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Oliva H, Pacheco R, Martinez-Navio JM, Rodríguez-García M, Naranjo-Gómez M, Climent N, Prado C, Gil C, Plana M, García F, Miró JM, Franco R, Borras FE, Navaratnam N, Gatell JM, Gallart T. Increased expression with differential subcellular location of cytidine deaminase APOBEC3G in human CD4(+) T-cell activation and dendritic cell maturation. Immunol Cell Biol 2016; 94:689-700. [PMID: 26987686 DOI: 10.1038/icb.2016.28] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 03/09/2016] [Accepted: 03/13/2016] [Indexed: 01/04/2023]
Abstract
APOBEC3G (apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G; A3G) is an innate defense protein showing activity against retroviruses and retrotransposons. Activated CD4(+) T cells are highly permissive for HIV-1 replication, whereas resting CD4(+) T cells are refractory. Dendritic cells (DCs), especially mature DCs, are also refractory. We investigated whether these differences could be related to a differential A3G expression and/or subcellular distribution. We found that A3G mRNA and protein expression is very low in resting CD4(+) T cells and immature DCs, but increases strongly following T-cell activation and DC maturation. The Apo-7 anti-A3G monoclonal antibody (mAb), which was specifically developed, confirmed these differences at the protein level and disclosed that A3G is mainly cytoplasmic in resting CD4(+) T cells and immature DCs. Nevertheless, A3G translocates to the nucleus in activated-proliferating CD4(+) T cells, yet remaining cytoplasmic in matured DCs, a finding confirmed by immunoblotting analysis of cytoplasmic and nuclear fractions. Apo-7 mAb was able to immunoprecipitate endogenous A3G allowing to detect complexes with numerous proteins in activated-proliferating but not in resting CD4(+) T cells. The results show for the first time the nuclear translocation of A3G in activated-proliferating CD4(+) T cells.
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Affiliation(s)
- Harold Oliva
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Rodrigo Pacheco
- Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.,Laboratorio de Neuroinmunología, Fundación Ciencia and Vida, Santiago, Chile
| | - José M Martinez-Navio
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Marta Rodríguez-García
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Service of Immunology, Hospital Clínic Universitari de Barcelona, Barcelona, Spain
| | - Mar Naranjo-Gómez
- LIRAD (Laboratory of Immunobiology for Research and Diagnostic Applications), Institut d'Investigació Germans Trias-Pujol, Autonomous University of Barcelona, Badalona (Barcelona), Spain
| | - Núria Climent
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Carolina Prado
- Laboratorio de Neuroinmunología, Fundación Ciencia and Vida, Santiago, Chile
| | - Cristina Gil
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Montserrat Plana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Felipe García
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Service of Infectious Diseases and AIDS Unit, Hospital Clínic de Barcelona, Barcelona, Spain
| | - José M Miró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Service of Infectious Diseases and AIDS Unit, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Rafael Franco
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain.,CIBERNED Centro de Investigación en Red, Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
| | - Francesc E Borras
- IVECAT-Group, Institut d'Investigació Germans Trias i Pujol (IGTP), Badalona, Spain.,Nephrology Service, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Naveenan Navaratnam
- MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - José M Gatell
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Service of Infectious Diseases and AIDS Unit, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Teresa Gallart
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-AIDS Research Group and HIV Vaccine Development in Catalonia (HIVACAT), Hospital Clínic de Barcelona, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Service of Immunology, Hospital Clínic Universitari de Barcelona, Barcelona, Spain
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Kim MS, Hur B, Kim S. RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data. BMC Genomics 2016; 17 Suppl 1:5. [PMID: 26817607 PMCID: PMC4895604 DOI: 10.1186/s12864-015-2301-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024] Open
Abstract
Background RNA-editing is an important post-transcriptional RNA sequence modification performed by two catalytic enzymes, "ADAR"(A-to-I) and "APOBEC"(C-to-U). By utilizing high-throughput sequencing technologies, the biological function of RNA-editing has been actively investigated. Currently, RNA-editing is considered to be a key regulator that controls various cellular functions, such as protein activity, alternative splicing pattern of mRNA, and substitution of miRNA targeting site. DARNED, a public RDD database, reported that there are more than 300-thousands RNA-editing sites detected in human genome(hg19). Moreover, multiple studies suggested that RNA-editing events occur in highly specific conditions. According to DARNED, 97.62 % of registered editing sites were detected in a single tissue or in a specific condition, which also supports that the RNA-editing events occur condition-specifically. Since RNA-seq can capture the whole landscape of transcriptome, RNA-seq is widely used for RDD prediction. However, significant amounts of false positives or artefacts can be generated when detecting RNA-editing from RNA-seq. Since it is difficult to perform experimental validation at the whole-transcriptome scale, there should be a powerful computational tool to distinguish true RNA-editing events from artefacts. Result We developed RDDpred, a Random Forest RDD classifier. RDDpred reports potentially true RNA-editing events from RNA-seq data. RDDpred was tested with two publicly available RNA-editing datasets and successfully reproduced RDDs reported in the two studies (90 %, 95 %) while rejecting false-discoveries (NPV: 75 %, 84 %). Conclusion RDDpred automatically compiles condition-specific training examples without experimental validations and then construct a RDD classifier. As far as we know, RDDpred is the very first machine-learning based automated pipeline for RDD prediction. We believe that RDDpred will be very useful and can contribute significantly to the study of condition-specific RNA-editing. RDDpred is available at http://biohealth.snu.ac.kr/software/RDDpred.
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Affiliation(s)
- Min-su Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
| | - Benjamin Hur
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea. .,Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
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APOBEC3 versus Retroviruses, Immunity versus Invasion: Clash of the Titans. Mol Biol Int 2012; 2012:974924. [PMID: 22720156 PMCID: PMC3375093 DOI: 10.1155/2012/974924] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 04/01/2012] [Indexed: 11/17/2022] Open
Abstract
Since the identification of APOBEC3G (A3G) as a potent restriction factor of HIV-1, a tremendous amount of effort has led to a broadened understanding of both A3G and the APOBEC3 (A3) family to which it belongs. In spite of the fine-tuned viral counterattack to A3 activity, in the form of the HIV-1 Vif protein, enthusiasm for leveraging the Vif : A3G axis as a point of clinical intervention remains high. In an impressive explosion of information over the last decade, additional A3 family members have been identified as antiviral proteins, mechanistic details of the restrictive capacity of these proteins have been elucidated, structure-function studies have revealed important molecular details of the Vif : A3G interaction, and clinical cohorts have been scrutinized for correlations between A3 expression and function and viral pathogenesis. In the last year, novel and unexpected findings regarding the role of A3G in immunity have refocused efforts on exploring the potential of harnessing the natural power of this immune defense. These most recent reports allude to functions of the A3 proteins that extend beyond their well-characterized designation as restriction factors. The emerging story implicates the A3 family as not only defense proteins, but also as participants in the broader innate immune response.
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Mous K, Jennes W, De Roo A, Pintelon I, Kestens L, Van Ostade X. Intracellular detection of differential APOBEC3G, TRIM5alpha, and LEDGF/p75 protein expression in peripheral blood by flow cytometry. J Immunol Methods 2011; 372:52-64. [PMID: 21784078 DOI: 10.1016/j.jim.2011.06.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/24/2011] [Accepted: 06/24/2011] [Indexed: 01/07/2023]
Abstract
Expression studies on specific host proteins predominantly use quantitative PCR and western blotting assays. In this study, we optimized a flow cytometry-based assay to study intracellular expression levels of three important host proteins involved in HIV-1 replication: apolipoprotein B mRNA-editing catalytic polypeptide-like 3G (APOBEC3G), tripartite motif 5alpha (TRIM5α), and lens epithelium-derived growth factor (LEDGF/p75). An indirect intracellular staining (ICS) method was optimized using antibodies designed for other applications like enzyme-linked immunosorbent assay (ELISA), confocal imaging, and western blotting. The median fluorescence intensity (MFI) value--a measure for the protein expression level--increased upon higher antibody concentration and longer incubation time, and was reduced following preincubation with recombinant proteins. Staining of stably transfected or knock-down cell lines supported the method's specificity. Moreover, confocal microscopy analysis of peripheral blood mononuclear cells (PBMC), when stained according to the ICS method, confirmed the localization of APOBEC3G and TRIM5α in the cytoplasm, and of LEDGF/p75 in the nucleus. Also, stimulation with mitogen, interferon-alpha, or interferon-beta resulted in detectable, albeit weak, increases in intracellular expression of APOBEC3G and TRIM5α. After optimization, the method was applied to healthy control and HIV-1 infected subjects. For all subjects studied, the memory subset of CD4+ T cells showed significantly higher expression levels of APOBEC3G, TRIM5α, and LEDGF/p75, while the CD16+ subset of monocytes was characterized by higher expression levels of LEDGF/p75. In addition, we observed that therapy-naïve HIV-1 patients tended to have lower expression levels of APOBEC3G and TRIM5α than HIV-1 negative controls. In summary, our data provide proof-of-principle for the detection of specific host factors at the level of a single cell, which may prove useful for our further understanding of their role in virus-host interactions.
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Affiliation(s)
- Kim Mous
- Laboratory for Proteinscience, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Smith HC. APOBEC3G: a double agent in defense. Trends Biochem Sci 2011; 36:239-44. [PMID: 21239176 DOI: 10.1016/j.tibs.2010.12.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/10/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
APOBEC3G (A3G) is an effective cellular host defense factor under experimental conditions in which a functional form of the HIV-encoded protein Vif cannot be expressed. Wild-type Vif targets A3G for proteasomal degradation and when this happens, any host defense advantage A3G might provide is severely diminished or lost. Recent evidence cast doubt on the potency of A3G in host defense and suggested that it could, under some circumstances, promote the emergence of more virulent HIV strains. In this article, I suggest that it is time to recognize that A3G has the potential to act as a double agent. Future research should focus on understanding how cellular and viral regulatory mechanisms enable the antiviral function of A3G, and on the development of novel research reagents to explore these pathways.
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Affiliation(s)
- Harold C Smith
- Department of Biochemistry and Biophysics, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA.
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