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Covino DA, Farina I, Catapano L, Sozzi S, Spadaro F, Cecchetti S, Purificato C, Gauzzi MC, Fantuzzi L. Induction of the antiviral factors APOBEC3A and RSAD2 upon CCL2 neutralization in primary human macrophages involves NF-κB, JAK/STAT, and gp130 signaling. J Leukoc Biol 2024; 116:876-889. [PMID: 38798090 DOI: 10.1093/jleuko/qiae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The CCL2/CC chemokine receptor 2 axis plays key roles in the pathogenesis of HIV-1 infection. We previously reported that exposure of monocyte-derived macrophages to CCL2 neutralizing antibody (αCCL2 Ab) restricted HIV-1 replication at postentry steps of the viral life cycle. This effect was associated with induction of transcripts coding for innate antiviral proteins, including APOBEC3A and RSAD2. This study aimed at identifying the signaling pathways involved in induction of these factors by CCL2 blocking in monocyte-derived macrophages. Through a combination of pharmacologic inhibition, quantitative reverse transcription polymerase chain reaction, Western blotting, and confocal laser-scanning microscopy, we demonstrated that CCL2 neutralization activates the canonical NF-κB and JAK/STAT pathways, as assessed by time-dependent phosphorylation of IκB, STAT1, and STAT3 and p65 nuclear translocation. Furthermore, pharmacologic inhibition of IκB kinase and JAKs strongly reduced APOBEC3A and RSAD2 transcript accumulation elicited by αCCL2 Ab treatment. Interestingly, exposure of monocyte-derived macrophages to αCCL2 Ab resulted in induction of IL-6 family cytokines, and interference with glycoprotein 130, the common signal-transducing receptor subunit shared by these cytokines, inhibited APOBEC3A and RSAD2 upregulation triggered by CCL2 neutralization. These results provide novel insights into the signal transduction pathways underlying the activation of innate responses triggered by CCL2 neutralization in macrophages. Since this response was found to be associated with protective antiviral effects, the new findings may help design innovative therapeutic approaches targeting CCL2 to strengthen host innate immunity.
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Affiliation(s)
- Daniela Angela Covino
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Iole Farina
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Laura Catapano
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Silvia Sozzi
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Francesca Spadaro
- Core Facilities, Microscopy Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Serena Cecchetti
- Core Facilities, Microscopy Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Cristina Purificato
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Maria Cristina Gauzzi
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Laura Fantuzzi
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
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2
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Dennis M, Hurley A, Bray N, Cordero C, Ilagan J, Mertz TM, Roberts SA. Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells. PLoS Genet 2024; 20:e1011293. [PMID: 38805570 PMCID: PMC11161071 DOI: 10.1371/journal.pgen.1011293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/07/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
APOBEC-induced mutations occur in 50% of sequenced human tumors, with APOBEC3A (A3A) being a major contributor to mutagenesis in breast cancer cells. The mechanisms that cause A3A activation and mutagenesis in breast cancers are still unknown. Here, we describe factors that influence basal A3A mRNA transcript levels in breast cancer cells. We found that basal A3A mRNA correlates with A3A protein levels and predicts the amount of APOBEC signature mutations in a panel of breast cancer cell lines, indicating that increased basal transcription may be one mechanism leading to breast cancer mutagenesis. We also show that alteration of ERBB2 expression can drive A3A mRNA levels, suggesting the enrichment of the APOBEC mutation signature in Her2-enriched breast cancer could in part result from elevated A3A transcription. Hierarchical clustering of transcripts in primary breast cancers determined that A3A mRNA was co-expressed with other genes functioning in viral restriction and interferon responses. However, reduction of STAT signaling via inhibitors or shRNA in breast cancer cell lines had only minor impact on A3A abundance. Analysis of single cell RNA-seq from primary tumors indicated that A3A mRNA was highest in infiltrating immune cells within the tumor, indicating that correlations of A3A with STAT signaling in primary tumors may be result from higher immune infiltrates and are not reflective of STAT signaling controlling A3A expression in breast cancer cells. Analysis of ATAC-seq data in multiple breast cancer cell lines identified two transcription factor sites in the APOBEC3A promoter region that could promote A3A transcription. We determined that Rel-A, and Bach1, which have binding sites in these peaks, elevated basal A3A expression. Our findings highlight a complex and variable set of transcriptional activators for A3A in breast cancer cells.
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Affiliation(s)
- Madeline Dennis
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Alyssa Hurley
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Nicholas Bray
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Cameron Cordero
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Jose Ilagan
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Tony M. Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
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Karakoese Z, Ingola M, Sitek B, Dittmer U, Sutter K. IFNα Subtypes in HIV Infection and Immunity. Viruses 2024; 16:364. [PMID: 38543729 PMCID: PMC10975235 DOI: 10.3390/v16030364] [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: 01/31/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Type I interferons (IFN), immediately triggered following most viral infections, play a pivotal role in direct antiviral immunity and act as a bridge between innate and adaptive immune responses. However, numerous viruses have evolved evasion strategies against IFN responses, prompting the exploration of therapeutic alternatives for viral infections. Within the type I IFN family, 12 IFNα subtypes exist, all binding to the same receptor but displaying significant variations in their biological activities. Currently, clinical treatments for chronic virus infections predominantly rely on a single IFNα subtype (IFNα2a/b). However, the efficacy of this therapeutic treatment is relatively limited, particularly in the context of Human Immunodeficiency Virus (HIV) infection. Recent investigations have delved into alternative IFNα subtypes, identifying certain subtypes as highly potent, and their antiviral and immunomodulatory properties have been extensively characterized. This review consolidates recent findings on the roles of individual IFNα subtypes during HIV and Simian Immunodeficiency Virus (SIV) infections. It encompasses their induction in the context of HIV/SIV infection, their antiretroviral activity, and the diverse regulation of the immune response against HIV by distinct IFNα subtypes. These insights may pave the way for innovative strategies in HIV cure or functional cure studies.
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Affiliation(s)
- Zehra Karakoese
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (Z.K.); (U.D.)
- Institute for the Research on HIV and AIDS-Associated Diseases, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Martha Ingola
- Medical Proteome Center, Ruhr University Bochum, 44801 Bochum, Germany; (M.I.); (B.S.)
| | - Barbara Sitek
- Medical Proteome Center, Ruhr University Bochum, 44801 Bochum, Germany; (M.I.); (B.S.)
- Department of Anesthesia, Intensive Care Medicine and Pain Therapy, University Hospital Knappschaftskrankenhaus Bochum, 44892 Bochum, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (Z.K.); (U.D.)
- Institute for the Research on HIV and AIDS-Associated Diseases, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (Z.K.); (U.D.)
- Institute for the Research on HIV and AIDS-Associated Diseases, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
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4
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Wahl SM. Howard A. Young's 4 Decades in Science: More Than Just Experiments. J Interferon Cytokine Res 2022; 42:611-617. [PMID: 35944271 PMCID: PMC9835286 DOI: 10.1089/jir.2022.0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 04/24/2022] [Indexed: 01/21/2023] Open
Affiliation(s)
- Sharon M. Wahl
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
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5
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Wittling MC, Cahalan SR, Levenson EA, Rabin RL. Shared and Unique Features of Human Interferon-Beta and Interferon-Alpha Subtypes. Front Immunol 2021; 11:605673. [PMID: 33542718 PMCID: PMC7850986 DOI: 10.3389/fimmu.2020.605673] [Citation(s) in RCA: 18] [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: 09/12/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Type I interferons (IFN-I) were first discovered as an antiviral factor by Isaacs and Lindenmann in 1957, but they are now known to also modulate innate and adaptive immunity and suppress proliferation of cancer cells. While much has been revealed about IFN-I, it remains a mystery as to why there are 16 different IFN-I gene products, including IFNβ, IFNω, and 12 subtypes of IFNα. Here, we discuss shared and unique aspects of these IFN-I in the context of their evolution, expression patterns, and signaling through their shared heterodimeric receptor. We propose that rather than investigating responses to individual IFN-I, these contexts can serve as an alternative approach toward investigating roles for IFNα subtypes. Finally, we review uses of IFNα and IFNβ as therapeutic agents to suppress chronic viral infections or to treat multiple sclerosis.
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Affiliation(s)
| | | | | | - Ronald L. Rabin
- Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
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Expression of APOBEC family members as regulators of endogenous retroelements and malignant transformation in systemic autoimmunity. Clin Immunol 2020; 223:108649. [PMID: 33326823 DOI: 10.1016/j.clim.2020.108649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To explore whether APOBEC family members are involved in the response to inappropriate expression of L1 retroelements in primary Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE), as well as in SS related lymphomagenesis. METHODS Minor salivary glands (MSG) and kidney biopsy (KB) specimens were obtained from 41 SS patients (10 with lymphoma) and 23 patients with SLE, respectively. PBMC and sera were also collected from 73 SLE patients. Full-length L1 transcripts, members of the APOBEC and IFN family were quantitated by real time PCR. Type I IFN activity was assessed in lupus plasma by a cell assay. RESULTS APOBEC3A was increased in SS MSG, SLE KB and PBMC and correlated with L1. AID and APOBEC3G were particularly overexpressed in MSG tissues derived from SS lymphoma patients. CONCLUSION These data reveal a previously unappreciated role of APOBEC family proteins in the pathogenesis of systemic autoimmunity and SS related lymphomagenesis.
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7
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Paul A, Sil J. Identification of Differentially Expressed Genes to Establish New Biomarker for Cancer Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1970-1985. [PMID: 29994718 DOI: 10.1109/tcbb.2018.2837095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The goal of the human genome project is to integrate genetic information into different clinical therapies. To achieve this goal, different computational algorithms are devised for identifying the biomarker genes, cause of complex diseases. However, most of the methods developed so far using DNA microarray data lack in interpreting biological findings and are less accurate in disease prediction. In the paper, we propose two parameters risk_factor and confusion_factor to identify the biologically significant genes for cancer development. First, we evaluate risk_factor of each gene and the genes with nonzero risk_factor result misclassification of data, therefore removed. Next, we calculate confusion_factor of the remaining genes which determines confusion of a gene in prediction due to closeness of the samples in the cancer and normal classes. We apply nondominated sorting genetic algorithm (NSGA-II) to select the maximally uncorrelated differentially expressed genes in the cancer class with minimum confusion_factor. The proposed Gene Selection Explore (GSE) algorithm is compared to well established feature selection algorithms using 10 microarray data with respect to sensitivity, specificity, and accuracy. The identified genes appear in KEGG pathway and have several biological importance.
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Li Y, Sun B, Esser S, Jessen H, Streeck H, Widera M, Yang R, Dittmer U, Sutter K. Expression Pattern of Individual IFNA Subtypes in Chronic HIV Infection. J Interferon Cytokine Res 2018; 37:541-549. [PMID: 29252127 DOI: 10.1089/jir.2017.0076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Interferon-α (IFN-α) plays an important role in HIV pathogenesis. IFN-α consists of 13 individual IFN-α subtypes, which exhibit individual antiviral and immunomodulatory activities in HIV infection. Here, we determined the expression profiles of all IFN-α subtypes in treated and treatment-naive HIV+ patients and their impact on the induction of distinct HIV restriction factors. We collected blood samples of chronic HIV+ patients, which underwent antiretroviral therapy or were treatment-naive, and determined the individual expression levels of different IFN-α subtypes and HIV restriction factors. HIV infection transiently enhanced the expression of IFNA mRNA. The IFN-α response was dominated by the most abundantly expressed subtypes IFNA4, A5, A7, and A14 in all individuals. HIV infection affected the expression pattern of the IFN-α response, in particular for IFNA2 and IFNA16, which were elevated by chronic HIV infection. Elevated expression of HIV restriction factors was observed in chronically HIV-infected patients, which partly decreased during successful antiretroviral treatment. In vitro stimulation of peripheral blood mononuclear cells revealed that IFN-α6, -α14, and -α21 were most effective in inducing the expression of HIV restriction factors. These results indicate that HIV infection induces a specific expression pattern of IFN-α subtypes, which in turn induce the expression of various HIV restriction factors.
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Affiliation(s)
- Yanpeng Li
- 1 Wuhan Institute of Virology , Chinese Academy of Sciences, Wuhan, PR China
| | - Binlian Sun
- 1 Wuhan Institute of Virology , Chinese Academy of Sciences, Wuhan, PR China
| | - Stefan Esser
- 2 Clinic of Dermatology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | | | - Hendrik Streeck
- 4 Institute for HIV Research, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Marek Widera
- 5 Institute for Virology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Rongge Yang
- 1 Wuhan Institute of Virology , Chinese Academy of Sciences, Wuhan, PR China
| | - Ulf Dittmer
- 5 Institute for Virology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Kathrin Sutter
- 5 Institute for Virology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
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9
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Abraham S, Choi JG, Ortega NM, Zhang J, Shankar P, Swamy NM. Gene therapy with plasmids encoding IFN-β or IFN-α14 confers long-term resistance to HIV-1 in humanized mice. Oncotarget 2018; 7:78412-78420. [PMID: 27729616 PMCID: PMC5346649 DOI: 10.18632/oncotarget.12512] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/02/2016] [Indexed: 01/31/2023] Open
Abstract
Because endogenous interferon type I (IFN-I) produced by HIV-1 infection might complicate the analysis of therapeutically administered IFN-I, we tested different humanized mouse models for induction of IFN-I during HIV-1 infection. While HIV-1 induced high levels of IFN-α in BLT mice, IFN-I was undetectable following infection in the Hu-PBL mouse model, in which only T cells expand. We therefore tested the effect of treatment with Pegylated IFN-2 (pegasys), in Hu-PBL mice. Pegasys prevented CD4 T cell depletion and reduced the viral load for 10 days, but the effect waned thereafter. We next expressed IFN-I subsets (IFN-α2, −α6, −α8, −α14, and −β) in Hu-PBL mice by hydrodynamic injection of plasmids encoding them and 2 days later infected the mice with HIV-1. CD4 T cell depletion was prevented in all subtypes of IFN-I-expressing mice by day 10. However, at day 40 post-infection, protection was seen in IFN-β- and IFN-α14-expressing mice, but not the others. The viral load followed an inverse pattern and was highest in control mice and lowest in IFN-β- and IFN-α14-expressing mice until day 40 after infection. These results show that gene therapy with plasmids encoding IFN-β and −α14, but not the commonly used −α2, confers long-term suppression of HIV-1 replication.
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Affiliation(s)
- Sojan Abraham
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Jang-Gi Choi
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA.,KM Application Center, Korea Institute of Oriental Medicine, Dong-gu, Daegu, Republic of Korea
| | - Nora M Ortega
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Junli Zhang
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Premlata Shankar
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - N Manjunath Swamy
- Center of Emphasis in Infectious Disease, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
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10
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Interferon α subtypes in HIV infection. Cytokine Growth Factor Rev 2018; 40:13-18. [PMID: 29475588 DOI: 10.1016/j.cytogfr.2018.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/09/2018] [Accepted: 02/09/2018] [Indexed: 02/06/2023]
Abstract
Type I interferons (IFN), which are immediately induced after most virus infections, are central for direct antiviral immunity and link innate and adaptive immune responses. However, several viruses have evolved strategies to evade the IFN response by preventing IFN induction or blocking IFN signaling pathways. Thus, therapeutic application of exogenous type I IFN or agonists inducing type I IFN responses are a considerable option for future immunotherapies against chronic viral infections. An important part of the type I IFN family are 12 IFNα subtypes, which all bind the same receptor, but significantly differ in their biological activities. Up to date only one IFNα subtype (IFNα2) is being used in clinical treatment against chronic virus infections, however its therapeutic success rate is rather limited, especially during Human Immunodeficiency Virus (HIV) infection. Recent studies addressed the important question if other IFNα subtypes would be more potent against retroviral infections in in vitro and in vivo experiments. Indeed, very potent IFNα subtypes were defined and their antiviral and immunomodulatory properties were characterized. In this review we summarize the recent findings on the role of individual IFNα subtypes during HIV and Simian Immunodeficiency Virus infection. This includes their induction during HIV/SIV infection, their antiretroviral activity and the regulation of immune response against HIV by different IFNα subtypes. The findings might facilitate novel strategies for HIV cure or functional cure studies.
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Covino DA, Gauzzi MC, Fantuzzi L. Understanding the regulation of APOBEC3 expression: Current evidence and much to learn. J Leukoc Biol 2017; 103:433-444. [DOI: 10.1002/jlb.2mr0717-310r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/28/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
| | | | - Laura Fantuzzi
- National Center for Global Health; Istituto Superiore di Sanità; Rome Italy
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12
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Chen C, Zhu X, Xu W, Yang F, Zhang G, Wu L, Zheng Y, Gao Z, Xie C, Peng L. IFNA2 p.Ala120Thr impairs the inhibitory activity of Interferon-α2 against the hepatitis B virus through altering its binding to the receptor. Antiviral Res 2017; 147:11-18. [PMID: 28958921 DOI: 10.1016/j.antiviral.2017.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/03/2017] [Accepted: 09/22/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Our previous study found that a rare genetic mutation IFNA2p.Ala120Thr affects the structure of IFN-α2 and contributes to increased host susceptibility to CHB. However, the way in which the single amino acid residue mutation affects IFN-α2 activity is unclear. The purpose of this research was to investigate the effects and mechanisms of IFNA2p.Ala120Thr on IFN-α2 activity. METHODS Plasmid transfection of BL-21 was used to construct both wild type IFNA2 (wt) and p.Ala120Thr IFNA2 (mut) proteins. The HepG2-NTCP model was established using a lentiviral vector (LV003). Anti-HBV activity of wt and mut were tested on HepG2-NTCP infected cells with HBV, through the detection of HBsAg and HBcAg using immunohistochemistry and by detecting HBV DNA with RT PCR. IF and Co-IP were performed in order to investigate the binding of the IFNA2 protein and its receptor. The changes in IFNAR density and signal molecule phosphorylation were measured with western blotting. We used qPCR to further explore anti-HBV protein expression including APOBEC3, MxA, OAS1, and PKR. RESULTS Cell model experiments confirmed that IFNA2p.Ala120Thr impairs anti-HBV activity of IFN-α2. Co-IP tests indicated that the binding of mut-IFNα to IFNR was weaker in the mut-treated group. IFNR density on the cells surface increased after treatment with wt-IFN-α2. Obvious differences in the STAT phosphorylation profiles were seen between the mut-treated and wt-treated groups. The expression of four main kinds of anti-HBV proteins induced by mut was higher in the HepG2-NTCP cells. Thus, IFNA2p.Ala120Thr affects anti-HBV activity of IFN-α2. CONCLUSION IFNA2p.Ala120Thr impairs the anti-HBV ability of IFN-a2, mainly by reducing its binding to the IFN receptor. Mut IFN-a2 has a very weak binding, barely inducing STAT phosphorylation, and induces the expression of only a low level of related anti-HBV ISG. This is quite different from the effects of wt IFN-a2, implying that modifying the key structural position of IFNa may lead to the modulation of targeted gene expression.
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Affiliation(s)
- Chuming Chen
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Department of Infectious Diseases, Third People's Hospital of Shenzhen, Shenzhen, Guangdong, China
| | - Xiang Zhu
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenxiong Xu
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fangji Yang
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Genglin Zhang
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lina Wu
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongyuan Zheng
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhiliang Gao
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chan Xie
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Liang Peng
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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Hieke S, Benner A, Schlenl RF, Schumacher M, Bullinger L, Binder H. Integrating multiple molecular sources into a clinical risk prediction signature by extracting complementary information. BMC Bioinformatics 2016; 17:327. [PMID: 27578050 PMCID: PMC5004308 DOI: 10.1186/s12859-016-1183-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 08/12/2016] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND High-throughput technology allows for genome-wide measurements at different molecular levels for the same patient, e.g. single nucleotide polymorphisms (SNPs) and gene expression. Correspondingly, it might be beneficial to also integrate complementary information from different molecular levels when building multivariable risk prediction models for a clinical endpoint, such as treatment response or survival. Unfortunately, such a high-dimensional modeling task will often be complicated by a limited overlap of molecular measurements at different levels between patients, i.e. measurements from all molecular levels are available only for a smaller proportion of patients. RESULTS We propose a sequential strategy for building clinical risk prediction models that integrate genome-wide measurements from two molecular levels in a complementary way. To deal with partial overlap, we develop an imputation approach that allows us to use all available data. This approach is investigated in two acute myeloid leukemia applications combining gene expression with either SNP or DNA methylation data. After obtaining a sparse risk prediction signature e.g. from SNP data, an automatically selected set of prognostic SNPs, by componentwise likelihood-based boosting, imputation is performed for the corresponding linear predictor by a linking model that incorporates e.g. gene expression measurements. The imputed linear predictor is then used for adjustment when building a prognostic signature from the gene expression data. For evaluation, we consider stability, as quantified by inclusion frequencies across resampling data sets. Despite an extremely small overlap in the application example with gene expression and SNPs, several genes are seen to be more stably identified when taking the (imputed) linear predictor from the SNP data into account. In the application with gene expression and DNA methylation, prediction performance with respect to survival also indicates that the proposed approach might work well. CONCLUSIONS We consider imputation of linear predictor values to be a feasible and sensible approach for dealing with partial overlap in complementary integrative analysis of molecular measurements at different levels. More generally, these results indicate that a complementary strategy for integrating different molecular levels can result in more stable risk prediction signatures, potentially providing a more reliable insight into the underlying biology.
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Affiliation(s)
- Stefanie Hieke
- Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Stefan-Meier-Str. 26, Freiburg, 79104, Germany. .,Freiburg Center for Data Analysis and Modeling, University Freiburg, Eckerstr. 1, Freiburg, 79104, Germany.
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Richard F Schlenl
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Ulm, 89081, Germany
| | - Martin Schumacher
- Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Stefan-Meier-Str. 26, Freiburg, 79104, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital of Ulm, Albert-Einstein-Allee 23, Ulm, 89081, Germany
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Johannes Gutenberg University Mainz, Obere Zahlbacher Str. 69, Mainz, 55131, Germany
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14
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AID/APOBEC-network reconstruction identifies pathways associated with survival in ovarian cancer. BMC Genomics 2016; 17:643. [PMID: 27527602 PMCID: PMC4986275 DOI: 10.1186/s12864-016-3001-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/08/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Building up of pathway-/disease-relevant signatures provides a persuasive tool for understanding the functional relevance of gene alterations and gene network associations in multifactorial human diseases. Ovarian cancer is a highly complex heterogeneous malignancy in respect of tumor anatomy, tumor microenvironment including pro-/antitumor immunity and inflammation; still, it is generally treated as single disease. Thus, further approaches to investigate novel aspects of ovarian cancer pathogenesis aiming to provide a personalized strategy to clinical decision making are of high priority. Herein we assessed the contribution of the AID/APOBEC family and their associated genes given the remarkable ability of AID and APOBECs to edit DNA/RNA, and as such, providing tools for genetic and epigenetic alterations potentially leading to reprogramming of tumor cells, stroma and immune cells. RESULTS We structured the study by three consecutive analytical modules, which include the multigene-based expression profiling in a cohort of patients with primary serous ovarian cancer using a self-created AID/APOBEC-associated gene signature, building up of multivariable survival models with high predictive accuracy and nomination of top-ranked candidate/target genes according to their prognostic impact, and systems biology-based reconstruction of the AID/APOBEC-driven disease-relevant mechanisms using transcriptomics data from ovarian cancer samples. We demonstrated that inclusion of the AID/APOBEC signature-based variables significantly improves the clinicopathological variables-based survival prognostication allowing significant patient stratification. Furthermore, several of the profiling-derived variables such as ID3, PTPRC/CD45, AID, APOBEC3G, and ID2 exceed the prognostic impact of some clinicopathological variables. We next extended the signature-/modeling-based knowledge by extracting top genes co-regulated with target molecules in ovarian cancer tissues and dissected potential networks/pathways/regulators contributing to pathomechanisms. We thereby revealed that the AID/APOBEC-related network in ovarian cancer is particularly associated with remodeling/fibrotic pathways, altered immune response, and autoimmune disorders with inflammatory background. CONCLUSIONS The herein study is, to our knowledge, the first one linking expression of entire AID/APOBECs and interacting genes with clinical outcome with respect to survival of cancer patients. Overall, data propose a novel AID/APOBEC-derived survival model for patient risk assessment and reconstitute mapping to molecular pathways. The established study algorithm can be applied further for any biologically relevant signature and any type of diseased tissue.
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15
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Interferon Alpha Subtype-Specific Suppression of HIV-1 Infection In Vivo. J Virol 2016; 90:6001-6013. [PMID: 27099312 DOI: 10.1128/jvi.00451-16] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/13/2016] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Although all 12 subtypes of human interferon alpha (IFN-α) bind the same receptor, recent results have demonstrated that they elicit unique host responses and display distinct efficacies in the control of different viral infections. The IFN-α2 subtype is currently in HIV-1 clinical trials, but it has not consistently reduced viral loads in HIV-1 patients and is not the most effective subtype against HIV-1 in vitro We now demonstrate in humanized mice that, when delivered at the same high clinical dose, the human IFN-α14 subtype has very potent anti-HIV-1 activity whereas IFN-α2 does not. In both postexposure prophylaxis and treatment of acute infections, IFN-α14, but not IFN-α2, significantly suppressed HIV-1 replication and proviral loads. Furthermore, HIV-1-induced immune hyperactivation, which is a prognosticator of disease progression, was reduced by IFN-α14 but not IFN-α2. Whereas ineffective IFN-α2 therapy was associated with CD8(+) T cell activation, successful IFN-α14 therapy was associated with increased intrinsic and innate immunity, including significantly higher induction of tetherin and MX2, increased APOBEC3G signature mutations in HIV-1 proviral DNA, and higher frequencies of TRAIL(+) NK cells. These results identify IFN-α14 as a potent new therapeutic that operates via mechanisms distinct from those of antiretroviral drugs. The ability of IFN-α14 to reduce both viremia and proviral loads in vivo suggests that it has strong potential as a component of a cure strategy for HIV-1 infections. The broad implication of these results is that the antiviral efficacy of each individual IFN-α subtype should be evaluated against the specific virus being treated. IMPORTANCE The naturally occurring antiviral protein IFN-α2 is used to treat hepatitis viruses but has proven rather ineffective against HIV in comparison to triple therapy with the antiretroviral (ARV) drugs. Although ARVs suppress the replication of HIV, they fail to completely clear infections. Since IFN-α acts by different mechanism than ARVs and has been shown to reduce HIV proviral loads, clinical trials are under way to test whether IFN-α2 combined with ARVs might eradicate HIV-1 infections. IFN-α is actually a family of 12 distinct proteins, and each IFN-α subtype has different efficacies toward different viruses. Here, we use mice that contain a human immune system, so they can be infected with HIV. With this model, we demonstrate that while IFN-α2 is only weakly effective against HIV, IFN-α14 is extremely potent. This discovery identifies IFN-α14 as a more powerful IFN-α subtype for use in combination therapy trials aimed toward an HIV cure.
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16
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Harper MS, Guo K, Gibbert K, Lee EJ, Dillon SM, Barrett BS, McCarter MD, Hasenkrug KJ, Dittmer U, Wilson CC, Santiago ML. Interferon-α Subtypes in an Ex Vivo Model of Acute HIV-1 Infection: Expression, Potency and Effector Mechanisms. PLoS Pathog 2015; 11:e1005254. [PMID: 26529416 PMCID: PMC4631339 DOI: 10.1371/journal.ppat.1005254] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/08/2015] [Indexed: 02/07/2023] Open
Abstract
HIV-1 is transmitted primarily across mucosal surfaces and rapidly spreads within the intestinal mucosa during acute infection. The type I interferons (IFNs) likely serve as a first line of defense, but the relative expression and antiviral properties of the 12 IFNα subtypes against HIV-1 infection of mucosal tissues remain unknown. Here, we evaluated the expression of all IFNα subtypes in HIV-1-exposed plasmacytoid dendritic cells by next-generation sequencing. We then determined the relative antiviral potency of each IFNα subtype ex vivo using the human intestinal Lamina Propria Aggregate Culture model. IFNα subtype transcripts from the centromeric half of the IFNA gene complex were highly expressed in pDCs following HIV-1 exposure. There was an inverse relationship between IFNA subtype expression and potency. IFNα8, IFNα6 and IFNα14 were the most potent in restricting HIV-1 infection. IFNα2, the clinically-approved subtype, and IFNα1 were both highly expressed but exhibited relatively weak antiviral activity. The relative potencies correlated with binding affinity to the type I IFN receptor and the induction levels of HIV-1 restriction factors Mx2 and Tetherin/BST-2 but not APOBEC3G, F and D. However, despite the lack of APOBEC3 transcriptional induction, the higher relative potency of IFNα8 and IFNα14 correlated with stronger inhibition of virion infectivity, which is linked to deaminase-independent APOBEC3 restriction activity. By contrast, both potent (IFNα8) and weak (IFNα1) subtypes significantly induced HIV-1 GG-to-AG hypermutation. The results unravel non-redundant functions of the IFNα subtypes against HIV-1 infection, with strong implications for HIV-1 mucosal immunity, viral evolution and IFNα-based functional cure strategies.
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Affiliation(s)
- Michael S. Harper
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Kejun Guo
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Kathrin Gibbert
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Eric J. Lee
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Stephanie M. Dillon
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Bradley S. Barrett
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Martin D. McCarter
- Department of Surgery, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- * E-mail: (UD); (CCW); (MLS)
| | - Cara C. Wilson
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail: (UD); (CCW); (MLS)
| | - Mario L. Santiago
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail: (UD); (CCW); (MLS)
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17
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Barrenas F, Palermo RE, Agricola B, Agy MB, Aicher L, Carter V, Flanary L, Green RR, McLain R, Li Q, Lu W, Murnane R, Peng X, Thomas MJ, Weiss JM, Anderson DM, Katze MG. Deep transcriptional sequencing of mucosal challenge compartment from rhesus macaques acutely infected with simian immunodeficiency virus implicates loss of cell adhesion preceding immune activation. J Virol 2014; 88:7962-72. [PMID: 24807713 PMCID: PMC4097788 DOI: 10.1128/jvi.00543-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/25/2014] [Indexed: 12/27/2022] Open
Abstract
Pathology resulting from human immunodeficiency virus (HIV) infection is driven by protracted inflammation; the primary loss of CD4(+) T cells is caused by activation-driven apoptosis. Recent studies of nonhuman primates (NHPs) have suggested that during the acute phase of infection, antiviral mucosal immunity restricts viral replication in the primary infection compartment. These studies imply that HIV achieves systemic infection as a consequence of a failure in host antiviral immunity. Here, we used high-dose intrarectal inoculation of rhesus macaques with simian immunodeficiency virus (SIV) SIVmac251 to examine how the mucosal immune system is overcome by SIV during acute infection. The host response in rectal mucosa was characterized by deep mRNA sequencing (mRNA-seq) at 3 and 12 days postinoculation (dpi) in 4 animals for each time point. While we observed a strong host transcriptional response at 3 dpi, functions relating to antiviral immunity were absent. Instead, we observed a significant number of differentially expressed genes relating to cell adhesion and reorganization of the cytoskeleton. We also observed downregulation of genes encoding members of the claudin family of cell adhesion molecules, which are coexpressed with genes associated with pathology in the colorectal mucosa, and a large number of noncoding transcripts. In contrast, at 12 dpi the differentially expressed genes were enriched in those involved with immune system functions, in particular, functions relating to T cells, B cells, and NK cells. Our findings indicate that host responses that negatively affect mucosal integrity occur before inflammation. Consequently, when inflammation is activated at peak viremia, mucosal integrity is already compromised, potentially enabling rapid tissue damage, driving further inflammation. Importance: The HIV pandemic is one of the major threats to human health, causing over a million deaths per year. Recent studies have suggested that mucosal antiviral immune responses play an important role in preventing systemic infection after exposure to the virus. Yet, despite their potential role in decreasing transmission rates between individuals, these antiviral mechanisms are poorly understood. Here, we carried out the first deep mRNA sequencing analysis of mucosal host responses in the primary infection compartment during acute SIV infection. We found that during acute infection, a significant host response was mounted in the mucosa before inflammation was triggered. Our analysis indicated that the response has a detrimental effect on tissue integrity, causing increased permeability, tissue damage, and recruitment of SIV target cells. These results emphasize the importance of mucosal host responses preceding immune activation in preventing systemic SIV infection.
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Affiliation(s)
- Fredrik Barrenas
- Department of Microbiology, University of Washington, Seattle, Washington, USA Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Robert E Palermo
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Brian Agricola
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Michael B Agy
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Lauri Aicher
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Victoria Carter
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Leon Flanary
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Richard R Green
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Randy McLain
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Wuxun Lu
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Robert Murnane
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Xinxia Peng
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Matthew J Thomas
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - David M Anderson
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, Washington, USA Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
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18
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Verhoeven D, George MD, Hu W, Dang AT, Smit-McBride Z, Reay E, Macal M, Fenton A, Sankaran-Walters S, Dandekar S. Enhanced innate antiviral gene expression, IFN-α, and cytolytic responses are predictive of mucosal immune recovery during simian immunodeficiency virus infection. THE JOURNAL OF IMMUNOLOGY 2014; 192:3308-18. [PMID: 24610016 DOI: 10.4049/jimmunol.1302415] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mucosa that lines the respiratory and gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the first line of innate immune defense against infections. Although an abundance of memory CD4(+) T cells at mucosal sites render them highly susceptible to HIV infection, the gut and not the lung experiences severe and sustained CD4(+) T cell depletion and tissue disruption. We hypothesized that distinct immune responses in the lung and gut during the primary and chronic stages of viral infection contribute to these differences. Using the SIV model of AIDS, we performed a comparative analysis of the molecular and cellular characteristics of host responses in the gut and lung. Our findings showed that both mucosal compartments harbor similar percentages of memory CD4(+) T cells and displayed comparable cytokine (IL-2, IFN-γ, and TNF-α) responses to mitogenic stimulations prior to infection. However, despite similar viral replication and CD4(+) T cell depletion during primary SIV infection, CD4(+) T cell restoration kinetics in the lung and gut diverged during acute viral infection. The CD4(+) T cells rebounded or were preserved in the lung mucosa during chronic viral infection, which correlated with heightened induction of type I IFN signaling molecules and innate viral restriction factors. In contrast, the lack of CD4(+) T cell restoration in the gut was associated with dampened immune responses and diminished expression of viral restriction factors. Thus, unique immune mechanisms contribute to the differential response and protection of pulmonary versus GI mucosa and can be leveraged to enhance mucosal recovery.
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Affiliation(s)
- David Verhoeven
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616
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19
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Roberts SA, Gordenin DA. Clustered and genome-wide transient mutagenesis in human cancers: Hypermutation without permanent mutators or loss of fitness. Bioessays 2014; 36:382-393. [PMID: 24615916 DOI: 10.1002/bies.201300140] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The gain of a selective advantage in cancer as well as the establishment of complex traits during evolution require multiple genetic alterations, but how these mutations accumulate over time is currently unclear. There is increasing evidence that a mutator phenotype perpetuates the development of many human cancers. While in some cases the increased mutation rate is the result of a genetic disruption of DNA repair and replication or environmental exposures, other evidence suggests that endogenous DNA damage induced by AID/APOBEC cytidine deaminases can result in transient localized hypermutation generating simultaneous, closely spaced (i.e. "clustered") multiple mutations. Here, we discuss mechanisms that lead to mutation cluster formation, the biological consequences of their formation in cancer and evidence suggesting that APOBEC mutagenesis can also occur genome-wide. This raises the possibility that dysregulation of these enzymes may enable rapid malignant transformation by increasing mutation rates without the loss of fitness associated with permanent mutators.
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Affiliation(s)
- Steven A Roberts
- Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Durham, NC, USA
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20
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Mavragani CP, Niewold TB, Chatzigeorgiou A, Danielides S, Thomas D, Kirou KA, Kamper E, Kaltsas G, Crow MK. Increased serum type I interferon activity in organ-specific autoimmune disorders: clinical, imaging, and serological associations. Front Immunol 2013; 4:238. [PMID: 23966997 PMCID: PMC3746787 DOI: 10.3389/fimmu.2013.00238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/02/2013] [Indexed: 01/27/2023] Open
Abstract
Background: Activation of the type I interferon (IFN) pathway has been implicated in the pathogenesis of systemic autoimmune disorders but its role in the pathogenesis of organ-specific autoimmunity is limited. We tested the hypothesis that endogenous expression of type I IFN functional activity contributes to the pathogenesis of autoimmune thyroid disease (ATD) and type I diabetes (T1DM). Methods: We studied 39 patients with ATD and 39 age and sex matched controls along with 88 T1DM patients and 46 healthy matched controls respectively. Available clinical and serological parameters were recorded by chart review, and thyroid ultrasound was performed in 17 ATD patients. Type I IFN serum activity was determined in all subjects using a reporter cell assay. The rs1990760 SNP of the interferon-induced helicase 1 gene was genotyped in ATD patients. Results: Serum type I IFN activity was increased in patients with ATD and T1DM compared to controls (p-values: 0.002 and 0.04, respectively). ATD patients with high type I IFN serum activity had increased prevalence of antibodies against thyroglobulin (anti-Tg) and cardiopulmonary manifestations compared to those with low IFN activity. Additionally, the presence of micronodules on thyroid ultrasound was associated with higher type I IFN levels. In patients with T1DM, high IFN levels were associated with increased apolipoprotein-B levels. Conclusion: Serum type I IFN activity is increased in ATD and T1DM and is associated with specific clinical, serological, and imaging features. These findings may implicate type I IFN pathway in the pathogenesis of specific features of organ-specific autoimmunity.
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Affiliation(s)
- Clio P Mavragani
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery , New York, NY , USA ; Department of Physiology, School of Medicine, University of Athens , Athens , Greece
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21
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Gibbert K, Schlaak JF, Yang D, Dittmer U. IFN-α subtypes: distinct biological activities in anti-viral therapy. Br J Pharmacol 2013; 168:1048-58. [PMID: 23072338 PMCID: PMC3594665 DOI: 10.1111/bph.12010] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/15/2012] [Accepted: 09/07/2012] [Indexed: 12/12/2022] Open
Abstract
During most viral infections, the immediate host response is characterized by an induction of type I IFN. These cytokines have various biological activities, including anti-viral, anti-proliferative and immunomodulatory effects. After induction, they bind to their IFN-α/β receptor, which leads to downstream signalling resulting in the expression of numerous different IFN-stimulated genes. These genes encode anti-viral proteins that directly inhibit viral replication as well as modulate immune function. Thus, the induction of type I IFN is a very powerful tool for the host to fight virus infections. Many viruses evade this response by various strategies like the direct suppression of IFN induction or inhibition of the IFN signalling pathway. Therefore, the therapeutic application of exogenous type I IFN or molecules that induce strong IFN responses should be of great potential for future immunotherapies against viral infections. Type I IFN is currently used as a treatment in chronic hepatitis B and C virus infection, but as yet is not widely utilized for other viral infections. One reason for this restricted clinical use is that type I IFN belongs to a multigene family that includes 13 different IFN-α subtypes and IFN-β, whose individual anti-viral and immunomodulatory properties have so far not been investigated in detail to improve IFN therapy against viral infections in humans. In this review, we summarize the recent achievements in defining the distinct biological functions of type I IFN subtypes in cell culture and in animal models of viral infection as well as their clinical usage in chronic hepatitis virus infections.
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Affiliation(s)
- K Gibbert
- Department of Virology, University Hospital Essen, Essen, Germany.
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22
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Harper MS, Barrett BS, Smith DS, Li SX, Gibbert K, Dittmer U, Hasenkrug KJ, Santiago ML. IFN-α treatment inhibits acute Friend retrovirus replication primarily through the antiviral effector molecule Apobec3. THE JOURNAL OF IMMUNOLOGY 2013; 190:1583-90. [PMID: 23315078 DOI: 10.4049/jimmunol.1202920] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Therapeutic administration of IFN-α in clinical trials significantly reduced HIV-1 plasma viral load and human T-lymphotropic virus type I proviral load in infected patients. The mechanism may involve the concerted action of multiple antiretroviral effectors collectively known as "restriction factors," which could vary in relative importance according to the magnitude of transcriptional induction. However, direct genetic approaches to identify the relevant IFN-α restriction factors will not be feasible in humans in vivo. Meanwhile, mice encode an analogous set of restriction factor genes and could be used to obtain insights on how IFN-α could inhibit retroviruses in vivo. As expected, IFN-α treatment of mice significantly upregulated the transcription of multiple restriction factors including Tetherin/BST2, SAMHD1, Viperin, ISG15, OAS1, and IFITM3. However, a dominant antiretroviral factor, Apobec3, was only minimally induced. To determine whether Apobec3 was necessary for direct IFN-α antiretroviral action in vivo, wild-type and Apobec3-deficient mice were infected with Friend retrovirus, then treated with IFN-α. Treatment of infected wild-type mice with IFN-α significantly reduced acute plasma viral load 28-fold, splenic proviral load 5-fold, bone marrow proviral load 14-fold, and infected bone marrow cells 7-fold, but no inhibition was observed in Apobec3-deficient mice. These findings reveal that IFN-α inhibits acute Friend retrovirus infection primarily through the antiviral effector Apobec3 in vivo, demonstrate that transcriptional induction levels did not predict the mechanism of IFN-α-mediated control, and highlight the potential of the human APOBEC3 proteins as therapeutic targets against pathogenic retrovirus infections.
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Affiliation(s)
- Michael S Harper
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
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23
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Piehler J, Thomas C, Garcia KC, Schreiber G. Structural and dynamic determinants of type I interferon receptor assembly and their functional interpretation. Immunol Rev 2012; 250:317-34. [PMID: 23046138 PMCID: PMC3986811 DOI: 10.1111/imr.12001] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Type I interferons (IFNs) form a network of homologous cytokines that bind to a shared, heterodimeric cell surface receptor and engage signaling pathways that activate innate and adaptive immune responses. The ability of IFNs to mediate differential responses through the same cell surface receptor has been subject of a controversial debate and has important medical implications. During the past decade, a comprehensive insight into the structure, energetics, and dynamics of IFN recognition by its two-receptor subunits, as well as detailed correlations with their functional properties on the level of signal activation, gene expression, and biological responses were obtained. All type I IFNs bind the two-receptor subunits at the same sites and form structurally very similar ternary complexes. Differential IFN activities were found to be determined by different lifetimes and ligand affinities toward the receptor subunits, which dictate assembly and dynamics of the signaling complex in the plasma membrane. We present a simple model, which explains differential IFN activities based on rapid endocytosis of signaling complexes and negative feedback mechanisms interfering with ternary complex assembly. More insight into signaling pathways as well as endosomal signaling and trafficking will be required for a comprehensive understanding, which will eventually lead to therapeutic applications of IFNs with increased efficacy.
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Affiliation(s)
- Jacob Piehler
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Christoph Thomas
- Departments of Molecular and Cellular Physiology, and Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - K. Christopher Garcia
- Departments of Molecular and Cellular Physiology, and Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Gideon Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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Zaritsky LA, Dery A, Leong WY, Gama L, Clements JE. Tissue-specific interferon alpha subtype response to SIV infection in brain, spleen, and lung. J Interferon Cytokine Res 2012; 33:24-33. [PMID: 23050948 DOI: 10.1089/jir.2012.0018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Interferon alpha (IFNalpha) is a type I interferon that plays a major role in host defense. There are 13 different IFNalpha genes in humans, but much of the work concerning their role in viral defense has been limited to studying either subtype 2 or pan IFNalpha due to the inability to distinguish between highly similar genetic and amino acid sequences. Because of recent advances in molecular and biochemical techniques, it is possible to study the regulation of individual subtypes. It has been reported that HIV/SIV infection results in impaired IFNalpha responses in certain tissues. Using a pigtailed macaque SIV model, we examined the subtype response during acute infection in 3 tissues that are known to be infected with HIV/SIV, but whose IFNalpha subtype response has not been extensively studied: the brain, spleen, and lung. We found that the expression and regulation of specific subtypes occur in a tissue-specific manner. There was more limited IFNalpha subtype expression in the lung and brain, where predominantly macrophages are infected compared to the spleen, which contains both infected CD4+ lymphocytes and macrophages. Understanding the IFNalpha subtype response in tissues known to be infected with HIV/SIV can help tailor adjunctive treatment regimens to highly active antiretroviral therapy.
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Affiliation(s)
- Luna Alammar Zaritsky
- Department of Molecular, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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25
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Abstract
Acquired immune deficiency syndrome (AIDS) was first described 30 years ago in a report from the US Centers for Disease Control. Two years later the causative virus was identified and afterwards named the human immunodeficiency virus (HIV). This article reviews the progress made in the three decades since the recognition of AIDS and the discovery of HIV, with respect to the virus, the infected cell, and the host, as well as directions for future studies.
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Affiliation(s)
- M Scott Killian
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143-1270, USA
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