1
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Correa-Medero LO, Jankowski SE, Hong HS, Armas ND, Vijendra AI, Reynolds MB, Fogo GM, Awad D, Dils AT, Inoki KA, Williams RG, Ye AM, Svezhova N, Gomez-Rivera F, Collins KL, O'Riordan MX, Sanderson TH, Lyssiotis CA, Carty SA. ER-associated degradation adapter Sel1L is required for CD8 + T cell function and memory formation following acute viral infection. Cell Rep 2024; 43:114156. [PMID: 38687642 DOI: 10.1016/j.celrep.2024.114156] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/06/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
The maintenance of antigen-specific CD8+ T cells underlies the efficacy of vaccines and immunotherapies. Pathways contributing to CD8+ T cell loss are not completely understood. Uncovering the pathways underlying the limited persistence of CD8+ T cells would be of significant benefit for developing novel strategies of promoting T cell persistence. Here, we demonstrate that murine CD8+ T cells experience endoplasmic reticulum (ER) stress following activation and that the ER-associated degradation (ERAD) adapter Sel1L is induced in activated CD8+ T cells. Sel1L loss limits CD8+ T cell function and memory formation following acute viral infection. Mechanistically, Sel1L is required for optimal bioenergetics and c-Myc expression. Finally, we demonstrate that human CD8+ T cells experience ER stress upon activation and that ER stress is negatively associated with improved T cell functionality in T cell-redirecting therapies. Together, these results demonstrate that ER stress and ERAD are important regulators of T cell function and persistence.
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Affiliation(s)
- Luis O Correa-Medero
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Hanna S Hong
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicholas D Armas
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mack B Reynolds
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Garrett M Fogo
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Dominik Awad
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander T Dils
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Reid G Williams
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Nadezhda Svezhova
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Kathleen L Collins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mary X O'Riordan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas H Sanderson
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shannon A Carty
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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2
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Collins KL. Physician-scientist development: a new category for supporting all stages of the physician-scientist pipeline. JCI Insight 2024; 9:e179940. [PMID: 38456507 DOI: 10.1172/jci.insight.179940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
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3
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McCauley M, Huston M, Condren AR, Pereira F, Cline J, Yaple-Maresh M, Painter MM, Zimmerman GE, Robertson AW, Carney N, Goodall C, Terry V, Müller R, Sherman DH, Collins KL. Structure-Activity Relationships of Natural and Semisynthetic Plecomacrolides Suggest Distinct Pathways for HIV-1 Immune Evasion and Vacuolar ATPase-Dependent Lysosomal Acidification. J Med Chem 2024. [PMID: 38452116 DOI: 10.1021/acs.jmedchem.3c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The human immunodeficiency virus (HIV)-encoded accessory protein Nef enhances pathogenicity by reducing major histocompatibility complex I (MHC-I) cell surface expression, protecting HIV-infected cells from immune recognition. Nef-dependent downmodulation of MHC-I can be reversed by subnanomolar concentrations of concanamycin A (1), a well-known inhibitor of vacuolar ATPase, at concentrations below those that interfere with lysosomal acidification or degradation. We conducted a structure-activity relationship study that assessed 76 compounds for Nef inhibition, 24 and 72 h viability, and lysosomal neutralization in Nef-expressing primary T cells. This analysis demonstrated that the most potent compounds were natural concanamycins and their derivatives. Comparison against a set of new, semisynthetic concanamycins revealed that substituents at C-8 and acylation of C-9 significantly affected Nef potency, target cell viability, and lysosomal neutralization. These findings provide important progress toward understanding the mechanism of action of these compounds and the identification of an advanced lead anti-HIV Nef inhibitory compound.
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Affiliation(s)
- Morgan McCauley
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Matthew Huston
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Alanna R Condren
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Filipa Pereira
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Joel Cline
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Marianne Yaple-Maresh
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Mark M Painter
- University of Michigan, Graduate Program in Immunology, Ann Arbor, Michigan 48109, United States
| | - Gretchen E Zimmerman
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Andrew W Robertson
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
- University of Michigan Natural Products Discovery Core, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Nolan Carney
- University of Michigan, Department of Chemistry, Ann Arbor, Michigan 48109, United States
| | - Christopher Goodall
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Valeri Terry
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken 66123, Germany
| | - David H Sherman
- University of Michigan, Department of Microbiology & Immunology, Ann Arbor, Michigan 48109, United States
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Medicinal Chemistry, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Chemistry, Ann Arbor, Michigan 48109, United States
| | - Kathleen L Collins
- University of Michigan, Graduate Program in Immunology, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Microbiology & Immunology, Ann Arbor, Michigan 48109, United States
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4
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Virgilio MC, Ramnani B, Chen T, Disbennett WM, Lubow J, Welch JD, Collins KL. HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. bioRxiv 2024:2023.03.21.533528. [PMID: 36993393 PMCID: PMC10055223 DOI: 10.1101/2023.03.21.533528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
HIV-1 Vpr promotes efficient spread of HIV-1 from macrophages to T cells by transcriptionally downmodulating restriction factors that target HIV-1 Envelope protein (Env). Here we find that Vpr induces broad transcriptomic changes by targeting PU.1, a transcription factor necessary for expression of host innate immune response genes, including those that target Env. Consistent with this, we find silencing PU.1 in infected macrophages lacking Vpr rescues Env. Vpr downmodulates PU.1 through a proteasomal degradation pathway that depends on physical interactions with PU.1 and DCAF1, a component of the Cul4A E3 ubiquitin ligase. The capacity for Vpr to target PU.1 is highly conserved across primate lentiviruses. In addition to impacting infected cells, we find that Vpr suppresses expression of innate immune response genes in uninfected bystander cells, and that virion-associated Vpr can degrade PU.1. Together, we demonstrate Vpr counteracts PU.1 in macrophages to blunt antiviral immune responses and promote viral spread.
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5
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Li C, Virgilio MC, Collins KL, Welch JD. Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction. Nat Biotechnol 2023; 41:387-398. [PMID: 36229609 PMCID: PMC10246490 DOI: 10.1038/s41587-022-01476-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/16/2022] [Indexed: 12/13/2022]
Abstract
Multi-omic single-cell datasets, in which multiple molecular modalities are profiled within the same cell, offer an opportunity to understand the temporal relationship between epigenome and transcriptome. To realize this potential, we developed MultiVelo, a differential equation model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression and improves the accuracy of cell fate prediction compared to velocity estimates from RNA only. Application to multi-omic single-cell datasets from brain, skin and blood cells reveals two distinct classes of genes distinguished by whether chromatin closes before or after transcription ceases. We also find four types of cell states: two states in which epigenome and transcriptome are coupled and two distinct decoupled states. Finally, we identify time lags between transcription factor expression and binding site accessibility and between disease-associated SNP accessibility and expression of the linked genes. MultiVelo is available on PyPI, Bioconda and GitHub ( https://github.com/welch-lab/MultiVelo ).
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Affiliation(s)
- Chen Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Maria C Virgilio
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen L Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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6
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Jackson S, Williams CL, Collins KL, McNally EM. Data we can trust. J Clin Invest 2022; 132:162884. [PMID: 35912864 PMCID: PMC9337817 DOI: 10.1172/jci162884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
“On behalf of all authors of the submission, I warrant that the work is original and scientifically accurate ...” If you’ve submitted a manuscript to the Journal of Clinical Investigation or JCI Insight, this phrase should sound familiar. This statement is the very first thing that we ask authors to verify for every new submission. While this may seem like a simple formality or just another screen to click through, certifying the accuracy of information presented to the journal is essential to the publishing process and scientific integrity. Data accuracy forms the foundation of the scientific enterprise, and without it, the enterprise risks crumbling.
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7
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Radisic G, Duncanson E, Le Leu R, Collins KL, Burke ALJ, Turner JK, Chur-Hansen A, Donnelly F, Hill K, McDonald S, Macauley L, Jesudason S. Improving management of needle distress during the journey to dialysis through psychological education and training-the INJECT study feasibility pilot protocol. Pilot Feasibility Stud 2022; 8:28. [PMID: 35120560 PMCID: PMC8815234 DOI: 10.1186/s40814-022-00989-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/02/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Needle-related distress is a common yet poorly recognised and managed problem among haemodialysis (HD) patients. The aim of this pilot study is to test the feasibility and acceptability of the INJECT Intervention-an innovative psychology-based intervention to empower patients to self-manage needle distress with the support of dialysis nurses. METHODS This investigator-initiated, single-arm, non-randomised feasibility study will take place in a large dialysis service in Adelaide, Australia. Participants will include patients aged ≥ 18 years, commencing or already receiving maintenance HD, recruited through dialysis physicians and nursing staff as individuals believed to be at risk of needle distress. They will be screened for inclusion using the Dialysis Fear of Injection Questionnaire (DFIQ) and enrolled into the study if the score is ≥ 2. The multi-pronged intervention encompasses (i) psychologist review, (ii) patient self-management program and (iii) nursing education program. The primary aim is to evaluate feasibility and acceptability of the intervention from patient and dialysis nurse perspectives, including recruitment, retention, engagement with the intervention and completion. Secondary exploratory outcomes will assess suitability of various tools for measuring needle distress, evaluate acceptability of the nursing education program and measure cannulation-related trauma and vascular access outcomes. CONCLUSION The results will inform the protocol for larger trials addressing needle distress in HD patients. TRIAL REGISTRATION Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12621000229875, approved 4 April 2021, https://www.anzctr.org.au/ .
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Affiliation(s)
- G Radisic
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia.
| | - E Duncanson
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia.,School of Psychology, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - R Le Leu
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - K L Collins
- School of Psychology, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia.,Psychology Department, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
| | - A L J Burke
- School of Psychology, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia.,Psychology Department, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
| | - J K Turner
- Psychology Department, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
| | - A Chur-Hansen
- School of Psychology, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - F Donnelly
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
| | - K Hill
- University of South Australia, South Australia, 5000, Adelaide, Australia
| | - S McDonald
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - L Macauley
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - S Jesudason
- Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, 5000, Australia
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8
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Terry VH, Zimmerman GE, Virgilio MC, Painter MM, Bixby D, Collins KL. Hematopoietic Stem and Progenitor Cells (HSPCs). Methods Mol Biol 2022; 2407:115-154. [PMID: 34985663 DOI: 10.1007/978-1-0716-1871-4_11] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cord blood is a readily available source of hematopoietic stem and progenitor cells (HSPCs) which can be infected with HIV-1 in vitro to produce inducible latently infected cells for reactivation studies. Infected HSPCs can also be found in the setting of clinically undetectable viremia in vivo. Here we describe an in vitro infection model utilizing cord blood derived HSPCs, as well as methods for isolating and characterizing provirus from bone marrow HSPCs from suppressed patients.
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Affiliation(s)
- Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Maria C Virgilio
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Dale Bixby
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen L Collins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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9
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Collins KL. Resource and Technical Advance papers: expanding our resources. JCI Insight 2021; 6:e151152. [PMID: 34100387 PMCID: PMC8262284 DOI: 10.1172/jci.insight.151152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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10
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Ware LB, Collins KL, Hawley JB, Ahima RS. A deliberate path toward diversity, equity, and inclusion within the ASCI. J Clin Invest 2021; 130:5031-5032. [PMID: 32831295 DOI: 10.1172/jci142423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Lorraine B Ware
- President, American Society for Clinical Investigation (ASCI), 2020-2021; Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathleen L Collins
- Editor, JCI Insight, , 2019-2024; University of Michigan, Ann Arbor, Michigan, USA
| | | | - Rexford S Ahima
- Editor, Journal of Clinical Investigation, , 2018-2022; Johns Hopkins University, Baltimore, Maryland, USA
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11
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Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL. Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes. Proc Natl Acad Sci U S A 2020; 117:23835-23846. [PMID: 32900948 PMCID: PMC7519347 DOI: 10.1073/pnas.2008615117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Indexed: 12/13/2022] Open
Abstract
Nef is an HIV-encoded accessory protein that enhances pathogenicity by down-regulating major histocompatibility class I (MHC-I) expression to evade killing by cytotoxic T lymphocytes (CTLs). A potent Nef inhibitor that restores MHC-I is needed to promote immune-mediated clearance of HIV-infected cells. We discovered that the plecomacrolide family of natural products restored MHC-I to the surface of Nef-expressing primary cells with variable potency. Concanamycin A (CMA) counteracted Nef at subnanomolar concentrations that did not interfere with lysosomal acidification or degradation and were nontoxic in primary cell cultures. CMA specifically reversed Nef-mediated down-regulation of MHC-I, but not CD4, and cells treated with CMA showed reduced formation of the Nef:MHC-I:AP-1 complex required for MHC-I down-regulation. CMA restored expression of diverse allotypes of MHC-I in Nef-expressing cells and inhibited Nef alleles from divergent clades of HIV and simian immunodeficiency virus, including from primary patient isolates. Lastly, we found that restoration of MHC-I in HIV-infected cells was accompanied by enhanced CTL-mediated clearance of infected cells comparable to genetic deletion of Nef. Thus, we propose CMA as a lead compound for therapeutic inhibition of Nef to enhance immune-mediated clearance of HIV-infected cells.
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Affiliation(s)
- Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | | | - Madeline S Merlino
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew W Robertson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Megan R McLeod
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Lyanne Gomez-Rodriguez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Kirsten A Garcia
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jolie A Leonard
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Kay E Leopold
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew J Neevel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Eli Olson
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Kathleen L Collins
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109
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13
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Abstract
HIV infects several cell types in the body, including CD4+ T cells and macrophages. Here we review the role of macrophages in HIV infection and describe complex interactions between viral proteins and host defenses in these cells. Macrophages exist in many forms throughout the body, where they play numerous roles in healthy and diseased states. They express pattern-recognition receptors (PRRs) that bind viral, bacterial, fungal, and parasitic pathogens, making them both a key player in innate immunity and a potential target of infection by pathogens, including HIV. Among these PRRs is mannose receptor, a macrophage-specific protein that binds oligosaccharides, restricts HIV replication, and is downregulated by the HIV accessory protein Vpr. Vpr significantly enhances infection in vivo, but the mechanism by which this occurs is controversial. It is well established that Vpr alters the expression of numerous host proteins by using its co-factor DCAF1, a component of the DCAF1-DDB1-CUL4 ubiquitin ligase complex. The host proteins targeted by Vpr and their role in viral replication are described in detail. We also discuss the structure and function of the viral protein Env, which is stabilized by Vpr in macrophages. Overall, this literature review provides an updated understanding of the contributions of macrophages and Vpr to HIV pathogenesis.
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Affiliation(s)
- Jay Lubow
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Kathleen L. Collins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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14
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Ahima RS, Jackson S, Casadevall A, Semenza GL, Tomaselli G, Collins KL, Lieberman AP, Martin DM, Reddy P. Changing the editorial process at JCI and JCI Insight in response to the COVID-19 pandemic. J Clin Invest 2020; 130:2147. [PMID: 32202513 DOI: 10.1172/jci138305] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The editors of JCI and JCI Insight are revisiting our editorial processes in light of the strain that the COVID-19 pandemic places on the worldwide scientific community. Here, we discuss adjustments to our decision framework in light of restrictions placed on laboratory working conditions for many of our authors.
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15
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Caldwell DJ, Cronin JA, Rao RPN, Collins KL, Weaver KE, Ko AL, Ojemann JG, Kutz JN, Brunton BW. Signal recovery from stimulation artifacts in intracranial recordings with dictionary learning. J Neural Eng 2020; 17:026023. [PMID: 32103828 PMCID: PMC7333778 DOI: 10.1088/1741-2552/ab7a4f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Electrical stimulation of the human brain is commonly used for eliciting and inhibiting neural activity for clinical diagnostics, modifying abnormal neural circuit function for therapeutics, and interrogating cortical connectivity. However, recording electrical signals with concurrent stimulation results in dominant electrical artifacts that mask the neural signals of interest. Here we develop a method to reproducibly and robustly recover neural activity during concurrent stimulation. We concentrate on signal recovery across an array of electrodes without channel-wise fine-tuning of the algorithm. Our goal includes signal recovery with trains of stimulation pulses, since repeated, high-frequency pulses are often required to induce desired effects in both therapeutic and research domains. We have made all of our code and data publicly available. APPROACH We developed an algorithm that automatically detects templates of artifacts across many channels of recording, creating a dictionary of learned templates using unsupervised clustering. The artifact template that best matches each individual artifact pulse is subtracted to recover the underlying activity. To assess the success of our method, we focus on whether it extracts physiologically interpretable signals from real recordings. MAIN RESULTS We demonstrate our signal recovery approach on invasive electrophysiologic recordings from human subjects during stimulation. We show the recovery of meaningful neural signatures in both electrocorticographic (ECoG) arrays and deep brain stimulation (DBS) recordings. In addition, we compared cortical responses induced by the stimulation of primary somatosensory (S1) by natural peripheral touch, as well as motor cortex activity with and without concurrent S1 stimulation. SIGNIFICANCE Our work will enable future advances in neural engineering with simultaneous stimulation and recording.
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Affiliation(s)
- D J Caldwell
- Department of Bioengineering, University of Washington, Seattle, WA, United States of America. Medical Scientist Training Program, University of Washington, Seattle, WA, United States of America. Center for Neurotechnology, Seattle, WA, United States of America. University of Washington Institute for Neuroengineering, Seattle, WA, United States of America. Author to whom any correspondence should be addressed
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16
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Abstract
Lessons from history underline the importance of having direct lines of communication to and from public health officials, who must remain free from policital bias in times of crisis.
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17
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Lubow J, Virgilio MC, Merlino M, Collins DR, Mashiba M, Peterson BG, Lukic Z, Painter MM, Gomez-Rivera F, Terry V, Zimmerman G, Collins KL. Mannose receptor is an HIV restriction factor counteracted by Vpr in macrophages. eLife 2020; 9:e51035. [PMID: 32119644 PMCID: PMC7051176 DOI: 10.7554/elife.51035] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 08/12/2019] [Accepted: 01/25/2020] [Indexed: 12/21/2022] Open
Abstract
HIV-1 Vpr is necessary for maximal HIV infection and spread in macrophages. Evolutionary conservation of Vpr suggests an important yet poorly understood role for macrophages in HIV pathogenesis. Vpr counteracts a previously unknown macrophage-specific restriction factor that targets and reduces the expression of HIV Env. Here, we report that the macrophage mannose receptor (MR), is a restriction factor targeting Env in primary human monocyte-derived macrophages. Vpr acts synergistically with HIV Nef to target distinct stages of the MR biosynthetic pathway and dramatically reduce MR expression. Silencing MR or deleting mannose residues on Env rescues Env expression in HIV-1-infected macrophages lacking Vpr. However, we also show that disrupting interactions between Env and MR reduces initial infection of macrophages by cell-free virus. Together these results reveal a Vpr-Nef-Env axis that hijacks a host mannose-MR response system to facilitate infection while evading MR's normal role, which is to trap and destroy mannose-expressing pathogens.
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Affiliation(s)
- Jay Lubow
- Department of Microbiology and Immunology, University of MichiganAnn ArborUnited States
| | - Maria C Virgilio
- Cellular and Molecular Biology Program, University of MichiganAnn ArborUnited States
| | - Madeline Merlino
- Department of Internal Medicine, University of MichiganAnn ArborUnited States
| | - David R Collins
- Department of Microbiology and Immunology, University of MichiganAnn ArborUnited States
| | - Michael Mashiba
- Graduate Program in Immunology, University of MichiganAnn ArborUnited States
| | - Brian G Peterson
- Department of Biological ChemistryUniversity of MichiganAnn ArborUnited States
| | - Zana Lukic
- Department of Internal Medicine, University of MichiganAnn ArborUnited States
| | - Mark M Painter
- Graduate Program in Immunology, University of MichiganAnn ArborUnited States
| | | | - Valeri Terry
- Department of Internal Medicine, University of MichiganAnn ArborUnited States
| | - Gretchen Zimmerman
- Graduate Program in Immunology, University of MichiganAnn ArborUnited States
| | - Kathleen L Collins
- Cellular and Molecular Biology Program, University of MichiganAnn ArborUnited States
- Department of Internal Medicine, University of MichiganAnn ArborUnited States
- Graduate Program in Immunology, University of MichiganAnn ArborUnited States
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18
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Abstract
Human immunodeficiency virus (HIV) is a chronic infection that destroys the immune system in infected individuals. Although antiretroviral therapy is effective at preventing infection of new cells, it is not curative. The inability to clear infection is due to the presence of a rare, but long-lasting latent cellular reservoir. These cells harboring silent integrated proviral genomes have the potential to become activated at any moment, making therapy necessary for life. Latently-infected cells can also proliferate and expand the viral reservoir through several methods including homeostatic proliferation and differentiation. The chromosomal location of HIV proviruses within cells influences the survival and proliferative potential of host cells. Proliferating, latently-infected cells can harbor proviruses that are both replication-competent and defective. Replication-competent proviral genomes contribute to viral rebound in an infected individual. The majority of available techniques can only assess the integration site or the proviral genome, but not both, preventing reliable evaluation of HIV reservoirs.
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Affiliation(s)
- Maria C. Virgilio
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathleen L. Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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19
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Zaikos TD, Terry VH, Sebastian Kettinger NT, Lubow J, Painter MM, Virgilio MC, Neevel A, Taschuk F, Onafuwa-Nuga A, McNamara LA, Riddell J, Bixby D, Markowitz N, Collins KL. Hematopoietic Stem and Progenitor Cells Are a Distinct HIV Reservoir that Contributes to Persistent Viremia in Suppressed Patients. Cell Rep 2019; 25:3759-3773.e9. [PMID: 30590047 DOI: 10.1016/j.celrep.2018.11.104] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 03/26/2018] [Revised: 09/12/2018] [Accepted: 11/29/2018] [Indexed: 01/03/2023] Open
Abstract
Long-lived reservoirs of persistent HIV are a major barrier to a cure. CD4+ hematopoietic stem and progenitor cells (HSPCs) have the capacity for lifelong survival, self-renewal, and the generation of daughter cells. Recent evidence shows that they are also susceptible to HIV infection in vitro and in vivo. Whether HSPCs harbor infectious virus or contribute to plasma virus (PV) is unknown. Here, we provide strong evidence that clusters of identical proviruses from HSPCs and their likely progeny often match residual PV. A higher proportion of these sequences match residual PV than proviral genomes from bone marrow and peripheral blood mononuclear cells that are observed only once. Furthermore, an analysis of near-full-length genomes isolated from HSPCs provides evidence that HSPCs harbor functional HIV proviral genomes that often match residual PV. These results support the conclusion that HIV-infected HSPCs form a distinct and functionally significant reservoir of persistent HIV in infected people.
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Affiliation(s)
- Thomas D Zaikos
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nadia T Sebastian Kettinger
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Maria C Virgilio
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Neevel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Frances Taschuk
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Lucy A McNamara
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Riddell
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Dale Bixby
- Division of Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Norman Markowitz
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, MI, USA
| | - Kathleen L Collins
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA; Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, USA.
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20
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Collins KL. A new editor and a new team for JCI Insight. JCI Insight 2019; 4:132119. [DOI: 10.1172/jci.insight.132119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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21
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Painter MM, Zaikos TD, Collins KL. Quiescence Promotes Latent HIV Infection and Resistance to Reactivation from Latency with Histone Deacetylase Inhibitors. J Virol 2017; 91:e01080-17. [PMID: 29021396 PMCID: PMC5709582 DOI: 10.1128/jvi.01080-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/02/2017] [Indexed: 12/28/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) establishes transcriptionally silent latent infections in resting memory T cells and hematopoietic stem and progenitor cells (HSPCs), which allows the virus to persist in infected individuals despite antiretroviral therapy. Developing in vitro models of HIV-1 latency that recapitulate the characteristics of latently infected cells in vivo is crucial to identifying and developing effective latency-reversing therapies. HSPCs exist in a quiescent state in vivo, and quiescence is correlated with latent infections in T cells. However, current models for culturing HSPCs and for infecting T cells in vitro require that the cells be maintained in an actively proliferating state. Here we describe a novel culture system in which primary human HSPCs cultured under hypothermic conditions are maintained in a quiescent state. We show that these quiescent HSPCs are susceptible to predominantly latent infection with HIV-1, while actively proliferating and differentiating HSPCs obtain predominantly active infections. Furthermore, we demonstrate that the most primitive quiescent HSPCs are more resistant to spontaneous reactivation from latency than more differentiated HSPCs and that quiescent HSPCs are resistant to reactivation by histone deacetylase inhibitors or P-TEFb activation but are susceptible to reactivation by protein kinase C (PKC) agonists. We also demonstrate that inhibition of HSP90, a known regulator of HIV transcription, recapitulates the quiescence and latency phenotypes of hypothermia, suggesting that hypothermia and HSP90 inhibition may regulate these processes by similar mechanisms. In summary, these studies describe a novel model for studying HIV-1 latency in human primary cells maintained in a quiescent state.IMPORTANCE Human immunodeficiency virus type 1 (HIV-1) establishes a persistent infection for which there remains no feasible cure. Current approaches are unable to clear the virus despite decades of therapy due to the existence of latent reservoirs of integrated HIV-1, which can reactivate and contribute to viral rebound following treatment interruption. Previous clinical attempts to reactivate the latent reservoirs in an individual so that they can be eliminated by the immune response or viral cytopathic effect have failed, indicating the need for a better understanding of the processes regulating HIV-1 latency. Here we characterize a novel in vitro model of HIV-1 latency in primary hematopoietic stem and progenitor cells isolated from human cord blood that may better recapitulate the behavior of latently infected cells in vivo This model can be used to study mechanisms regulating latency and potential therapeutic approaches to reactivate latent infections in quiescent cells.
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Affiliation(s)
- Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas D Zaikos
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kathleen L Collins
- Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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22
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Sebastian NT, Zaikos TD, Terry V, Taschuk F, McNamara LA, Onafuwa-Nuga A, Yucha R, Signer RAJ, Riddell IV J, Bixby D, Markowitz N, Morrison SJ, Collins KL. CD4 is expressed on a heterogeneous subset of hematopoietic progenitors, which persistently harbor CXCR4 and CCR5-tropic HIV proviral genomes in vivo. PLoS Pathog 2017; 13:e1006509. [PMID: 28732051 PMCID: PMC5540617 DOI: 10.1371/journal.ppat.1006509] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 06/01/2017] [Revised: 08/02/2017] [Accepted: 07/04/2017] [Indexed: 12/27/2022] Open
Abstract
Latent HIV infection of long-lived cells is a barrier to viral clearance. Hematopoietic stem and progenitor cells are a heterogeneous population of cells, some of which are long-lived. CXCR4-tropic HIVs infect a broad range of HSPC subtypes, including hematopoietic stem cells, which are multi-potent and long-lived. However, CCR5-tropic HIV infection is limited to more differentiated progenitor cells with life spans that are less well understood. Consistent with emerging data that restricted progenitor cells can be long-lived, we detected persistent HIV in restricted HSPC populations from optimally treated people. Further, genotypic and phenotypic analysis of amplified env alleles from donor samples indicated that both CXCR4- and CCR5-tropic viruses persisted in HSPCs. RNA profiling confirmed expression of HIV receptor RNA in a pattern that was consistent with in vitro and in vivo results. In addition, we characterized a CD4high HSPC sub-population that was preferentially targeted by a variety of CXCR4- and CCR5-tropic HIVs in vitro. Finally, we present strong evidence that HIV proviral genomes of both tropisms can be transmitted to CD4-negative daughter cells of multiple lineages in vivo. In some cases, the transmitted proviral genomes contained signature deletions that inactivated the virus, eliminating the possibility that coincidental infection explains the results. These data support a model in which both stem and non-stem cell progenitors serve as persistent reservoirs for CXCR4- and CCR5-tropic HIV proviral genomes that can be passed to daughter cells. People who are effectively treated with antiretroviral medication harbor persistent forms of HIV that are integrated into the cellular genome. While HIV is cytopathic to most cells, transcriptionally silent, latent forms do not express toxic HIV gene products and can survive in the host for years. When conditions change, the latent virus can be activated to reinitiate infection. Because of the capacity for virus to spread, cure of HIV will require that we identify and eradicate all cells harboring functional HIV provirus. CD4+ T cells are abundant and easily identified as harboring proviral genomes. However, rare cell types that express HIV receptors, such as bone marrow hematopoietic progenitor and stem cells can also be infected by the virus potentially serving as barriers to cure strategies. We found that HIV can infect and persist in progenitor sub-types that were previously thought to be short lived, which expands the types of cells that can support reservoir formation. In addition, we found that HIV can spread by proliferation and cellular differentiation without the need for viral gene expression and virion production that could reveal the infection to the immune system. A deeper understanding of viral reservoirs is critically important for developing strategies that will succeed in viral eradication.
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Affiliation(s)
- Nadia T. Sebastian
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas D. Zaikos
- Department of Microbiology and Immunology University of Michigan, Ann Arbor, Michigan, United States of America
| | - Valeri Terry
- Division of Infectious Disease, Department of Internal Medicine University of Michigan, Ann Arbor, Michigan, United States of America
| | - Frances Taschuk
- Division of Infectious Disease, Department of Internal Medicine University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lucy A. McNamara
- Department of Microbiology and Immunology University of Michigan, Ann Arbor, Michigan, United States of America
| | - Adewunmi Onafuwa-Nuga
- Division of Infectious Disease, Department of Internal Medicine University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ryan Yucha
- Division of Infectious Disease, Department of Internal Medicine University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert A. J. Signer
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - James Riddell IV
- Division of Infectious Disease, Department of Internal Medicine University of Michigan, Ann Arbor, Michigan, United States of America
| | - Dale Bixby
- Division of Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Norman Markowitz
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, Michigan, United States of America
| | - Sean J. Morrison
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kathleen L. Collins
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology University of Michigan, Ann Arbor, Michigan, United States of America
- Division of Infectious Disease, Department of Internal Medicine University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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23
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Baxter SD, Smith AF, Hitchcock DB, Collins KL, Guinn CH, Smith AL, Finney CJ. The National Health and Nutrition Examination Survey's Food Insecurity Questionnaire Completed by Children: Effects of Assessment Mode (Classroom versus Interview). J Hunger Environ Nutr 2017; 13:205-227. [PMID: 29904506 PMCID: PMC5995461 DOI: 10.1080/19320248.2017.1315325] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The National Health and Nutrition Examination Survey's food insecurity questionnaire was administered to 155 children (77 African American, 65 White, 13 "Other" [7 Hispanic; 6 mixed races]) in grade 4 twice, 28-32 days apart. Test-retest reliabilities were modest and somewhat similar for assessment mode (classroom, interview) and subgroup variables (gender, race, socioeconomic status, academic achievement, body mass index percentile, social desirability). As academic achievement increased, White and Other children reported less food insecurity, and African-American children reported slightly less. As social desirability increased, White and African-American children reported slightly more food insecurity, and Other children reported substantially more. Although the questionnaire may be acceptable for use with diverse groups of children in grade 4, validation is needed.
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Affiliation(s)
- Suzanne D Baxter
- Research Professor, Institute for Families in Society, College of Social Work, University of South Carolina, 1600 Hampton Street, Suite 507, Columbia, SC, USA, 29208, orcid.org/0000-0002-9031-9087
| | - Albert F Smith
- Associate Professor, Department of Psychology, Cleveland State University, Cleveland, OH, USA, 44115, orcid.org/0000-0002-3442-8123
| | - David B Hitchcock
- Associate Professor, Department of Statistics, University of South Carolina, Columbia, SC, USA, 29208
| | - Kathleen L Collins
- Research Specialist (at the time of the study), Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208
| | - Caroline H Guinn
- Research Dietitian, Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208
| | - Alyssa L Smith
- Research Specialist II (at the time of the study), Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208
| | - Christopher J Finney
- Analyst, Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208; Manager, South Carolina Revenue and Fiscal Affairs Office, Health and Demographics, Columbia, SC, USA, 29201
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Baxter SD, Guinn CH, Smith AF, Hitchcock DB, Royer JA, Puryear MP, Collins KL, Smith AL. Children's school-breakfast reports and school-lunch reports (in 24-h dietary recalls): conventional and reporting-error-sensitive measures show inconsistent accuracy results for retention interval and breakfast location. Br J Nutr 2016; 115:1301-15. [PMID: 26865356 PMCID: PMC5546838 DOI: 10.1017/s0007114515005413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Validation-study data were analysed to investigate retention interval (RI) and prompt effects on the accuracy of fourth-grade children's reports of school-breakfast and school-lunch (in 24-h recalls), and the accuracy of school-breakfast reports by breakfast location (classroom; cafeteria). Randomly selected fourth-grade children at ten schools in four districts were observed eating school-provided breakfast and lunch, and were interviewed under one of eight conditions created by crossing two RIs ('short'--prior-24-hour recall obtained in the afternoon and 'long'--previous-day recall obtained in the morning) with four prompts ('forward'--distant to recent, 'meal name'--breakfast, etc., 'open'--no instructions, and 'reverse'--recent to distant). Each condition had sixty children (half were girls). Of 480 children, 355 and 409 reported meals satisfying criteria for reports of school-breakfast and school-lunch, respectively. For breakfast and lunch separately, a conventional measure--report rate--and reporting-error-sensitive measures--correspondence rate and inflation ratio--were calculated for energy per meal-reporting child. Correspondence rate and inflation ratio--but not report rate--showed better accuracy for school-breakfast and school-lunch reports with the short RI than with the long RI; this pattern was not found for some prompts for each sex. Correspondence rate and inflation ratio showed better school-breakfast report accuracy for the classroom than for cafeteria location for each prompt, but report rate showed the opposite. For each RI, correspondence rate and inflation ratio showed better accuracy for lunch than for breakfast, but report rate showed the opposite. When choosing RI and prompts for recalls, researchers and practitioners should select a short RI to maximise accuracy. Recommendations for prompt selections are less clear. As report rates distort validation-study accuracy conclusions, reporting-error-sensitive measures are recommended.
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Affiliation(s)
- Suzanne Domel Baxter
- Institute for Families in Society, College of Social Work, University of South Carolina, 1600 Hampton St., Suite 507, Columbia, SC 29208
| | - Caroline H. Guinn
- Institute for Families in Society, College of Social Work, University of South Carolina, 1600 Hampton St., Suite 507, Columbia, SC 29208
| | - Albert F. Smith
- Department of Psychology, Cleveland State University, Cleveland, OH 44114
| | - David B. Hitchcock
- Department of Statistics, University of South Carolina, Columbia, SC 29208
| | - Julie A. Royer
- Institute for Families in Society, College of Social Work, University of South Carolina, 1600 Hampton St., Suite 507, Columbia, SC 29208
| | - Megan P. Puryear
- Institute for Families in Society, College of Social Work, University of South Carolina, 1600 Hampton St., Suite 507, Columbia, SC 29208
| | - Kathleen L. Collins
- Institute for Families in Society, College of Social Work, University of South Carolina, 1600 Hampton St., Suite 507, Columbia, SC 29208
| | - Alyssa L. Smith
- Institute for Families in Society, College of Social Work, University of South Carolina, 1600 Hampton St., Suite 507, Columbia, SC 29208
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25
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Baxter SD, Smith AF, Hitchcock DB, Collins KL, Guinn CH, Finney CJ, Royer JA, Miller PH. Test-Retest Reliability of the National Health and Nutrition Examination Survey's 5-Item Food Insecurity Questionnaire Completed by Fourth-Grade Children. J Nutr Educ Behav 2015; 47:459-64.e1. [PMID: 26363937 PMCID: PMC4570025 DOI: 10.1016/j.jneb.2015.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 04/14/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To examine test-retest reliability and internal consistency of a 5-item food insecurity questionnaire used in the National Health and Nutrition Examination Survey (NHANES). METHODS Researchers administered NHANES's questionnaire in the classroom to 92 fourth-grade children (74 African American; 48 girls) in 2 sessions 27-30 days apart in spring, 2011. Each classroom administration lasted 5-10 minutes. RESULTS Test-retest reliability was 0.66 (Kendall tau), which is modest. Internal consistency (Cronbach alpha) was .67 and .70 for respective administrations. Food insecurity scores were related to gender (adjusted P = .05) and academic achievement (adjusted P = .004) but not to socioeconomic status or body mass index percentile (binomial regression). On average, boys reported higher food insecurity than girls. Children with lower academic achievement scores reported higher food insecurity than children with higher academic achievement scores. CONCLUSIONS AND IMPLICATIONS NHANES's 5-item questionnaire may be group administered to assess food insecurity efficiently as reported by individual fourth-grade children.
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Affiliation(s)
- Suzanne D Baxter
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC.
| | - Albert F Smith
- Department of Psychology, Cleveland State University, Cleveland, OH
| | - David B Hitchcock
- Department of Statistics, University of South Carolina, Columbia, SC
| | - Kathleen L Collins
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC
| | - Caroline H Guinn
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC
| | - Christopher J Finney
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC; South Carolina Revenue and Fiscal Affairs Office-Health and Demographics, Columbia, SC
| | - Julie A Royer
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC; South Carolina Revenue and Fiscal Affairs Office-Health and Demographics, Columbia, SC
| | - Patricia H Miller
- Department of Psychology, San Francisco State University, San Francisco, CA
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26
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Baxter SD, Smith AF, Hitchcock DB, Guinn CH, Royer JA, Collins KL, Smith AL, Puryear MP, Vaadi KK, Finney CJ, Miller PH. Effectiveness of Prompts on Fourth-Grade Children's Dietary Recall Accuracy Depends on Retention Interval and Varies by Gender. J Nutr 2015; 145:2185-92. [PMID: 26224752 PMCID: PMC4548165 DOI: 10.3945/jn.115.213298] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 03/06/2015] [Accepted: 06/29/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Dietary recall accuracy is related to retention interval (RI) (i.e., time between to-be-reported meals and the interview), and possibly to prompts. To the best of our knowledge, no study has evaluated their combined effect. OBJECTIVE The combined influence of RI and prompts on children's recall accuracy was investigated in this study. Two RIs [short (prior-24-h recall obtained in afternoon) and long (previous-day recall obtained in morning)] were crossed with 4 prompts [forward (distant-to-recent), meal-name (breakfast, lunch, etc.), open (no instructions), and reverse (recent-to-distant)], creating 8 conditions. METHODS Fourth-grade children (n = 480; 50% girls) were randomly selected from consenting children at 10 schools in 4 districts in a southern state during 3 school years (2011-2012, 2012-2013, and 2013-2014). Each child was observed eating school-provided breakfast and lunch, and interviewed one time under 1 of the 8 conditions. Condition assignment was constrained so that each had 60 children (30 girls). Accuracy measures were food-item omission and intrusion rates, and energy correspondence rate and inflation ratio. For each measure, linear models determined effects of RI, prompt, gender, and interactions (2-way, 3-way); race/ethnicity, school year, and district were control variables. RESULTS RI (P values < 0.015) and prompt (P values < 0.005) were significant for all 4 accuracy measures. RI × prompt (P values < 0.001) was significant for 3 accuracy measures (not intrusion rate). Prompt × gender (P = 0.005) was significant for omission rate. RI × prompt × gender was significant for intrusion rate and inflation ratio (P values < 0.001). For the short vs. long RI across prompts and genders, accuracy was better by 33-50% for each accuracy measure. CONCLUSIONS To obtain the most accurate recalls possible from children, studies should be designed to use a short rather than long RI. Prompts affect children's recall accuracy, although the effectiveness of different prompts depends on RI and varies by gender: at a short RI, the choice of prompts has little systematic effect on accuracy, whereas at a long RI, reverse prompts may elicit the most accurate recalls.
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Affiliation(s)
| | - Albert F Smith
- Department of Psychology, Cleveland State University, Cleveland, OH; and
| | - David B Hitchcock
- Department of Statistics, University of South Carolina, Columbia, SC
| | | | - Julie A Royer
- Institute for Families in Society, College of Social Work, and
| | | | - Alyssa L Smith
- Institute for Families in Society, College of Social Work, and
| | - Megan P Puryear
- Institute for Families in Society, College of Social Work, and
| | - Kate K Vaadi
- Institute for Families in Society, College of Social Work, and
| | | | - Patricia H Miller
- Department of Psychology, San Francisco State University, San Francisco, CA
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Miller PH, Baxter SD, Royer JA, Hitchcock DB, Smith AF, Collins KL, Guinn CH, Smith AL, Puryear MP, Vaadi KK, Finney CJ. Children's Social Desirability: Effects of Test Assessment Mode. Pers Individ Dif 2015; 83:85-90. [PMID: 25870465 PMCID: PMC4392397 DOI: 10.1016/j.paid.2015.03.039] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study examined a recently developed short version of the Children's Social Desirability (CSD-S) scale with 157 fourth-grade children. Of interest was a) whether one-month test-retest reliability would vary as a function of test assessment mode (interview or classroom), gender, race, SES, and BMI percentile, and b) whether the degree of social desirability would vary as a function of these same variables. The CSD-S scale showed good test-retest reliability for both interview and classroom assessment modes (.85 and .83, respectively). Internal consistency also was good (first interview administration = .84; first classroom administration = .81). Reliability was good and did not vary significantly over assessment mode or any child subgroup variables, suggesting that the CSD-S scale is appropriate for general use. The interview mode elicited significantly more socially desirable answers than did the classroom mode. Social desirability did not differ across child subgroups. Some of these findings were examined, and replicated, on another sample. Thus, the CSD-S scale may be used with diverse groups of children to a) reliably assess a social desirability bias that may systematically bias other self-reports of interest to researchers and b) examine individual differences in degree of social desirability.
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Affiliation(s)
- Patricia H. Miller
- Department of Psychology, San Francisco State University, San Francisco, CA, USA, 94132
| | - Suzanne D. Baxter
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
| | - Julie A. Royer
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
- South Carolina Revenue and Fiscal Affairs Office, Health and Demographics Section, Columbia, SC, USA, 29201
| | - David B. Hitchcock
- Department of Statistics, University of South Carolina, Columbia, SC, USA, 29208
| | - Albert F. Smith
- Department of Psychology, Cleveland State University, Cleveland, OH, USA, 44115
| | - Kathleen L. Collins
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
| | - Caroline H. Guinn
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
| | - Alyssa L. Smith
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
| | - Megan P. Puryear
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
| | - Kate K. Vaadi
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
| | - Christopher J. Finney
- Institute for Families in Society, College of Social Work, University of South Carolina, Columbia, SC, USA, 29208 (Baxter, 803-777-1824 extension 12)
- South Carolina Revenue and Fiscal Affairs Office, Health and Demographics Section, Columbia, SC, USA, 29201
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Collins DR, Lubow J, Lukic Z, Mashiba M, Collins KL. Vpr Promotes Macrophage-Dependent HIV-1 Infection of CD4+ T Lymphocytes. PLoS Pathog 2015; 11:e1005054. [PMID: 26186441 PMCID: PMC4506080 DOI: 10.1371/journal.ppat.1005054] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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: 03/03/2015] [Accepted: 06/29/2015] [Indexed: 11/18/2022] Open
Abstract
Vpr is a conserved primate lentiviral protein that promotes infection of T lymphocytes in vivo by an unknown mechanism. Here we demonstrate that Vpr and its cellular co-factor, DCAF1, are necessary for efficient cell-to-cell spread of HIV-1 from macrophages to CD4+ T lymphocytes when there is inadequate cell-free virus to support direct T lymphocyte infection. Remarkably, Vpr functioned to counteract a macrophage-specific intrinsic antiviral pathway that targeted Env-containing virions to LAMP1+ lysosomal compartments. This restriction of Env also impaired virological synapses formed through interactions between HIV-1 Env on infected macrophages and CD4 on T lymphocytes. Treatment of infected macrophages with exogenous interferon-alpha induced virion degradation and blocked synapse formation, overcoming the effects of Vpr. These results provide a mechanism that helps explain the in vivo requirement for Vpr and suggests that a macrophage-dependent stage of HIV-1 infection drives the evolutionary conservation of Vpr.
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Affiliation(s)
- David R. Collins
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jay Lubow
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Zana Lukic
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael Mashiba
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kathleen L. Collins
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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Mashiba M, Collins DR, Terry VH, Collins KL. Vpr Overcomes Macrophage-Specific Restriction of HIV-1 Env Expression and Virion Production. Cell Host Microbe 2015; 17:414. [PMID: 29669271 DOI: 10.1016/j.chom.2015.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Mashiba M, Collins DR, Terry VH, Collins KL. Vpr overcomes macrophage-specific restriction of HIV-1 Env expression and virion production. Cell Host Microbe 2014; 16:722-35. [PMID: 25464830 DOI: 10.1016/j.chom.2014.10.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/21/2014] [Accepted: 10/06/2014] [Indexed: 12/30/2022]
Abstract
The HIV-1 accessory protein Vpr enhances infection of primary macrophages through unknown mechanisms. Recent studies demonstrated that Vpr interactions with the cellular DCAF1-DDB1-CUL4 E3 ubiquitin ligase complex limit activation of innate immunity and interferon (IFN) induction. We describe a restriction mechanism that targets the HIV-1 envelope protein Env, but is overcome by Vpr and its interaction with DCAF1. This restriction is active in the absence of Vpr in HIV-1-infected primary macrophages and macrophage-epithelial cell heterokaryons, but not epithelial cell lines. HIV-1-infected macrophages lacking Vpr express more IFN following infection, target Env for lysosomal degradation, and produce fewer Env-containing virions. Conversely, Vpr expression reduces IFN induction, rescues Env expression, and enhances virion release. Addition of IFN or silencing DCAF1 reduces the amount of cell-associated Env and virion production in wild-type HIV-1-infected primary macrophages. These findings provide insight into an IFN-stimulated macrophage-specific restriction pathway targeting HIV-1 Env that is counteracted by Vpr.
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Affiliation(s)
- Michael Mashiba
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - David R Collins
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathleen L Collins
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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Abstract
Current therapy for HIV effectively suppresses viral replication and prolongs life, but the infection persists due, at least in part, to latent infection of long-lived cells. One favored strategy toward a cure targets latent virus in resting memory CD4(+) T cells by stimulating viral production. However, the existence of an additional reservoir in bone marrow hematopoietic progenitor cells has been detected in some treated HIV-infected people. This review describes approaches investigators have used to reactivate latent proviral genomes in resting CD4(+) T cells and hematopoietic progenitor cells. In addition, the authors review approaches for clearance of these reservoirs along with other important topics related to HIV eradication.
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Affiliation(s)
- Nadia T Sebastian
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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32
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Affiliation(s)
- David R. Collins
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kathleen L. Collins
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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McNamara LA, Onafuwa-Nuga A, Sebastian NT, Riddell J, Bixby D, Collins KL. CD133+ hematopoietic progenitor cells harbor HIV genomes in a subset of optimally treated people with long-term viral suppression. J Infect Dis 2013; 207:1807-16. [PMID: 23554378 DOI: 10.1093/infdis/jit118] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Hematopoietic progenitor cells (HPCs) in the bone marrow of human immunodeficiency virus (HIV)-infected individuals have been proposed as a persistent reservoir of virus. However, some studies have suggested that HIV genomes detected in HPCs arise from T-cell contamination. METHODS CD133-sorted HPCs and CD133-depleted bone marrow cells were purified from bone marrow specimens obtained from 11 antiretroviral-treated donors in whom the HIV load had been <48 copies/mL for at least 6 months. CD133 and CD3 expression on the cells was assessed by flow cytometry. HIV DNA was quantified by real-time polymerase chain reaction analysis. RESULTS HIV genomes were detected in CD133-sorted samples from 6 donors, including 2 in whom viral loads were undetectable for >8 years. CD3(+) T cells represented <1% of cells in all CD133-sorted samples. For 5 of 6 CD133-sorted samples with detectable HIV DNA, the HIV genomes could not be explained by contaminating CD3(+) T cells. Donors with detectable HIV DNA in HPCs received their diagnosis significantly more recently than the remaining donors but had had undetectable viral loads for similar periods. CONCLUSIONS HIV genomes can be detected in CD133-sorted cells from a subset of donors with long-term viral suppression and, in most cases, cannot be explained by contamination with CD3(+) T cells.
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Affiliation(s)
- Lucy A McNamara
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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35
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Abstract
Recently, genome-wide association studies have identified the major histocompatibility complex class I protein HLA-C as an important molecule that affects HIV disease progression. The association between HLA-C and HIV disease outcome was originally determined through a single nucleotide polymorphism (SNP) 35 kb upstream of the HLA-C locus. More recent work has focused on elucidating the functional significance of the -35 SNP, and several groups now have demonstrated HLA-C surface expression to be a key element in control of HIV viral load, with higher surface expression associating with slower disease progression. Most recently, control of HLA-C surface expression has been correlated with the presence of microRNA binding sites that affect HLA-C expression and control of HIV disease. This review highlights these results and explores the ways in which HLA-C surface expression could affect immune system function in the setting of HIV disease.
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Affiliation(s)
- Deanna A Kulpa
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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Abstract
The Human Immunodeficiency Virus (HIV) Nef protein is necessary for high viral loads and for timely progression to AIDS. Nef plays a number of roles, but its effect on antigen presentation and immune evasion are among the best characterized. Cytotoxic T lymphocytes (CTLs) recognize and lyse virally infected cells by detecting viral antigens in complex with host major histocompatibility complex class I (MHC-I) molecules on the infected cell surface. The HIV Nef protein disrupts antigen presentation at the cell surface by interfering with the normal trafficking pathway of MHC-I and thus reduces CTL recognition and lysis of infected cells. The molecular mechanism by which Nef causes MHC-I downmodulation is becoming more clear, but some questions remain. A better understanding of how Nef disrupts antigen presentation may lead to the development of drugs that enhance the ability of the anti-HIV CTLs to control HIV disease.
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Affiliation(s)
- Elizabeth R Wonderlich
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
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Thammavongsa V, Schaefer M, Filzen T, Collins KL, Carrington M, Bangia N, Raghavan M. Assembly and intracellular trafficking of HLA-B*3501 and HLA-B*3503. Immunogenetics 2010; 61:703-16. [PMID: 19838694 DOI: 10.1007/s00251-009-0399-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Residue 116 of major histocompatibility complex (MHC) class I heavy chains is an important determinant of assembly, that can influence rates of ER-Golgi trafficking, binding to the transporter associated with antigen processing (TAP), tapasin dependence of assembly, and the efficiency and specificity of peptide binding. Here, we investigated assembly and peptide-binding differences between HLA-B*3501(S116) and HLA-B*3503(F116), two alleles differing only at position 116 of the MHC class I heavy chain, that are associated respectively with normal or rapid AIDS progression. A reduced intracellular maturation rate was observed for HLA-B*3503 in HIV-infected and uninfected cells, which correlated with enhanced binding of HLA-B*3503 to TAP. No significant differences in the intrinsic efficiency of in vitro peptide binding by HLA-B*3501 and HLA-B*3503 were measurable with several common peptides or peptide libraries, and both allotypes were relatively tapasin-independent for their assembly. However, thermostability differences between the two allotypes were measurable in a CD4(+) T cell line. These findings suggest that compared to HLA-B*3501, a reduced intracellular peptide repertoire for HLA-B*3503 could contribute to its slower intracellular trafficking and stronger association with rapid AIDS progression.
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Affiliation(s)
- Vilasack Thammavongsa
- Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, Ann Arbor, MI 48109-0620, USA
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Abstract
Successful viruses must overcome the body's immune defenses. In this issue of Cell Host & Microbe, Goffinet et al. (2009) provide evidence that the host protein CD317, the target of the HIV Vpu protein, is part of an ancient innate immune response directed against budding viruses.
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Affiliation(s)
- Kathleen L Collins
- Department of Internal Medicine and Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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Schaefer MR, Williams M, Kulpa DA, Blakely PK, Yaffee AQ, Collins KL. A novel trafficking signal within the HLA-C cytoplasmic tail allows regulated expression upon differentiation of macrophages. J Immunol 2008; 180:7804-17. [PMID: 18523244 DOI: 10.4049/jimmunol.180.12.7804] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
MHC class I molecules (MHC-I) present peptides to CTLs. In addition, HLA-C allotypes are recognized by killer cell Ig-like receptors (KIR) found on NK cells and effector CTLs. Compared with other classical MHC-I allotypes, HLA-C has low cell surface expression and an altered intracellular trafficking pattern. We present evidence that this results from effects of both the extracellular domain and the cytoplasmic tail. Notably, we demonstrate that the cytoplasmic tail contains a dihydrophobic (LI) internalization and lysosomal targeting signal that is partially attenuated by an aspartic acid residue (DXSLI). In addition, we provide evidence that this signal is specifically inhibited by hypophosphorylation of the adjacent serine residue upon macrophage differentiation and that this allows high HLA-C expression in this cell type. We propose that tightly regulated HLA-C surface expression facilitates immune surveillance and allows HLA-C to serve a specialized role in macrophages.
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Affiliation(s)
- Malinda R Schaefer
- Graduate Program Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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Wonderlich ER, Williams M, Collins KL. The tyrosine binding pocket in the adaptor protein 1 (AP-1) mu1 subunit is necessary for Nef to recruit AP-1 to the major histocompatibility complex class I cytoplasmic tail. J Biol Chem 2007; 283:3011-3022. [PMID: 18073204 DOI: 10.1074/jbc.m707760200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
To evade the anti-human immunodeficiency virus (HIV) immune response, the HIV Nef protein disrupts major histocompatibility complex class I (MHC-I) trafficking by recruiting the clathrin adaptor protein 1 (AP-1) to the MHC-I cytoplasmic tail. Under normal conditions AP-1 binds dileucine and tyrosine signals (YXX phi motifs) via physically separate binding sites. In the case of the Nef-MHC-I complex, a tyrosine in the human leukocyte antigen (HLA)-A2 cytoplasmic tail ((320)YSQA) and a methionine in Nef (Met(20)) are absolutely required for AP-1 binding. Also present in Nef is a dileucine motif, which does not normally affect MHC-I trafficking and is not needed to recruit AP-1 to the Nef-MHC-I-complex. However, evidence is presented here that this dileucine motif can be activated by fusing Nef to the HLA-A2 tail in cis. Thus, the inability of this motif to function in trans likely results from a structural change that occurs when Nef binds to the MHC-I cytoplasmic tail. The physiologically relevant tyrosine-dependent recruitment of AP-1 to MHC-I, which occurs whether Nef is present in cis or trans, was stabilized by the acidic and polyproline domains within Nef. Additionally, amino acids Ala(324) and Asp(327) in the cytoplasmic tails of HLA-A and (but not HLA-C and HLA-E) molecules also stabilized AP-1 binding. Finally, mutation of the tyrosine binding pocket in the mu subunit of AP-1 created a dominant negative inhibitor of Nef-induced down-modulation of HLA-A2 that disrupted binding of wild type AP-1 to the Nef-MHC-I complex. Thus, these data provide evidence that Nef binding to the MHC-I cytoplasmic tail stabilizes the interaction of a tyrosine in the MHC-I cytoplasmic tail with the natural tyrosine binding pocket in AP-1.
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Affiliation(s)
- Elizabeth R Wonderlich
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Maya Williams
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Kathleen L Collins
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109.
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Thammavongsa V, Raghuraman G, Filzen TM, Collins KL, Raghavan M. HLA-B44 polymorphisms at position 116 of the heavy chain influence TAP complex binding via an effect on peptide occupancy. J Immunol 2006; 177:3150-61. [PMID: 16920953 DOI: 10.4049/jimmunol.177.5.3150] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A single residue polymorphism distinguishes HLA-B*4402(D116) from HLA-B*4405(Y116), which was suggested to allow HLA-B*4405 to acquire peptides without binding to tapasin-TAP complexes. We show that HLA-B*4405 is not inherently unable to associate with tapasin-TAP complexes. Under conditions of peptide deficiency, both allotypes bound efficiently to TAP and tapasin, and furthermore, random nonamer peptides conferred higher thermostability to HLA-B*4405 than to HLA-B*4402. Correspondingly, under conditions of peptide sufficiency, more rapid peptide-loading, dissociation from TAP complexes, and endoplasmic reticulum exit were observed for HLA-B*4405, whereas HLA-B*4402 showed greater endoplasmic reticulum retention and enhanced tapasin-TAP binding. Together, these studies suggest that position 116 HLA polymorphisms influence peptide occupancy, which in turn determines binding to tapasin and TAP. Relative to HLA-B*4405, inefficient peptide loading of HLA-B*4402 is likely to underlie its stronger tapasin dependence for cell surface expression and thermostability, and its enhanced susceptibility to pathogen interference strategies.
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Affiliation(s)
- Vilasack Thammavongsa
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor 48109-0620, USA
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Abstract
The Nef protein of primate lentiviruses is a unique protein that has evolved in several ways to manipulate the biology of an infected cell to support viral replication, immune evasion, pathogenesis, and viral spread. Nef is a small (25- to 34-kDa), myristoylated protein that binds to a collection of cellular factors and acts as an adaptor to generate novel protein interactions to accomplish specific functions. Of the many biological activities attributed to Nef, the reduction of surface levels of the viral receptor (CD4) and antigen-presenting molecules (major histocompatibility complex class I) has been intensely examined; recent evidence demonstrates that Nef utilizes multiple, distinct pathways to affect these proteins. To accomplish this, Nef promotes the formation of multiprotein complexes, recruiting host adaptor proteins to commandeer intracellular vesicular trafficking routes. The altered trafficking of several other host molecules has also been reported, and an emerging theory suggests that Nef generates pleiotrophic effects in the secretory and endocytic pathways that reprogram intracellular protein trafficking and may ultimately provide an efficient platform for viral assembly. This review critically discusses some of the major findings regarding the impact of human immunodeficiency virus type 1 Nef on host protein transport and addresses some emerging directions in this area of human immunodeficiency virus biology.
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Affiliation(s)
- Jeremiah F Roeth
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Williams M, Roeth JF, Kasper MR, Filzen TM, Collins KL. Human immunodeficiency virus type 1 Nef domains required for disruption of major histocompatibility complex class I trafficking are also necessary for coprecipitation of Nef with HLA-A2. J Virol 2005; 79:632-6. [PMID: 15596859 PMCID: PMC538737 DOI: 10.1128/jvi.79.1.632-636.2005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) Nef is a critical protein that is necessary for HIV pathogenesis. Its roles include the disruption of major histocompatibility complex class I (MHC-I) and CD4 trafficking to promote immune evasion and viral spread. Mutational analyses have revealed that separate domains of Nef are required to affect these two molecules. To further elucidate how Nef disrupts MHC-I trafficking in T cells, we examined the role of protein domains that are required for this function (N-terminal alpha helix, polyproline, acidic, and oligomerization domains). We found that each of these regions was required for Nef to disrupt the transport of HLA-A2 to the cell surface and for Nef to coprecipitate with HLA-A2.
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Affiliation(s)
- Maya Williams
- Graduate Program in Cellular and Molecular Biology, The University of Michigan, Ann Arbor, Michigan 48109, USA
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44
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Abstract
Human immunodeficiency virus, type 1 Nef disrupts viral antigen presentation and promotes viral immune evasion from cytotoxic T lymphocytes. There is evidence that Nef acts early in the secretory pathway to redirect major histocompatibility complex class I (MHC-I) from the trans-Golgi network to the endolysosomal pathway. However, a competing model suggests that Nef acts much later by accelerating MHC-I turnover at the cell surface. Here we demonstrate that Nef targets early forms of MHC-I molecules in the endoplasmic reticulum by preferentially binding hypophosphorylated cytoplasmic tails. The Nef-MHC-I complex migrates normally into the Golgi apparatus but subsequently fails to arrive at the cell surface and become phosphorylated. Cell type-specific differences in the rate of MHC-I transport through the secretory pathway correlate with responsiveness to Nef and co-precipitation of adaptor protein 1 with the Nef.MHC-I complex. We propose that the assembly of a Nef.MHC-I.adaptor protein 1 complex early in the secretory pathway is important for Nef activity.
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Affiliation(s)
- Matthew R Kasper
- Department of Microbiology, The University of Michigan, Ann Arbor, Michigan 48109, USA
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45
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Abstract
To avoid immune recognition by cytotoxic T lymphocytes (CTLs), human immunodeficiency virus (HIV)-1 Nef disrupts the transport of major histocompatibility complex class I molecules (MHC-I) to the cell surface in HIV-infected T cells. However, the mechanism by which Nef does this is unknown. We report that Nef disrupts MHC-I trafficking by rerouting newly synthesized MHC-I from the trans-Golgi network (TGN) to lysosomal compartments for degradation. The ability of Nef to target MHC-I from the TGN to lysosomes is dependent on expression of the μ1 subunit of adaptor protein (AP) AP-1A, a cellular protein complex implicated in TGN to endolysosomal pathways. We demonstrate that in HIV-infected primary T cells, Nef promotes a physical interaction between endogenous AP-1 and MHC-I. Moreover, we present data that this interaction uses a novel AP-1 binding site that requires amino acids in the MHC-I cytoplasmic tail. In sum, our evidence suggests that binding of AP-1 to the Nef–MHC-I complex is an important step required for inhibition of antigen presentation by HIV.
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Affiliation(s)
- Jeremiah F Roeth
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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46
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Abstract
Although cytotoxic T lymphocytes (CTLs) are important for controlling HIV, CTLs are not effective at eradicating HIV infection. Recent studies have revealed a combination of factors that together make HIV-infected cells resistant to CTLs and make anti-HIV CTLs ineffective. These factors likely contribute to prolonged survival of infected target cells, which in turn increases the probability of antigenic variation and immune escape.
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Affiliation(s)
- Kathleen L Collins
- Department of Internal Medicine, The University of Michigan, Ann Arbor 48109, USA.
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47
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Abstract
Human immunodeficiency virus type 1 (HIV-1) Nef is a key pathogenic factor necessary for the development of AIDS. One important function of Nef is to reduce cell surface levels of major histocompatibility complex class I (MHC-I) molecules, thereby protecting HIV-infected cells from recognition by cytotoxic T lymphocytes. The mechanism of MHC-I downmodulation by Nef has not been clearly elucidated, and its reported effect on MHC-I steady-state levels ranges widely, from 2-fold in HeLa cells to 200-fold in HIV-infected primary T cells. Here, we directly compared downmodulation of HLA-A2 in HIV-infected HeLa cells to that in T cells. We found that similar amounts of Nef protein resulted in a much more dramatic downmodulation of HLA-A2 in T cells than in HeLa cells. A comparison of Nef's effects on HLA-A2 endocytosis, recycling, and transport rates indicated that the most prominent effect of Nef on HLA-A2 in T cells was to inhibit transport to the cell surface. The phosphatidylinositol 3-kinase inhibitor, LY294002, previously reported to inhibit Nef-mediated MHC-I downmodulation in astrocytic cells, did not directly affect Nef's ability to block transport of MHC-I to the cell surface in T cells.
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Affiliation(s)
- Matthew R Kasper
- Department of Microbiology and Immunology, The University of Michigan, Ann Arbor, Michigan 48109, USA
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48
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Bobbitt KR, Addo MM, Altfeld M, Filzen T, Onafuwa AA, Walker BD, Collins KL. Rev activity determines sensitivity of HIV-1-infected primary T cells to CTL killing. Immunity 2003; 18:289-99. [PMID: 12594955 DOI: 10.1016/s1074-7613(03)00031-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The HIV Nef protein is thought to promote HIV immune evasion by downmodulating MHC-I and protecting infected cells from CTL killing. In addition, we demonstrated that Rev, an HIV regulatory protein needed for expression of the HIV late genes, can influence CTL killing. When Rev activity level was reduced by virtue of amino acid alterations in the Rev protein sequence, infected cells were more resistant to anti-Gag and anti-Env CTL killing. A screen of primary viral isolates revealed that viruses derived from asymptomatic, infected people had lower Rev activity, lower Gag levels, and greater resistance to anti-Gag CTL killing. Thus, rev alleles with low activity may have a selective advantage in infected people with effective immune responses.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Base Sequence
- Cells, Cultured
- Cytotoxicity Tests, Immunologic
- DNA, Viral/genetics
- Gene Products, rev/genetics
- Gene Products, rev/metabolism
- Genes, rev
- HIV Infections/immunology
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/immunology
- HIV-1/metabolism
- Humans
- Models, Immunological
- Molecular Sequence Data
- Sequence Homology, Amino Acid
- T-Lymphocytes/immunology
- T-Lymphocytes/virology
- T-Lymphocytes, Cytotoxic/immunology
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Kevin R Bobbitt
- Department of Internal Medicine, The University of Michigan, Ann Arbor, MI 48109, USA
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49
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Abstract
The human immunodeficiency virus (HIV) is unique in its capacity to produce chronic disease in almost all infected hosts. To accomplish this, it has evolved multiple mechanisms to effectively evade the immune response. HIV encodes at least one protein that makes infected cells resistant to CTL killing by downmodulating epitope (peptide plus MHC-I protein) density on the infected cell surface. In addition, HIV encodes several mechanisms to promote apoptosis of HIV-specific CTLs. The end result is that infected cells have a reduced susceptibility to CTLs, survive longer and produce more viral antigenic variants that can further evade the immune response.
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Affiliation(s)
- Kathleen L Collins
- Department of Internal Medicine, 4301 MSRB III Box 0638, 1150 West Medical Center Drive, The University of Michigan, Ann Arbor, MI 48109, USA.
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50
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Williams M, Roeth JF, Kasper MR, Fleis RI, Przybycin CG, Collins KL. Direct binding of human immunodeficiency virus type 1 Nef to the major histocompatibility complex class I (MHC-I) cytoplasmic tail disrupts MHC-I trafficking. J Virol 2002; 76:12173-84. [PMID: 12414957 PMCID: PMC136906 DOI: 10.1128/jvi.76.23.12173-12184.2002] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2002] [Accepted: 08/19/2002] [Indexed: 11/20/2022] Open
Abstract
Nef, an essential pathogenic determinant for human immunodeficiency virus type 1, has multiple functions that include disruption of major histocompatibility complex class I molecules (MHC-I) and CD4 and CD28 cell surface expression. The effects of Nef on MHC-I have been shown to protect infected cells from cytotoxic T-lymphocyte recognition by downmodulation of a subset of MHC-I (HLA-A and -B). The remaining HLA-C and -E molecules prevent recognition by natural killer (NK) cells, which would otherwise lyse cells expressing small amounts of MHC-I. Specific amino acid residues in the MHC-I cytoplasmic tail confer sensitivity to Nef, but their function is unknown. Here we show that purified Nef binds directly to the HLA-A2 cytoplasmic tail in vitro and that Nef forms complexes with MHC-I that can be isolated from human cells. The interaction between Nef and MHC-I appears to be weak, indicating that it may be transient or stabilized by other factors. Supporting the fact that these molecules interact in vivo, we found that Nef colocalizes with HLA-A2 molecules in a perinuclear distribution inside cells. In addition, we demonstrated that Nef fails to bind the HLA-E tail and also fails to bind HLA-A2 tails with deletions of amino acids necessary for MHC-I downmodulation. These data provide an explanation for differential downmodulation of MHC-I allotypes by Nef. In addition, they provide the first direct evidence indicating that Nef functions as an adaptor molecule able to link MHC-I to cellular trafficking proteins.
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Affiliation(s)
- Maya Williams
- Graduate Program in Cellular and Molecular Biology, University of Michigan. University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
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