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Seo D, Brito Oliveira S, Rex EA, Ye X, Rice LM, da Fonseca FG, Gammon DB. Poxvirus A51R proteins regulate microtubule stability and antagonize a cell-intrinsic antiviral response. Cell Rep 2024; 43:113882. [PMID: 38457341 PMCID: PMC11023057 DOI: 10.1016/j.celrep.2024.113882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/28/2024] [Accepted: 02/13/2024] [Indexed: 03/10/2024] Open
Abstract
Numerous viruses alter host microtubule (MT) networks during infection, but how and why they induce these changes is unclear in many cases. We show that the vaccinia virus (VV)-encoded A51R protein is a MT-associated protein (MAP) that directly binds MTs and stabilizes them by both promoting their growth and preventing their depolymerization. Furthermore, we demonstrate that A51R-MT interactions are conserved across A51R proteins from multiple poxvirus genera, and highly conserved, positively charged residues in A51R proteins mediate these interactions. Strikingly, we find that viruses encoding MT interaction-deficient A51R proteins fail to suppress a reactive oxygen species (ROS)-dependent antiviral response in macrophages that leads to a block in virion morphogenesis. Moreover, A51R-MT interactions are required for VV virulence in mice. Collectively, our data show that poxviral MAP-MT interactions overcome a cell-intrinsic antiviral ROS response in macrophages that would otherwise block virus morphogenesis and replication in animals.
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Affiliation(s)
- Dahee Seo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sabrynna Brito Oliveira
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Emily A Rex
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuecheng Ye
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luke M Rice
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Don B Gammon
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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2
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Albarnaz JD, Kite J, Oliveira M, Li H, Di Y, Christensen MH, Paulo JA, Antrobus R, Gygi SP, Schmidt FI, Huttlin EL, Smith GL, Weekes MP. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection. Nat Commun 2023; 14:8134. [PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Modified vaccinia Ankara (MVA) virus does not replicate in human cells and is the vaccine deployed to curb the current outbreak of mpox. Here, we conduct a multiplexed proteomic analysis to quantify >9000 cellular and ~80% of viral proteins throughout MVA infection of human fibroblasts and macrophages. >690 human proteins are down-regulated >2-fold by MVA, revealing a substantial remodelling of the host proteome. >25% of these MVA targets are not shared with replication-competent vaccinia. Viral intermediate/late gene expression is necessary for MVA antagonism of innate immunity, and suppression of interferon effectors such as ISG20 potentiates virus gene expression. Proteomic changes specific to infection of macrophages indicate modulation of the inflammatory response, including inflammasome activation. Our approach thus provides a global view of the impact of MVA on the human proteome and identifies mechanisms that may underpin its abortive infection. These discoveries will prove vital to design future generations of vaccines.
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Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK.
| | - Joanne Kite
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Marisa Oliveira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Hanqi Li
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Ying Di
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Florian I Schmidt
- Institute of Innate Immunity, University of Bonn, 53127, Bonn, Germany
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
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3
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Saghazadeh A, Rezaei N. Poxviruses and the immune system: Implications for monkeypox virus. Int Immunopharmacol 2022; 113:109364. [PMID: 36283221 PMCID: PMC9598838 DOI: 10.1016/j.intimp.2022.109364] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Poxviruses (PXVs) are mostly known for the variola virus, being the cause of smallpox; however, re-emerging PXVs have also shown a great capacity to develop outbreaks of pox-like infections in humans. The situation is alarming; PXV outbreaks have been involving both endemic and non-endemic areas in recent decades. Stopped smallpox vaccination is a reason offered mainly for this changing epidemiology that implies the protective role of immunity in the pathology of PXV infections. The immune system recognizes PXVs and elicits responses, but PXVs can antagonize these responses. Here, we briefly review the immunology of PXV infections, with emphasis on the role of pattern-recognition receptors, macrophages, and natural killer cells in the early response to PXV infections and PXVs’ strategies influencing these responses, as well as taking a glance at other immune cells, which discussion over them mainly occurs in association with PXV immunization rather than PXV infection. Throughout the review, numerous evasion mechanisms are highlighted, which might have implications for designing specific immunotherapies for PXV in the future.
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Affiliation(s)
- Amene Saghazadeh
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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4
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Leite Pereira A, Jouhault Q, Marcos Lopez E, Cosma A, Lambotte O, Le Grand R, Lehmann MH, Tchitchek N. Modulation of Cell Surface Receptor Expression by Modified Vaccinia Virus Ankara in Leukocytes of Healthy and HIV-Infected Individuals. Front Immunol 2020; 11:2096. [PMID: 33013882 PMCID: PMC7506042 DOI: 10.3389/fimmu.2020.02096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/03/2020] [Indexed: 11/19/2022] Open
Abstract
Viral vectors are increasingly used as delivery means to induce a specific immunity in humans and animals. However, they also impact the immune system, and it depends on the given context whether this is beneficial or not. The attenuated vaccinia virus strain modified vaccinia virus Ankara (MVA) has been used as a viral vector in clinical studies intended to treat and prevent cancer and infectious diseases. The adjuvant property of MVA is thought to be due to its capability to stimulate innate immunity. Here, we confirmed that MVA induces interleukin-8 (IL-8), and this chemokine was upregulated significantly more in monocytes and HLA-DRbright dendritic cells (DCs) of HIV-infected patients on combined antiretroviral therapy (ART) than in cells of healthy persons. The effect of MVA on cell surface receptors is mostly unknown. Using mass cytometry profiling, we investigated the expression of 17 cell surface receptors in leukocytes after ex vivo infection of human whole-blood samples with MVA. We found that MVA downregulates most of the characteristic cell surface markers in particular types of leukocytes. In contrast, C-X-C motif chemokine receptor 4 (CXCR4) was significantly upregulated in each leukocyte type of healthy persons. Additionally, we detected a relative higher cell surface expression of the HIV-1 co-receptors C-C motif chemokine receptor 5 (CCR5) and CXCR4 in leukocytes of HIV-ART patients than in healthy persons. Importantly, we showed that MVA infection significantly downregulated CCR5 in CD4+ T cells, CD8+ T cells, B cells, and three different DC populations. CD86, a costimulatory molecule for T cells, was significantly upregulated in HLA-DRbright DCs after MVA infection of whole blood from HIV-ART patients. However, MVA was unable to downregulate cell surface expression of CD11b and CD32 in monocytes and neutrophils of HIV-ART patients to the same extent as in monocytes and neutrophils of healthy persons. In summary, MVA modulates the expression of many different kinds of cell surface receptors in leukocytes, which can vary in cells originating from persons previously infected with other pathogens.
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Affiliation(s)
- Adrien Leite Pereira
- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Infrastructure, CEA-Université Paris Sud 11, Fontenay-aux-Roses, France
| | - Quentin Jouhault
- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Infrastructure, CEA-Université Paris Sud 11, Fontenay-aux-Roses, France
| | - Ernesto Marcos Lopez
- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Infrastructure, CEA-Université Paris Sud 11, Fontenay-aux-Roses, France
| | - Antonio Cosma
- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Infrastructure, CEA-Université Paris Sud 11, Fontenay-aux-Roses, France
| | - Olivier Lambotte
- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Infrastructure, CEA-Université Paris Sud 11, Fontenay-aux-Roses, France.,INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, Le Kremlin-Bicêtre, France.,APHP, Service de Médecine Interne et Immunologie Clinique, Hôpitaux Universitaires Paris Saclay, Le Kremlin-Bicêtre, France
| | - Roger Le Grand
- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Infrastructure, CEA-Université Paris Sud 11, Fontenay-aux-Roses, France
| | - Michael H Lehmann
- Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicolas Tchitchek
- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Infrastructure, CEA-Université Paris Sud 11, Fontenay-aux-Roses, France
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5
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Zhang WC, Du LJ, Zheng XJ, Chen XQ, Shi C, Chen BY, Sun XN, Li C, Zhang YY, Liu Y, Xiao H, Leng Q, Jiang X, Zhang Z, Sun S, Duan SZ. Elevated sodium chloride drives type I interferon signaling in macrophages and increases antiviral resistance. J Biol Chem 2017; 293:1030-1039. [PMID: 29203528 DOI: 10.1074/jbc.m117.805093] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 11/28/2017] [Indexed: 12/20/2022] Open
Abstract
Type I IFN production and signaling in macrophages play critical roles in innate immune responses. High salt (i.e. high concentrations of NaCl) has been proposed to be an important environmental factor that influences immune responses in multiple ways. However, it remains unknown whether high salt regulates type I IFN production and signaling in macrophages. Here, we demonstrated that high salt promoted IFNβ production and its signaling in both human and mouse macrophages, and consequentially primed macrophages for strengthened immune sensing and signaling when challenged with viruses or viral nucleic acid analogues. Using both pharmacological inhibitors and RNA interference we showed that these effects of high salt on IFNβ signaling were mediated by the p38 MAPK/ATF2/AP1 signaling pathway. Consistently, high salt increased resistance to vesicle stomatitis virus (VSV) infection in vitro. In vivo data indicated that a high-salt diet protected mice from lethal VSV infection. Taken together, these results identify high salt as a crucial regulator of type I IFN production and signaling, shedding important new light on the regulation of innate immune responses.
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Affiliation(s)
- Wu-Chang Zhang
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
| | - Lin-Juan Du
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011.,the Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031
| | - Xiao-Jun Zheng
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011.,the Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031
| | - Xiao-Qing Chen
- the Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, and
| | - Chaoji Shi
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
| | - Bo-Yan Chen
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
| | - Xue-Nan Sun
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011.,the Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031
| | - Chao Li
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011.,the Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031
| | - Yu-Yao Zhang
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011.,the Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031
| | - Yan Liu
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
| | - Hui Xiao
- the Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qibin Leng
- the Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinquan Jiang
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
| | - Zhiyuan Zhang
- From the Ninth People's Hospital, School of Stomatology and.,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
| | - Shuyang Sun
- From the Ninth People's Hospital, School of Stomatology and .,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
| | - Sheng-Zhong Duan
- From the Ninth People's Hospital, School of Stomatology and .,the Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011
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6
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Differential Innate Immune Signaling in Macrophages by Wild-Type Vaccinia Mature Virus and a Mutant Virus with a Deletion of the A26 Protein. J Virol 2017; 91:JVI.00767-17. [PMID: 28659486 DOI: 10.1128/jvi.00767-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/23/2017] [Indexed: 12/13/2022] Open
Abstract
The Western Reserve (WR) strain of mature vaccinia virus contains an A26 envelope protein that mediates virus binding to cell surface laminin and subsequent endocytic entry into HeLa cells. Removal of the A26 protein from the WR strain mature virus generates a mutant, WRΔA26, that enters HeLa cells through plasma membrane fusion. Here, we infected murine bone marrow-derived macrophages (BMDM) with wild-type strain WR and the WRΔA26 mutant and analyzed viral gene expression and cellular innate immune signaling. In contrast to previous studies, in which both HeLa cells infected with WR and HeLa cells infected with WRΔA26 expressed abundant viral late proteins, we found that WR expressed much less viral late protein than WRΔA26 in BMDM. Microarray analysis of the cellular transcripts in BMDM induced by virus infection revealed that WR preferentially activated type 1 interferon receptor (IFNAR)-dependent signaling but WRΔA26 did not. We consistently detected a higher level of soluble beta interferon secretion and phosphorylation of the STAT1 protein in BMDM infected with WR than in BMDM infected with WRΔA26. When IFNAR-knockout BMDM were infected with WR, late viral protein expression increased, confirming that IFNAR-dependent signaling was differentially induced by WR and, in turn, restricted viral late gene expression. Finally, wild-type C57BL/6 mice were more susceptible to mortality from WRΔA26 infection than to that from WR infection, whereas IFNAR-knockout mice were equally susceptible to WR and WRΔA26 infection, demonstrating that the ability of WRΔA26 to evade IFNAR signaling has an important influence on viral pathogenesis in vivoIMPORTANCE The vaccinia virus A26 protein was previously shown to mediate virus attachment and to regulate viral endocytosis. Here, we show that infection with strain WR induces a robust innate immune response that activates type 1 interferon receptor (IFNAR)-dependent cellular genes in BMDM, whereas infection with the WRΔA26 mutant does not. We further demonstrated that the differential activation of IFNAR-dependent cellular signaling between WR and WRΔA26 not only is important for differential host restriction in BMDM but also is important for viral virulence in vivo Our study reveals a new property of WRΔA26, which is in regulating host antiviral innate immunity in vitro and in vivo.
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7
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Fortin C, Yang Y, Huang X. Monocytic myeloid-derived suppressor cells regulate T-cell responses against vaccinia virus. Eur J Immunol 2017; 47:1022-1031. [PMID: 28383204 DOI: 10.1002/eji.201646797] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/20/2017] [Accepted: 03/29/2017] [Indexed: 01/07/2023]
Abstract
Vaccinia virus (VV) can potently activate NK- and T-cell responses, leading to efficient viral control and generation of long-lasting protective immunity. However, immune responses against viral infections are often tightly controlled to avoid collateral damage and systemic inflammation. We have previously shown that granulocytic myeloid-derived suppressor cells (g-MDSCs) can suppress the NK-cell response to VV infection. It remains unknown what regulates T-cell responses to VV infection in vivo. In this study, we first showed that monocytic MDSCs (m-MDSCs), but not g-MDSCs, from VV-infected mice could directly suppress CD4+ and CD8+ T-cell activation in vitro. We then demonstrated that defective recruitment of m-MDSCs to the site of VV infection in CCR2-/- mice enhanced VV-specific CD8+ T-cell response and that adoptive transfer of m-MDSCs into VV-infected mice suppressed VV-specific CD8+ T-cell activation, leading to a delay in viral clearance. Mechanistically, we further showed that T-cell suppression by m-MDSCs is mediated by indication of iNOS and production of NO upon VV infection, and that IFN-γ is required for activation of m-MDSCs. Collectively, our results highlight a critical role for m-MDSCs in regulating T-cell responses against VV infection and may suggest potential strategies using m-MDSCs to modulate T-cell responses during viral infections.
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Affiliation(s)
- Carl Fortin
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Yiping Yang
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA.,Division of Hematologic Malignancies and Cellular Therapy, Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Xiaopei Huang
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
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8
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An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data. Genes Immun 2016; 17:244-50. [PMID: 27052692 DOI: 10.1038/gene.2016.15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/06/2015] [Accepted: 01/04/2016] [Indexed: 12/17/2022]
Abstract
Expression quantitative trait loci (eQTL) studies have functionalized nucleic acid variants through the regulation of gene expression. Although most eQTL studies only examine the effects of single variants on transcription, a more complex process of variant-variant interaction (epistasis) may regulate transcription. Herein, we describe a tool called interaction QTL (iQTL) designed to efficiently detect epistatic interactions that regulate gene expression. To maximize biological relevance and minimize the computational and hypothesis testing burden, iQTL restricts interactions such that one variant is within a user-defined proximity of the transcript (cis-regulatory). We apply iQTL to a data set of 183 smallpox vaccine study participants with genome-wide association study and gene expression data from unstimulated samples and samples stimulated by inactivated vaccinia virus. While computing only 0.15% of possible interactions, we identify 11 probe sets whose expression is regulated through a variant-variant interaction. We highlight the functional epistatic interactions among apoptosis-related genes, DIABLO, TRAPPC4 and FADD, in the context of smallpox vaccination. We also use an integrative network approach to characterize these iQTL interactions in a posterior network of known prior functional interactions. iQTL is an efficient, open-source tool to analyze variant interactions in eQTL studies, providing better understanding of the function of epistasis in immune response and other complex phenotypes.
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9
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Lehmann MH, Torres-Domínguez LE, Price PJR, Brandmüller C, Kirschning CJ, Sutter G. CCL2 expression is mediated by type I IFN receptor and recruits NK and T cells to the lung during MVA infection. J Leukoc Biol 2016; 99:1057-64. [DOI: 10.1189/jlb.4ma0815-376rr] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 03/01/2016] [Indexed: 12/16/2022] Open
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10
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Brenner TA, Rice TA, Anderson ED, Percopo CM, Rosenberg HF. Immortalized MH-S cells lack defining features of primary alveolar macrophages and do not support mouse pneumovirus replication. Immunol Lett 2016; 172:106-12. [PMID: 26916143 DOI: 10.1016/j.imlet.2016.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 12/15/2022]
Abstract
The SV-40-transformed MH-S cell line maintains some, but not all, features of primary alveolar macrophages (AMs) from BALB/c mice. We show here that MH-S cells produce inflammatory cytokines IL-6 and CXCL10 in response to challenge with Gram-positive Lactobacillus reuteri, and to TLR2 and NOD2 ligands Pam3CSK4 and MDP, respectively. In contrast, although wild-type AMs are infected in vivo by pneumonia virus of mice (PVM), no virus replication was detected in MH-S cells. Interestingly, the surface immunophenotype of MH-S cells (CD11c(+)Siglec F(-)) differs from that of wild-type AMs (CD11c(+) Siglec F(+)) and is similar to that of immature AMs isolated from granulocyte macrophage-colony stimulating factor (GM-CSF) gene-deleted mice; AMs from GM-CSF(-/-) mice also support PVM replication. However, MH-S cells do not express the GM-CSF receptor alpha chain (CD116) and do not respond to GM-CSF. Due to these unusual features, MH-S cells should be used with caution as experimental models of AMs.
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Affiliation(s)
- Todd A Brenner
- Inflammation Immunobiology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Tyler A Rice
- Inflammation Immunobiology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Erik D Anderson
- Inflammation Immunobiology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Caroline M Percopo
- Inflammation Immunobiology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Helene F Rosenberg
- Inflammation Immunobiology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States.
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