory of Innate Immunity and Signal Transduction, Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
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3
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Nandakumar V, Profaizer T, Lozier BK, Elgort MG, Larragoite ET, Williams ESCP, Solis-Leal A, Lopez JB, Berges BK, Planelles V, Rychert J, Slev PR, Delgado JC. Evaluation of a Surrogate ELISA- Based Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) cPass Neutralization Antibody Detection Assay and Correlation with IgG Commercial Serology Assays. Arch Pathol Lab Med 2021; 145:1212-1220. [PMID: 34181714 DOI: 10.5858/arpa.2021-0213-sa] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT Emerging evidence shows correlation between the presence of neutralization antibodies (nAbs) and protective immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently available commercial serology assays lack the ability to specifically identify nAbs. An ELISAbased nAb assay (GenScript cPass neutralization antibody assay) has recently received emergency use authorization from the Food and Drug Administration (FDA). OBJECTIVE To evaluate the performance characteristics of this assay and compare and correlate it with the commercial assays that detect SARS-CoV-2 specific IgG. DESIGN Specimens from SARS-COV-2 infected patients (n=124), healthy donors obtained pre-pandemic (n=100), and from patients with non-COVID (coronavirus disease 2019) respiratory infections (n=92) were analyzed using this assay. Samples with residual volume were also tested on three commercial serology platforms (Abbott, EUROIMMUN, Siemens). Twenty-eight randomly selected specimens from patients with COVID-19 and 10 healthy controls were subjected to a Plaque Reduction Neutralization Test (PRNT). RESULTS The cPass assay exhibited 96.1% (95% CI, 94.9%-97.3%) sensitivity (at >14 days post- positive PCR), 100% (95% CI, 98.0%-100.0%) specificity and zero cross-reactivity for the presence of non- COVID respiratory infections. When compared to the plaque reduction assay, 97.4% (95% CI, 96.2%-98.5%) qualitative agreement and a positive correlation (R2 =0.76) was observed. Comparison of IgG signals from each of the commercial assays with the nAb results from PRNT/cPass assays displayed >94.7% qualitative agreement and correlations with R2=0.43/0.68 (Abbott), R2=0.57/0.85 (EUROIMMUN) and R2=0.39/0.63 (Siemens), respectively. CONCLUSIONS The combined data support the use of cPass assay for accurate detection of the nAb response. Positive IgG results from commercial assays associated reasonably with nAbs presence and can serve as a substitute.
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Affiliation(s)
- Vijayalakshmi Nandakumar
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA (Nandakumar, Profaizer, Lozier, Elgort, Rychert, Slev, Delgado).,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA (Nandakumar, Larragoite, Williams, Planelles, Rychert, Slev, Delgado)
| | - Tracie Profaizer
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA (Nandakumar, Profaizer, Lozier, Elgort, Rychert, Slev, Delgado)
| | - Bucky K Lozier
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA (Nandakumar, Profaizer, Lozier, Elgort, Rychert, Slev, Delgado)
| | - Marc G Elgort
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA (Nandakumar, Profaizer, Lozier, Elgort, Rychert, Slev, Delgado)
| | - Erin T Larragoite
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA (Nandakumar, Larragoite, Williams, Planelles, Rychert, Slev, Delgado)
| | - Elizabeth S C P Williams
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA (Nandakumar, Larragoite, Williams, Planelles, Rychert, Slev, Delgado)
| | - Antonio Solis-Leal
- Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UTAH, USA (Solis-Leal, Lopez, Berges)
| | - J Brandon Lopez
- Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UTAH, USA (Solis-Leal, Lopez, Berges)
| | - Bradford K Berges
- Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UTAH, USA (Solis-Leal, Lopez, Berges)
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA (Nandakumar, Larragoite, Williams, Planelles, Rychert, Slev, Delgado)
| | - Jenna Rychert
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA (Nandakumar, Profaizer, Lozier, Elgort, Rychert, Slev, Delgado).,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA (Nandakumar, Larragoite, Williams, Planelles, Rychert, Slev, Delgado)
| | - Patricia R Slev
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA (Nandakumar, Profaizer, Lozier, Elgort, Rychert, Slev, Delgado).,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA (Nandakumar, Larragoite, Williams, Planelles, Rychert, Slev, Delgado)
| | - Julio C Delgado
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA (Nandakumar, Profaizer, Lozier, Elgort, Rychert, Slev, Delgado).,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA (Nandakumar, Larragoite, Williams, Planelles, Rychert, Slev, Delgado)
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4
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Zheng Y, Larragoite ET, Williams ESCP, Lama J, Cisneros I, Delgado JC, Slev P, Rychert J, Innis EA, Coiras M, Rondina MT, Spivak AM, Planelles V. Neutralization assay with SARS-CoV-1 and SARS-CoV-2 spike pseudotyped murine leukemia virions. Virol J 2021; 18:1. [PMID: 33397387 PMCID: PMC7780907 DOI: 10.1186/s12985-020-01472-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Virus neutralization by antibodies is an important prognostic factor in many viral diseases. To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal murine leukemia virus genome encoding firefly luciferase. This assay design is intended for use in laboratories with biocontainment level 2 and therefore circumvents the need for the biocontainment level 3 that would be required for replication-competent SARS-CoV-2 virus. To validate the pseudovirion assay, we set up comparisons with other available antibody tests including those from Abbott, Euroimmun and Siemens, using archived, known samples. RESULTS 11 out of 12 SARS-CoV-2-infected patient serum samples showed neutralizing activity against SARS-CoV-2-spike pseudotyped MLV viruses, with neutralizing titers-50 (NT50) that ranged from 1:25 to 1:1,417. Five historical samples from patients hospitalized for severe influenza infection in 2016 tested negative in the neutralization assay (NT50 < 25). Three serum samples with high neutralizing activity against SARS-CoV-2/MLV pseudoviruses showed no detectable neutralizing activity (NT50 < 25) against SARS-CoV-1/MLV pseudovirions. We also compared the semiquantitative Siemens SARS-CoV-2 IgG test, which measures binding of IgG to recombinantly expressed receptor binding domain of SARS-CoV-2 spike glycoprotein with the neutralization titers obtained in the pseudovirion assay and the results show high concordance between the two tests (R2 = 0.9344). CONCLUSIONS SARS-CoV-2 spike/MLV pseudovirions provide a practical means of assessing neutralizing activity of antibodies in serum or plasma from infected patients under laboratory conditions consistent with biocontainment level 2. This assay offers promise also in evaluating immunogenicity of spike glycoprotein-based candidate vaccines in the near future.
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Affiliation(s)
- Yue Zheng
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Erin T Larragoite
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Juan Lama
- RetroVirox, Inc., San Diego, CA, USA
| | | | - Julio C Delgado
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA
| | - Patricia Slev
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA
| | - Jenna Rychert
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA
| | - Emily A Innis
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mayte Coiras
- AIDS Immunopathology Unit, National Center of Microbiology (CNM), Instituto de Salud Carlos III, Madrid, Spain
| | - Matthew T Rondina
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Adam M Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
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5
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Luetkens T, Metcalf R, Planelles V, Zheng Y, Larragoite ET, Spivak ES, Spivak AM, Steinbach M, Blaylock RC, Avila SV, Hankey KG, Martins TB, Slev PR, Mannuel HD, Sajadi M, Rapoport AP, Atanackovic D. Successful transfer of anti-SARS-CoV-2 immunity using convalescent plasma in an MM patient with hypogammaglobulinemia and COVID-19. Blood Adv 2020; 4:4864-4868. [PMID: 33031540 PMCID: PMC7556131 DOI: 10.1182/bloodadvances.2020002595] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/14/2020] [Indexed: 12/26/2022] Open
Abstract
A severely immunocompromised patient with MM and COVID19 who received a convalescent plasma product showed SARS-CoV-2 clearance. The convalescent plasma showed humoral immunity against all structural SARS-CoV-2 proteins, which was successfully transferred to the patient.
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Affiliation(s)
- Tim Luetkens
- Hematology and Hematologic Malignancies, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
- Blood and Marrow Transplantation Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Ryan Metcalf
- Department of Pathology, University of Utah, Salt Lake City, UT
- ARUP Laboratories, Salt Lake City, UT
| | | | - Yue Zheng
- Department of Pathology, University of Utah, Salt Lake City, UT
| | | | - Emily S Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Adam M Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Mary Steinbach
- Hematology and Hematologic Malignancies, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Robert C Blaylock
- Department of Pathology, University of Utah, Salt Lake City, UT
- ARUP Laboratories, Salt Lake City, UT
| | - Stephanie V Avila
- Hematology and Hematologic Malignancies, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Kim G Hankey
- Blood and Marrow Transplantation Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Thomas B Martins
- Department of Pathology, University of Utah, Salt Lake City, UT
- ARUP Laboratories, Salt Lake City, UT
| | - Patricia R Slev
- Department of Pathology, University of Utah, Salt Lake City, UT
- ARUP Laboratories, Salt Lake City, UT
| | - Heather D Mannuel
- Hematology/Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD
- Baltimore Veterans Affairs Medical Center, Baltimore, MD; and
| | - Mohammad Sajadi
- Institute of Human Virology, University of Maryland, Baltimore, MD
| | - Aaron P Rapoport
- Blood and Marrow Transplantation Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Djordje Atanackovic
- Hematology and Hematologic Malignancies, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
- Blood and Marrow Transplantation Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD
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6
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Zheng Y, Larragoite ET, Lama J, Cisneros I, Delgado JC, Slev P, Rychert J, Innis EA, Williams ES, Coiras M, Rondina MT, Spivak AM, Planelles V. Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions. bioRxiv 2020:2020.07.17.207563. [PMID: 32995778 PMCID: PMC7523104 DOI: 10.1101/2020.07.17.207563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antibody neutralization is an important prognostic factor in many viral diseases. To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal MLV genome encoding firefly luciferase. These pseudovirions provide a practical means of assessing immune responses under laboratory conditions consistent with biocontainment level 2.
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Affiliation(s)
- Yue Zheng
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Erin T. Larragoite
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | | | | | - Julio C. Delgado
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT
| | - Patricia Slev
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT
| | - Jenna Rychert
- Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, UT
| | - Emily A. Innis
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | | | - Mayte Coiras
- AIDS Immunopathology Unit, National Center of Microbiology (CNM), Instituto de Salud Carlos III, Madrid, Spain
| | - Matthew T. Rondina
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT
| | - Adam M. Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
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7
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Larragoite ET, Spivak AM. Down but not out. eLife 2019; 8:53363. [PMID: 31868581 PMCID: PMC6927739 DOI: 10.7554/elife.53363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
A new study in monkeys suggests that treating HIV infection early with antiretroviral therapy reduces the number of latent viruses, but has little impact on viral reactivation when treatment stops.
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Affiliation(s)
- Erin T Larragoite
- School of Medicine, University of Utah, Salt Lake City, United States
| | - Adam M Spivak
- School of Medicine, University of Utah, Salt Lake City, United States
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8
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Read DF, Atindaana E, Pyaram K, Yang F, Emery S, Cheong A, Nakama KR, Burnett C, Larragoite ET, Battivelli E, Verdin E, Planelles V, Chang CH, Telesnitsky A, Kidd JM. Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis. PLoS Pathog 2019; 15:e1007903. [PMID: 31584995 PMCID: PMC6795456 DOI: 10.1371/journal.ppat.1007903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/16/2019] [Accepted: 09/04/2019] [Indexed: 12/17/2022] Open
Abstract
HIV-1 gene expression is regulated by host and viral factors that interact with viral motifs and is influenced by proviral integration sites. Here, expression variation among integrants was followed for hundreds of individual proviral clones within polyclonal populations throughout successive rounds of virus and cultured cell replication, with limited findings using CD4+ cells from donor blood consistent with observations in immortalized cells. Tracking clonal behavior by proviral “zip codes” indicated that mutational inactivation during reverse transcription was rare, while clonal expansion and proviral expression states varied widely. By sorting for provirus expression using a GFP reporter in the nef open reading frame, distinct clone-specific variation in on/off proportions were observed that spanned three orders of magnitude. Tracking GFP phenotypes over time revealed that as cells divided, their progeny alternated between HIV transcriptional activity and non-activity. Despite these phenotypic oscillations, the overall GFP+ population within each clone was remarkably stable, with clones maintaining clone-specific equilibrium mixtures of GFP+ and GFP- cells. Integration sites were analyzed for correlations between genomic features and the epigenetic phenomena described here. Integrants inserted in the sense orientation of genes were more frequently found to be GFP negative than those in the antisense orientation, and clones with high GFP+ proportions were more distal to repressive H3K9me3 peaks than low GFP+ clones. Clones with low frequencies of GFP positivity appeared to expand more rapidly than clones for which most cells were GFP+, even though the tested proviruses were Vpr-. Thus, much of the increase in the GFP- population in these polyclonal pools over time reflected differential clonal expansion. Together, these results underscore the temporal and quantitative variability in HIV-1 gene expression among proviral clones that are conferred in the absence of metabolic or cell-type dependent variability, and shed light on cell-intrinsic layers of regulation that affect HIV-1 population dynamics. Very few HIV-1 infected cells persist in patients for more than a couple days, but those that do pose life-long health risks. Strategies designed to eliminate these cells have been based on assumptions about what viral properties allow infected cell survival. However, such approaches for HIV-1 eradication have not yet shown therapeutic promise, possibly because many assumptions about virus persistence are based on studies involving a limited number of infected cell types, the averaged behavior of cells in diverse populations, or snapshot views. Here, we developed a high-throughput approach to study hundreds of distinct HIV-1 infected cells and their progeny over time in an unbiased way. This revealed that each virus established its own pattern of gene expression that, upon infected cell division, was stably transmitted to all progeny cells. Expression patterns consisted of alternating waves of activity and inactivity, with the extent of activity differing among infected cell families over a 1000-fold range. The dynamics and variability among infected cells and within complex populations that the work here revealed has not previously been evident, and may help establish more accurate correlates of persistent HIV-1 infection.
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Affiliation(s)
- David F. Read
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Edmond Atindaana
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) and Department of Biochemistry, Cell & Molecular Biology, University of Ghana, Legon, Greater Accra Region, Ghana
| | - Kalyani Pyaram
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Feng Yang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sarah Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Anna Cheong
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Katherine R. Nakama
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Erin T. Larragoite
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Emilie Battivelli
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Eric Verdin
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Vicente Planelles
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Cheong-Hee Chang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (C-HC); (AT); (JMK)
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (C-HC); (AT); (JMK)
| | - Jeffrey M. Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail: (C-HC); (AT); (JMK)
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Spivak AM, Larragoite ET, Coletti ML, Macedo AB, Martins LJ, Bosque A, Planelles V. Janus kinase inhibition suppresses PKC-induced cytokine release without affecting HIV-1 latency reversal ex vivo. Retrovirology 2016; 13:88. [PMID: 27998278 PMCID: PMC5175306 DOI: 10.1186/s12977-016-0319-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/25/2016] [Indexed: 11/10/2022] Open
Abstract
Background Despite the durable viral suppression afforded by antiretroviral therapy, HIV-1 eradication will require strategies to target latently infected cells that persist in infected individuals. Protein kinase C (PKC) activation is a promising strategy to reactivate latent proviruses and allow for subsequent recognition and clearance of infected cells by the immune system. Ingenol derivatives are PKC agonists that induce latency reversal but also lead to T cell activation and the release of pro-inflammatory cytokines, which would be undesirable in vivo. In this work, we sought to identify compounds that would suppress pro-inflammatory cytokine production in the context of PKC activation. Design and methods We performed an in vitro screen to identify compounds that could dampen pro-inflammatory cytokine release associated with T cell activation, using IL-6 as a model cytokine. We then tested the ability of the most promising screening hit, the FDA-approved Janus Kinase (JAK) inhibitor ruxolitinib, to diminish release of multiple cytokines and its effect on latency reversal using cells from HIV-1-positive, aviremic participants. Results We demonstrate that co-administration of ruxolitinib with ingenol-3,20-dibenzoate significantly reduces pro-inflammatory cytokine release without impairing latency reversal ex vivo. Conclusion The combination of ingenol compounds and JAK inhibition represents a novel strategy for HIV-1 eradication. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam M Spivak
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Erin T Larragoite
- Department of Pathology, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building Room 2520, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA
| | - McKenna L Coletti
- Department of Pathology, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building Room 2520, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA
| | - Amanda B Macedo
- Department of Pathology, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building Room 2520, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA
| | - Laura J Martins
- Department of Pathology, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building Room 2520, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA
| | - Alberto Bosque
- Department of Pathology, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building Room 2520, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Emma Eccles Jones Medical Research Building Room 2520, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA.
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Larragoite ET, Tacchi L, LaPatra SE, Salinas I. An attenuated virus vaccine appears safe to the central nervous system of rainbow trout (Oncorhynchus mykiss) after intranasal delivery. Fish Shellfish Immunol 2016; 49:351-4. [PMID: 26772477 PMCID: PMC4871134 DOI: 10.1016/j.fsi.2016.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/02/2016] [Accepted: 01/05/2016] [Indexed: 05/13/2023]
Abstract
Nasal vaccines are very effective but the olfactory organ provides direct access of antigens to the brain. Infectious hematopoietic necrosis virus (IHNV) is known to cause high mortalities in salmonids. The purpose of this study is to evaluate the safety of a live attenuated IHNV nasal (I.N) vaccine in rainbow trout (Oncorhynchus mykiss). In the olfactory organ, the vaccine was detected 1 and 4 days after primary I.N vaccination but not in the intramuscular (i.m) or control groups. In the brain, IHNV was detected by RT-qPCR 4 and 21 days after i.m primary vaccination. One i.m and one I.N vaccinated trout were positive at days 4 and 28 days post-boost, respectively. Presence of IHNV in the brain of i.m vaccinated fish correlated with moderate increases in IL-1β and TNF-α expression in this tissue. These results demonstrate that IHNV vaccine lasts for 4 days in the local nasal environment and that nasal vaccination appears to be safe to the CNS of rainbow trout.
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Affiliation(s)
- Erin T Larragoite
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, USA.
| | - Luca Tacchi
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, USA.
| | | | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, USA.
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Tacchi L, Larragoite ET, Muñoz P, Amemiya CT, Salinas I. African Lungfish Reveal the Evolutionary Origins of Organized Mucosal Lymphoid Tissue in Vertebrates. Curr Biol 2015; 25:2417-24. [PMID: 26344090 DOI: 10.1016/j.cub.2015.07.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/19/2015] [Accepted: 07/28/2015] [Indexed: 11/25/2022]
Abstract
One of the most remarkable innovations of the vertebrate adaptive immune system is the progressive organization of the lymphoid tissues that leads to increased efficiency of immune surveillance and cell interactions. The mucosal immune system of endotherms has evolved organized secondary mucosal lymphoid tissues (O-MALT) such as Peyer's patches, tonsils, and adenoids. Primitive semi-organized lymphoid nodules or aggregates (LAs) were found in the mucosa of anuran amphibians, suggesting that O-MALT evolved from amphibian LAs ∼250 million years ago. This study shows for the first time the presence of O-MALT in the mucosa of the African lungfish, an extant representative of the closest ancestral lineage to all tetrapods. Lungfish LAs are lymphocyte-rich structures associated with a modified covering epithelium and express all IGH genes except for IGHW2L. In response to infection, nasal LAs doubled their size and increased the expression of CD3 and IGH transcripts. Additionally, de novo organogenesis of inducible LAs resembling mammalian tertiary lymphoid structures was observed. Using deep-sequencing transcriptomes, we identified several members of the tumor necrosis factor (TNF) superfamily, and subsequent phylogenetic analyses revealed its extraordinary diversification within sarcopterygian fish. Attempts to find AICDA in lungfish transcriptomes or by RT-PCR failed, indicating the possible absence of somatic hypermutation in lungfish LAs. These findings collectively suggest that the origin of O-MALT predates the emergence of tetrapods and that TNF family members play a conserved role in the organization of vertebrate mucosal lymphoid organs.
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Affiliation(s)
- Luca Tacchi
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Erin T Larragoite
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Pilar Muñoz
- Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, Murcia 30100, Spain
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA; Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA.
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Tacchi L, Lowrey L, Musharrafieh R, Crossey K, Larragoite ET, Salinas I. Effects of transportation stress and addition of salt to transport water on the skin mucosal homeostasis of rainbow trout ( Oncorhynchus mykiss). Aquaculture 2015; 435:120-127. [PMID: 25705060 PMCID: PMC4332845 DOI: 10.1016/j.aquaculture.2014.09.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transportation of live fish is a common practice among aquaculture facilities. Many studies have previously reported how transport elicits physiological stress responses and increases disease susceptibility in farmed fish. The aim of this work is to investigate the changes that the skin of rainbow trout (Oncorhynchus mykiss) experiences due to stress. Since NaCl is commonly added to transport water as a stress mitigator, the effects of salt addition on the skin mucosa and skin-associated bacteria were also examined. Three experimental groups (Control, post-transport no salt (PTNS) and post-transport with salt (PTS)) were analyzed in a 5-hour transport acute stress model. Results indicate that the skin mucosa and the skin-associated bacteria are affected by transport stress. Total numbers of culturable skin-associated bacteria increased by ~10-fold and ~50-fold in the PTS and PTNS groups, respectively. Compared to controls, MUC2 expression was increased by 5-fold and 2-fold in the PTNS and PTS groups, respectively. Claudin-7, 8d and 12 expression levels were higher in both PTNS and PTS groups whereas antimicrobial peptide gene expression was lower than controls. Expression of the anti-inflammatory cytokine TGF-β but not IL-1β, IL-6 and TNF-α was up-regulated 2-3 fold in both the PTS and PTNS groups. The addition of salt diminished some of the physiological responses measured including the numbers of skin-associated bacteria. The responses recorded here appeared to be efficient at controlling bacterial translocation since stress did not lead to significant presence of bacteria in the liver or spleen of rainbow trout. When examining the ability of skin mucus to inhibit or promote growth of the bacterial pathogen Vibrio anguillarum, the skin mucus of PTS trout was more efficient at inhibiting V. anguillarum growth (20% inhibition) compared to control or PTNS mucus (11-12% inhibition). Our data clearly indicate the skin and skin microbiota of rainbow trout undergo important physiological responses during stress. The reduction in the magnitude of the skin responses recorded when salt was added to the transport water explains a new mechanism by which salt is an effective stress mitigator in some fish species. Aquaculture specialists will benefit from the present study by taking into consideration the importance of skin health during live transport.
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Tacchi L, Musharrafieh R, Larragoite ET, Crossey K, Erhardt EB, Martin SAM, LaPatra SE, Salinas I. Nasal immunity is an ancient arm of the mucosal immune system of vertebrates. Nat Commun 2014; 5:5205. [PMID: 25335508 DOI: 10.1038/ncomms6205] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/09/2014] [Indexed: 01/14/2023] Open
Abstract
The mucosal surfaces of all vertebrates have been exposed to similar evolutionary pressures for millions of years. In terrestrial vertebrates such as birds and mammals, the nasopharynx-associated lymphoid tissue (NALT) represents a first line of immune defence. Here we propose that NALT is an ancient arm of the mucosal immune system not restricted to terrestrial vertebrates. We find that NALT is present in rainbow trout and that it resembles other teleost mucosa-associated lymphoid tissues. Trout NALT consists of diffuse lymphoid cells and lacks tonsils and adenoids. The predominant B-cell subset found in trout NALT are IgT(+) B cells, similar to skin and gut. The trout olfactory organ is colonized by abundant symbiotic bacteria, which are coated by trout secretory immunoglobulin. Trout NALT is capable of mounting strong anti-viral immune responses following nasal delivery of a live attenuated viral vaccine. Our results open up a new tool for the control of aquatic infectious diseases via nasal vaccination.
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Affiliation(s)
- Luca Tacchi
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Rami Musharrafieh
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Erin T Larragoite
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Kyle Crossey
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Erik B Erhardt
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, Scotland
| | | | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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