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Sadri Nahand J, Khanaliha K, Khatami A, Aminjavaheri P, Abbasi-Kolli M, Mirzaei H, Motlaghzadeh S, Nahid-Samiei R, Bokharaei-Salim F. Expression pattern analysis of the long non-coding RNAs (TINCR, RP11-573D15.8, RP11-156E8.1), and their target genes (AKT1, FOXO1 and MAPK3) in patients with HIV infection, and elite controllers. Heliyon 2024; 10:e30900. [PMID: 38803943 PMCID: PMC11128862 DOI: 10.1016/j.heliyon.2024.e30900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Elite controllers (ECs) defined as a small subclass of subjects with HIV capable of controlling human immunodeficiency virus (HIV) replication in the lack of antiretroviral treatment. One class of RNA molecules that serve as vital components in the network of HIV-related transcriptional regulation, are long noncoding RNAs (lncRNAs). The critical part that they take is in transcriptional regulation of HIV through monitoring various cellular signaling pathways. Reportedly, AKT and MAPK signaling pathways serve a crucial role in modulation of HIV infection. In the current investigation, we utilized bioinformatics tools to predict the lncRNAs that have the ability to interact with MAPK3, AKT, and FOXO1. Then, PBMC expression levels of lncRNAs and their target genes (AKT, FOXO1 and MAPK3) measured in the ECs (n = 15), HIV-positive (n = 40) patients and healthy control subjects (n = 40). We found a significant increase and decrease in the level of AKT and FOXO1 expression within the ECs group, respectively than in the HIV + group (P-value <0.0001 and 0.04, respectively). In the ECs group, the level of TINCR and RP11-156E8.1 was overexpressed compared to the HIV + group (P-value: 0.004 and 0.001, respectively). While RP11-573D15.8 level in ECs exhibited a significant suppression in contrast to HIV + group (P-value: 0.02). According to the receiver-operating characteristic (ROC) curve results, AKT and TINCR could serve as useful biomarkers for screening ECs groups from HIV + patients and healthy control groups. Overall, different expression patterns of selected factors and ROC curve results showed these factors could critically contribute to HIV controlling and be considered as diagnostic markers for ECs from HIV + samples.
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Affiliation(s)
- Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khadijeh Khanaliha
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - AliReza Khatami
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Parisasadat Aminjavaheri
- Department of Microbial Biotechnology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
| | - Mohammad Abbasi-Kolli
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Saeed Motlaghzadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rahil Nahid-Samiei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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De La Torre-Tarazona E, Ayala-Suárez R, Díez-Fuertes F, Alcamí J. Omic Technologies in HIV: Searching Transcriptional Signatures Involved in Long-Term Non-Progressor and HIV Controller Phenotypes. Front Immunol 2022; 13:926499. [PMID: 35844607 PMCID: PMC9284212 DOI: 10.3389/fimmu.2022.926499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
This article reviews the main discoveries achieved by transcriptomic approaches on HIV controller (HIC) and long-term non-progressor (LTNP) individuals, who are able to suppress HIV replication and maintain high CD4+ T cell levels, respectively, in the absence of antiretroviral therapy. Different studies using high throughput techniques have elucidated multifactorial causes implied in natural control of HIV infection. Genes related to IFN response, calcium metabolism, ribosome biogenesis, among others, are commonly differentially expressed in LTNP/HIC individuals. Additionally, pathways related with activation, survival, proliferation, apoptosis and inflammation, can be deregulated in these individuals. Likewise, recent transcriptomic studies include high-throughput sequencing in specific immune cell subpopulations, finding additional gene expression patterns associated to viral control and/or non-progression in immune cell subsets. Herein, we provide an overview of the main differentially expressed genes and biological routes commonly observed on immune cells involved in HIV infection from HIC and LTNP individuals, analyzing also different technical aspects that could affect the data analysis and the future perspectives and gaps to be addressed in this field.
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Affiliation(s)
- Erick De La Torre-Tarazona
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rubén Ayala-Suárez
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Francisco Díez-Fuertes
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Francisco Díez-Fuertes,
| | - José Alcamí
- Acquired Immunodeficiency Syndrome (AIDS) Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Human Immunodeficiency Virus (HIV) Unit, Hospital Clínic de Barcelona, Barcelona, Spain
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3
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Minami Y, Yuan Y, Ueda HR. Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling. Biophys Rev 2021; 13:1113-1126. [PMID: 35059031 PMCID: PMC8724464 DOI: 10.1007/s12551-021-00859-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023] Open
Abstract
The system-level identification and analysis of molecular and cellular networks in mammals can be accelerated by "next-generation" genetics, which is defined as genetics that can achieve desired genetic makeup in a single generation without any animal crossing. We recently established a highly efficient procedure for producing knock-out (KO) mice using the "Triple-CRISPR" method, which targets a single gene by triple gRNAs in the CRISPR/Cas9 system. This procedure achieved an almost perfect KO efficiency (96-100%). We also established a highly efficient procedure, the "ES-mouse" method, for producing knock-in (KI) mice within a single generation. In this method, ES cells were treated with three inhibitors to keep their potency and then injected into 8-cell-stage embryos. These procedures dramatically shortened the time required to produce KO or KI mice from years down to about 3 months. The produced KO and KI mice can also be systematically profiled at a single-cell resolution by the "whole-organ cell profiling," which was realized by tissue-clearing methods, such as CUBIC, and an advanced light-sheet microscopy. The review describes the establishment and application of these technologies above in analyzing the three states (NREM sleep, REM sleep, and awake) of mammalian brains. It also discusses the role of calcium and muscarinic receptors in these states as well as the current challenges and future opportunities in the next-generation mammalian genetics and whole-organ cell profiling for organism-level systems biology.
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Affiliation(s)
- Yoichi Minami
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yufei Yuan
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
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4
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Jochems SP, Jacquelin B, Tchitchek N, Busato F, Pichon F, Huot N, Liu Y, Ploquin MJ, Roché E, Cheynier R, Dereuddre-Bosquet N, Stahl-Henning C, Le Grand R, Tost J, Müller-Trutwin M. DNA methylation changes in metabolic and immune-regulatory pathways in blood and lymph node CD4 + T cells in response to SIV infections. Clin Epigenetics 2020; 12:188. [PMID: 33298174 PMCID: PMC7724887 DOI: 10.1186/s13148-020-00971-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The molecular mechanisms underlying HIV-induced inflammation, which persists even during effective long-term treatment, remain incompletely defined. Here, we studied pathogenic and nonpathogenic simian immunodeficiency virus (SIV) infections in macaques and African green monkeys, respectively. We longitudinally analyzed genome-wide DNA methylation changes in CD4 + T cells from lymph node and blood, using arrays. DNA methylation changes after SIV infection were more pronounced in lymph nodes than blood and already detected in primary infection. Differentially methylated genes in pathogenic SIV infection were enriched for Th1-signaling (e.g., RUNX3, STAT4, NFKB1) and metabolic pathways (e.g., PRKCZ). In contrast, nonpathogenic SIVagm infection induced DNA methylation in genes coding for regulatory proteins such as LAG-3, arginase-2, interleukin-21 and interleukin-31. Between 15 and 18% of genes with DNA methylation changes were differentially expressed in CD4 + T cells in vivo. Selected identified sites were validated using bisulfite pyrosequencing in an independent cohort of uninfected, viremic and SIV controller macaques. Altered DNA methylation was confirmed in blood and lymph node CD4 + T cells in viremic macaques but was notably absent from SIV controller macaques. Our study identified key genes differentially methylated already in primary infection and in tissues that could contribute to the persisting metabolic disorders and inflammation in HIV-infected individuals despite effective treatment.
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Affiliation(s)
- Simon P Jochems
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
- Sorbonne Paris Cité, Université Paris Diderot, Paris, France
- Leiden University Medical Center, Leiden, The Netherlands
| | - Beatrice Jacquelin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Nicolas Tchitchek
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Fabien Pichon
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Nicolas Huot
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Yi Liu
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Mickaël J Ploquin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Elodie Roché
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Rémi Cheynier
- UMR8104, CNRS, U1016, INSERM, Institut Cochin, Université de Paris, 75014, Paris, France
| | - Nathalie Dereuddre-Bosquet
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | | | - Roger Le Grand
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Michaela Müller-Trutwin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France.
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Dysfunctional Immunometabolism in HIV Infection: Contributing Factors and Implications for Age-Related Comorbid Diseases. Curr HIV/AIDS Rep 2020; 17:125-137. [PMID: 32140979 DOI: 10.1007/s11904-020-00484-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW An increasing body of evidence indicates that persons living with HIV (PLWH) display dysfunctional immunometabolism. Here, we provide an updated review of this topic and its relationship to HIV-associated immune stimuli and age-related disease. RECENT FINDINGS HIV infection alters immunometabolism by increasing reliance on aerobic glycolysis for energy and productive infection and repurposing oxidative phosphorylation machinery for immune cell proliferation and survival. Recent studies in PLWH with diabetes mellitus or cardiovascular disease have identified an association with elevated T cell and monocyte glucose metabolism, respectively. Immunometabolic dysfunction has also been observed in PLWH in frailty and additional studies suggest a role for immunometabolism in non-AIDS defining cancers and neurocognitive disease. There is a plethora of HIV-associated immune stimuli that could drive immunometabolic dysfunction and age-related disease in PLWH, but studies directly examining their relationship are lacking. Immunometabolic dysfunction is characteristic of HIV infection and is a potential link between HIV-associated stimuli and age-related comorbidities.
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A novel prognostic two-gene signature for triple negative breast cancer. Mod Pathol 2020; 33:2208-2220. [PMID: 32404959 DOI: 10.1038/s41379-020-0563-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022]
Abstract
The absence of a robust risk stratification tool for triple negative breast cancer (TNBC) underlies imprecise and nonselective treatment of these patients with cytotoxic chemotherapy. This study aimed to interrogate transcriptomes of TNBC resected samples using next generation sequencing to identify novel biomarkers associated with disease outcomes. A subset of cases (n = 112) from a large, well-characterized cohort of primary TNBC (n = 333) were subjected to RNA-sequencing. Reads were aligned to the human reference genome (GRCH38.83) using the STAR aligner and gene expression quantified using HTSEQ. We identified genes associated with distant metastasis-free survival and breast cancer-specific survival by applying supervised artificial neural network analysis with gene selection to the RNA-sequencing data. The prognostic ability of these genes was validated using the Breast Cancer Gene-Expression Miner v4. 0 and Genotype 2 outcome datasets. Multivariate Cox regression analysis identified a prognostic gene signature that was independently associated with poor prognosis. Finally, we corroborated our results from the two-gene prognostic signature by their protein expression using immunohistochemistry. Artificial neural network identified two gene panels that strongly predicted distant metastasis-free survival and breast cancer-specific survival. Univariate Cox regression analysis of 21 genes common to both panels revealed that the expression level of eight genes was independently associated with poor prognosis (p < 0.05). Adjusting for clinicopathological factors including patient's age, grade, nodal stage, tumor size, and lymphovascular invasion using multivariate Cox regression analysis yielded a two-gene prognostic signature (ACSM4 and SPDYC), which was associated with poor prognosis (p < 0.05) independent of other prognostic variables. We validated the protein expression of these two genes, and it was significantly associated with patient outcome in both independent and combined manner (p < 0.05). Our study identifies a prognostic gene signature that can predict prognosis in TNBC patients and could potentially be used to guide the clinical management of TNBC patients.
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7
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Kaddour H, Panzner TD, Welch JL, Shouman N, Mohan M, Stapleton JT, Okeoma CM. Electrostatic Surface Properties of Blood and Semen Extracellular Vesicles: Implications of Sialylation and HIV-Induced Changes on EV Internalization. Viruses 2020; 12:E1117. [PMID: 33019624 PMCID: PMC7601085 DOI: 10.3390/v12101117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Although extracellular vesicle (EV) surface electrostatic properties (measured as zeta potential, ζ-potential) have been reported by many investigators, the biophysical implications of charge and EV origin remains uncertain. Here, we compared the ζ-potential of human blood EVs (BEVs) and semen EVs (SEVs) from 26 donors that were HIV-infected (HIV+, n = 13) or HIV uninfected (HIV-, n = 13). We found that, compared to BEVs that bear neutral surface charge, SEVs were significantly more negatively charged, even when BEVs and SEVs were from the same individual. Comparison of BEVs and SEVs from HIV- and HIV+ groups revealed subtle HIV-induced alteration in the ζ-potential of EVs, with the effect being more significant in SEVs (∆ζ-potential = -8.82 mV, p-value = 0.0062) than BEVs (∆ζ-potential = -1.4 mV, p-value = 0.0462). These observations were validated by differences in the isoelectric point (IEP) of EVs, which was in the order of HIV + SEV ≤ HIV-SEV ≪ HIV + BEV ≤ HIV-BEV. Functionally, the rate and efficiency of SEV internalization by the human cervical epithelial cell line, primary peripheral blood lymphocytes, and primary blood-derived monocytes were significantly higher than those of BEVs. Mechanistically, removal of sialic acids from the surface of EVs using neuraminidase treatment significantly decreased SEV's surface charge, concomitant with a substantial reduction in SEV's internalization. The neuraminidase effect was independent of HIV infection and insignificant for BEVs. Finally, these results were corroborated by enrichment of glycoproteins in SEVs versus BEVs. Taken together, these findings uncover fundamental tissue-specific differences in surface electrostatic properties of EVs and highlight the critical role of surface charge in EV/target cell interactions.
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Affiliation(s)
- Hussein Kaddour
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; (H.K.); (T.D.P.); (N.S.)
| | - Tyler D. Panzner
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; (H.K.); (T.D.P.); (N.S.)
| | - Jennifer L. Welch
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (J.L.W.); (J.T.S.)
- Medical Service, Iowa City Veterans Affairs Medical Center, Iowa City, IA 52246, USA
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nadia Shouman
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; (H.K.); (T.D.P.); (N.S.)
| | - Mahesh Mohan
- Host Pathogen Interaction Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Jack T. Stapleton
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (J.L.W.); (J.T.S.)
- Medical Service, Iowa City Veterans Affairs Medical Center, Iowa City, IA 52246, USA
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Chioma M. Okeoma
- Department of Pharmacology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA; (H.K.); (T.D.P.); (N.S.)
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Comparison of miRNA Expression Profiles between HIV-1 and HIV-2 Infected Monocyte-Derived Macrophages (MDMs) and Peripheral Blood Mononuclear Cells (PBMCs). Int J Mol Sci 2020; 21:ijms21186970. [PMID: 32971935 PMCID: PMC7556008 DOI: 10.3390/ijms21186970] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
During the progression of HIV-1 infection, macrophage tropic HIV-1 that use the CCR5 co-receptor undergoes a change in co-receptor use to CXCR4 that is predominately T cell tropic. This change in co-receptor preference makes the virus able to infect T cells. HIV-2 is known to infect MDMs and T cells and is dual tropic. The aim of this study was to elucidate the differential expression profiles of host miRNAs and their role in cells infected with HIV-1/HIV-2. To achieve this goal, a comparative global miRNA expression profile was determined in human PBMCs and MDMs infected with HIV-1/HIV-2. Differentially expressed miRNAs were identified in HIV-1/HIV-2 infected PBMCs and MDMs using the next-generation sequencing (NGS) technique. A comparative global miRNA expression profile in infected MDMs and PBMCs with HIV-1 and HIV-2 identified differential expression of several host miRNAs. These differentially expressed miRNAs are likely to be involved in many signaling pathways, like the p53 signaling pathway, PI3K-Akt signaling pathways, MAPK signaling pathways, FoxO signaling pathway, and viral carcinogenesis. Thus, a comparative study of the differential expression of host miRNAs in MDMs and T cell in response to HIV-1 and HIV-2 infection will help us to identify unique biomarkers that can differentiate HIV-1 and HIV-2 infection.
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9
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Wallace J, Narasipura SD, Sha BE, French AL, Al-Harthi L. Canonical Wnts Mediate CD8 + T Cell Noncytolytic Anti-HIV-1 Activity and Correlate with HIV-1 Clinical Status. THE JOURNAL OF IMMUNOLOGY 2020; 205:2046-2055. [PMID: 32887752 DOI: 10.4049/jimmunol.1801379] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/04/2020] [Indexed: 11/19/2022]
Abstract
CD8+ T cells do not rely solely on cytotoxic functions for significant HIV control. Moreover, the noncytotoxic CD8+ T cell antiviral response is a primary mediator of natural HIV control such as that seen in HIV elite controllers and long-term nonprogressors that does not require combined antiretroviral therapy. In this study, we investigated the biological factors contributing to the noncytotoxic control of HIV replication mediated by primary human CD8+ T cells. We report that canonical Wnt signaling inhibits HIV transcription in an MHC-independent, noncytotoxic manner and that mediators of this pathway correlate with HIV controller clinical status. We show that CD8+ T cells express all 19 Wnts and CD8+ T cell-conditioned medium (CM) induced canonical Wnt signaling in infected recipient cells while simultaneously inhibiting HIV transcription. Antagonizing canonical Wnt activity in CD8+ T cell CM resulted in increased HIV transcription in infected cells. Further, Wnt2b expression was upregulated in HIV controllers versus viremic patients, and in vitro depletion of Wnt2b and/or Wnt9b from CD8+ CM reversed HIV inhibitory activity. Finally, plasma concentration of Dkk-1, an antagonist of canonical Wnt signaling, was higher in viremic patients with lower CD4 counts. This study demonstrates that canonical Wnt signaling inhibits HIV and significantly correlates with HIV controller status.
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Affiliation(s)
- Jennillee Wallace
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612
| | - Srinivas D Narasipura
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612
| | - Beverly E Sha
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL 60612
| | - Audrey L French
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL 60612.,Stroger Hospital of Cook County, Cook County Health and Hospitals System, Chicago, IL 60612; and.,Ruth M. Rothstein CORE Center, Cook County Health and Hospitals System, Chicago, IL 60612
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612;
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10
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García M, López-Fernández L, Mínguez P, Morón-López S, Restrepo C, Navarrete-Muñoz MA, López-Bernaldo JC, Benguría A, García MI, Cabello A, Fernández-Guerrero M, De la Hera FJ, Estrada V, Barros C, Martínez-Picado J, Górgolas M, Benito JM, Rallón N. Transcriptional signature of resting-memory CD4 T cells differentiates spontaneous from treatment-induced HIV control. J Mol Med (Berl) 2020; 98:1093-1105. [PMID: 32556382 DOI: 10.1007/s00109-020-01930-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 01/29/2023]
Abstract
The HIV reservoir is the main barrier to eradicating HIV infection, and resting memory CD4 T (Trm) cells are one of the most relevant cellular component harboring latent proviruses. This is the first study analyzing the transcriptional profile of Trm cells, in two well-characterized groups of HIV patients with distinct mechanisms of viral replication control (spontaneous versus treatment-induced). We use a systems biology approach to unravel subtle but important differences in the molecular mechanisms operating at the cellular level that could be associated with the host's ability to control virus replication and persistence. Despite the absence of significant differences in the transcriptome of Trm cells between Elite Controllers (ECs) and cART-treated (TX) patients at the single gene level, we found 353 gene ontology (GO) categories upregulated in EC compared with TX. Our results suggest the existence of mechanisms at two different levels: first boosting both adaptive and innate immune responses, and second promoting active viral replication and halting HIV latency in the Trm cell compartment of ECs as compared with TX patients. These differences in the transcriptional profile of Trm cells could be involved in the lower HIV reservoir observed in ECs compared with TX individuals, although mechanistic studies are needed to confirm this hypothesis. Combining transcriptome analysis and systems biology methods is likely to provide important findings to help us in the design of therapeutic strategies aimed at purging the HIV reservoir. KEY MESSAGES: HIV-elite controllers have the lowest HIV-DNA content in resting memory CD4 T cells. HIV-ECs show a particular transcriptional profile in resting memory CD4 T cells. Molecular mechanisms of enhanced adaptative and innate immune response in HIV-ECs. High viral replication and low viral latency establishment associate to the EC status.
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Affiliation(s)
- Marcial García
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Luis López-Fernández
- Pharmacy Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pablo Mínguez
- Bioinformatics Unit, Genetics Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | | | - Clara Restrepo
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - María A Navarrete-Muñoz
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | | | - Alberto Benguría
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - María Isabel García
- Pharmacy Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alfonso Cabello
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | | | | | | | | | - Javier Martínez-Picado
- irsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Miguel Górgolas
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - José M Benito
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
| | - Norma Rallón
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
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11
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Abstract
Gene expression profiling of the host response to HIV infection has promised to fill the gaps in our knowledge and provide new insights toward vaccine and cure. However, despite 20 years of research, the biggest questions remained unanswered. A literature review identified 62 studies examining gene expression dysregulation in samples from individuals living with HIV. Changes in gene expression were dependent on cell/tissue type, stage of infection, viremia, and treatment status. Some cell types, notably CD4+ T cells, exhibit upregulation of cell cycle, interferon-related, and apoptosis genes consistent with depletion. Others, including CD8+ T cells and natural killer cells, exhibit perturbed function in the absence of direct infection with HIV. Dysregulation is greatest during acute infection. Differences in study design and data reporting limit comparability of existing research and do not as yet provide a coherent overview of gene expression in HIV. This review outlines the extraordinarily complex host response to HIV and offers recommendations to realize the full potential of HIV host transcriptomics.
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12
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Key Players in HIV-1 Transcriptional Regulation: Targets for a Functional Cure. Viruses 2020; 12:v12050529. [PMID: 32403278 PMCID: PMC7291152 DOI: 10.3390/v12050529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 establishes a life-long infection when proviral DNA integrates into the host genome. The provirus can then either actively transcribe RNA or enter a latent state, without viral production. The switch between these two states is governed in great part by the viral protein, Tat, which promotes RNA transcript elongation. Latency is also influenced by the availability of host transcription factors, integration site, and the surrounding chromatin environment. The latent reservoir is established in the first few days of infection and serves as the source of viral rebound upon treatment interruption. Despite effective suppression of HIV-1 replication by antiretroviral therapy (ART), to below the detection limit, ART is ineffective at reducing the latent reservoir size. Elimination of this reservoir has become a major goal of the HIV-1 cure field. However, aside from the ideal total HIV-1 eradication from the host genome, an HIV-1 remission or functional cure is probably more realistic. The “block-and-lock” approach aims at the transcriptional silencing of the viral reservoir, to render suppressed HIV-1 promoters extremely difficult to reactivate from latency. There are unfortunately no clinically available HIV-1 specific transcriptional inhibitors. Understanding the mechanisms that regulate latency is expected to provide novel targets to be explored in cure approaches.
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13
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Zhang X, Liu L, Yuan X, Wei Y, Wei X. JMJD3 in the regulation of human diseases. Protein Cell 2019; 10:864-882. [PMID: 31701394 PMCID: PMC6881266 DOI: 10.1007/s13238-019-0653-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/11/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, many studies have shown that histone methylation plays an important role in maintaining the active and silent state of gene expression in human diseases. The Jumonji domain-containing protein D3 (JMJD3), specifically demethylate di- and trimethyl-lysine 27 on histone H3 (H3K27me2/3), has been widely studied in immune diseases, infectious diseases, cancer, developmental diseases, and aging related diseases. We will focus on the recent advances of JMJD3 function in human diseases, and looks ahead to the future of JMJD3 gene research in this review.
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Affiliation(s)
- Xiangxian Zhang
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Liu
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xia Yuan
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuquan Wei
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiawei Wei
- Laboratory of Aging Research and Nanotoxicology, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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14
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Chowdhury FZ, Ouyang Z, Buzon M, Walker BD, Lichterfeld M, Yu XG. Metabolic pathway activation distinguishes transcriptional signatures of CD8+ T cells from HIV-1 elite controllers. AIDS 2018; 32:2669-2677. [PMID: 30289807 DOI: 10.1097/qad.0000000000002007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Elite controllers, defined as persons maintaining undetectable levels of HIV-1 replication in the absence of antiretroviral therapy, represent living evidence that sustained, natural control of HIV-1 is possible, at least in relatively rare instances. Understanding the complex immunologic and virologic characteristics of these specific patients holds promise for inducing drug-free control of HIV-1 in broader populations of HIV-1 infected patients. DESIGN We used an unbiased transcriptional profiling approach to characterize CD8+ T cells, the strongest correlate of HIV-1 immune control identified thus far, in a large cohort of elite controllers (n = 51); highly active antiretrovial therapy (HAART)-treated patients (n = 32) and HIV-1 negative (n = 10) served as reference cohorts. METHODS We isolated mRNA from total CD8+ T cells isolated from peripheral blood mononuclear cell (PBMC) of each individual followed by microarray analysis of the transcriptional signatures. RESULTS We observed profound transcriptional differences [590 transcripts, false discovery rate (FDR)-adjusted P < 0.05] between elite controller and HAART-treated patients. Interestingly, metabolic and signalling pathways governed by mammalian target of rapamycin (mTOR) and eIF2, known for their key roles in regulating cellular growth, proliferation and metabolism, were among the top functions enriched in the differentially expressed genes, suggesting a therapeutically actionable target as a distinguishing feature of spontaneous HIV-1 immune control. A subsequent bootstrapping approach distinguished five different subgroups of elite controller, each characterized by distinct transcriptional signatures. However, despite this marked heterogeneity, differential regulation of mTOR and eIF2 signalling remained the dominant functional pathway in three of these elite controller subgroups. CONCLUSION These studies suggest that mTOR and eIF2 signalling may play a remarkably universal role for regulating CD8 T-cell function from elite controllers.
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15
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Seeking “protective” and “harmful” immune genes during chronic HIV-1 infection by transcriptome analysis. JOURNAL OF BIO-X RESEARCH 2018. [DOI: 10.1097/jbr.0000000000000015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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16
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Masson JJR, Cherry CL, Murphy NM, Sada-Ovalle I, Hussain T, Palchaudhuri R, Martinson J, Landay AL, Billah B, Crowe SM, Palmer CS. Polymorphism rs1385129 Within Glut1 Gene SLC2A1 Is Linked to Poor CD4+ T Cell Recovery in Antiretroviral-Treated HIV+ Individuals. Front Immunol 2018; 9:900. [PMID: 29867928 PMCID: PMC5966582 DOI: 10.3389/fimmu.2018.00900] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/11/2018] [Indexed: 01/14/2023] Open
Abstract
Untreated HIV infection is associated with progressive CD4+ T cell depletion, which is generally recovered with combination antiretroviral therapy (cART). However, a significant proportion of cART-treated individuals have poor CD4+ T cell reconstitution. We investigated associations between HIV disease progression and CD4+ T cell glucose transporter-1 (Glut1) expression. We also investigated the association between these variables and specific single nucleotide polymorphisms (SNPs) within the Glut1 regulatory gene AKT (rs1130214, rs2494732, rs1130233, and rs3730358) and in the Glut1-expressing gene SLC2A1 (rs1385129 and rs841853) and antisense RNA 1 region SLC2A1-AS1 (rs710218). High CD4+Glut1+ T cell percentage is associated with rapid CD4+ T cell decline in HIV-positive treatment-naïve individuals and poor T cell recovery in HIV-positive individuals on cART. Evidence suggests that poor CD4+ T cell recovery in treated HIV-positive individuals is linked to the homozygous genotype (GG) associated with SLC2A1 SNP rs1385129 when compared to those with a recessive allele (GA/AA) (odds ratio = 4.67; P = 0.04). Furthermore, poor response to therapy is less likely among Australian participants when compared against American participants (odds ratio: 0.12; P = 0.01) despite there being no difference in prevalence of a specific genotype for any of the SNPs analyzed between nationalities. Finally, CD4+Glut1+ T cell percentage is elevated among those with a homozygous dominant genotype for SNPs rs1385129 (GG) and rs710218 (AA) when compared to those with a recessive allele (GA/AA and AT/TT respectively) (P < 0.04). The heterozygous genotype associated with AKT SNP 1130214 (GT) had a higher CD4+Glut1+ T cell percentage when compared to the dominant homozygous genotype (GG) (P = 0.0068). The frequency of circulating CD4+Glut1+ T cells and the rs1385129 SLC2A1 SNP may predict the rate of HIV disease progression and CD4+ T cell recovery in untreated and treated infection, respectively.
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Affiliation(s)
- Jesse J R Masson
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia
| | - Catherine L Cherry
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicholas M Murphy
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.,Preimplantation Genetic Diagnosis, Monash IVF, Melbourne, VIC, Australia
| | - Isabel Sada-Ovalle
- Unidad de Investigación Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Tabinda Hussain
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Riya Palchaudhuri
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia
| | - Jeffrey Martinson
- Department of Immunology-Microbiology, Rush University Medical Centre, Chicago, IL, United States
| | - Alan L Landay
- Department of Immunology-Microbiology, Rush University Medical Centre, Chicago, IL, United States
| | - Baki Billah
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Suzanne M Crowe
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Clovis S Palmer
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
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17
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Jiang G, Nguyen D, Archin NM, Yukl SA, Méndez-Lagares G, Tang Y, Elsheikh MM, Thompson GR, Hartigan-O'Connor DJ, Margolis DM, Wong JK, Dandekar S. HIV latency is reversed by ACSS2-driven histone crotonylation. J Clin Invest 2018; 128:1190-1198. [PMID: 29457784 DOI: 10.1172/jci98071] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022] Open
Abstract
Eradication of HIV-1 (HIV) is hindered by stable viral reservoirs. Viral latency is epigenetically regulated. While the effects of histone acetylation and methylation at the HIV long-terminal repeat (LTR) have been described, our knowledge of the proviral epigenetic landscape is incomplete. We report that a previously unrecognized epigenetic modification of the HIV LTR, histone crotonylation, is a regulator of HIV latency. Reactivation of latent HIV was achieved following the induction of histone crotonylation through increased expression of the crotonyl-CoA-producing enzyme acyl-CoA synthetase short-chain family member 2 (ACSS2). This reprogrammed the local chromatin at the HIV LTR through increased histone acetylation and reduced histone methylation. Pharmacologic inhibition or siRNA knockdown of ACSS2 diminished histone crotonylation-induced HIV replication and reactivation. ACSS2 induction was highly synergistic in combination with either a protein kinase C agonist (PEP005) or a histone deacetylase inhibitor (vorinostat) in reactivating latent HIV. In the SIV-infected nonhuman primate model of AIDS, the expression of ACSS2 was significantly induced in intestinal mucosa in vivo, which correlated with altered fatty acid metabolism. Our study links the HIV/SIV infection-induced fatty acid enzyme ACSS2 to HIV latency and identifies histone lysine crotonylation as a novel epigenetic regulator for HIV transcription that can be targeted for HIV eradication.
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Affiliation(s)
- Guochun Jiang
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Don Nguyen
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Nancie M Archin
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Steven A Yukl
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gema Méndez-Lagares
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Yuyang Tang
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - Maher M Elsheikh
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
| | | | - David M Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joseph K Wong
- Department of Medicine, UCSF, and San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, UCD, Davis, California, USA
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18
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Zhang LL, Zhang ZN, Wu X, Jiang YJ, Fu YJ, Shang H. Transcriptomic meta-analysis identifies gene expression characteristics in various samples of HIV-infected patients with nonprogressive disease. J Transl Med 2017; 15:191. [PMID: 28899396 PMCID: PMC5596944 DOI: 10.1186/s12967-017-1294-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A small proportion of HIV-infected patients remain clinically and/or immunologically stable for years, including elite controllers (ECs) who have undetectable viremia (<50 copies/ml) and long-term nonprogressors (LTNPs) who maintain normal CD4+ T cell counts for prolonged periods (>10 years). However, the mechanism of nonprogression needs to be further resolved. In this study, a transcriptome meta-analysis was performed on nonprogressor and progressor microarray data to identify differential transcriptome pathways and potential biomarkers. METHODS Using the INMEX (integrative meta-analysis of expression data) program, we performed the meta-analysis to identify consistently differentially expressed genes (DEGs) in nonprogressors and further performed functional interpretation (gene ontology analysis and pathway analysis) of the DEGs identified in the meta-analysis. Five microarray datasets (81 cases and 98 controls in total), including whole blood, CD4+ and CD8+ T cells, were collected for meta-analysis. RESULTS We determined that nonprogressors have reduced expression of important interferon-stimulated genes (ISGs), CD38, lymphocyte activation gene 3 (LAG-3) in whole blood, CD4+ and CD8+ T cells. Gene ontology (GO) analysis showed a significant enrichment in DEGs that function in the type I interferon signaling pathway. Upregulated pathways, including the PI3K-Akt signaling pathway in whole blood, cytokine-cytokine receptor interaction in CD4+ T cells and the MAPK signaling pathway in CD8+ T cells, were identified in nonprogressors compared with progressors. In each metabolic functional category, the number of downregulated DEGs was more than the upregulated DEGs, and almost all genes were downregulated DEGs in the oxidative phosphorylation (OXPHOS) and tricarboxylic acid (TCA) cycle in the three types of samples. CONCLUSIONS Our transcriptomic meta-analysis provides a comprehensive evaluation of the gene expression profiles in major blood types of nonprogressors, providing new insights in the understanding of HIV pathogenesis and developing strategies to delay HIV disease progression.
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Affiliation(s)
- Le-Le Zhang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, No 155, Nanjingbei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zi-Ning Zhang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, No 155, Nanjingbei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xian Wu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, No 155, Nanjingbei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yong-Jun Jiang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, No 155, Nanjingbei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Ya-Jing Fu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, No 155, Nanjingbei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hong Shang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, No 155, Nanjingbei Street, Heping District, Shenyang, 110001, Liaoning Province, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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19
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van Zuylen WJ, Rawlinson WD, Ford CE. The Wnt pathway: a key network in cell signalling dysregulated by viruses. Rev Med Virol 2016; 26:340-55. [PMID: 27273590 DOI: 10.1002/rmv.1892] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/04/2016] [Accepted: 05/12/2016] [Indexed: 12/19/2022]
Abstract
Viruses are obligate parasites dependent on host cells for survival. Viral infection of a cell activates a panel of pattern recognition receptors that mediate antiviral host responses to inhibit viral replication and dissemination. Viruses have evolved mechanisms to evade and subvert this antiviral host response, including encoding proteins that hijack, mimic and/or manipulate cellular processes such as the cell cycle, DNA damage repair, cellular metabolism and the host immune response. Currently, there is an increasing interest whether viral modulation of these cellular processes, including the cell cycle, contributes to cancer development. One cellular pathway related to cell cycle signalling is the Wnt pathway. This review focuses on the modulation of this pathway by human viruses, known to cause (or associated with) cancer development. The main mechanisms where viruses interact with the Wnt pathway appear to be through (i) epigenetic modification of Wnt genes; (ii) cellular or viral miRNAs targeting Wnt genes; (iii) altering specific Wnt pathway members, often leading to (iv) nuclear translocation of β-catenin and activation of Wnt signalling. Given that diverse viruses affect this signalling pathway, modulating Wnt signalling could be a generalised critical process for the initiation or maintenance of viral pathogenesis, with resultant dysregulation contributing to virus-induced cancers. Further study of this virus-host interaction may identify options for targeted therapy against Wnt signalling molecules as a means to reduce virus-induced pathogenesis and the downstream consequences of infection. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Wendy J van Zuylen
- Serology and Virology Division, SEALS Microbiology, Prince of Wales Hospital, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - William D Rawlinson
- Serology and Virology Division, SEALS Microbiology, Prince of Wales Hospital, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Caroline E Ford
- Metastasis Research Group, School of Women's and Children's Health, University of New South Wales, Sydney, Australia.
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20
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MicroRNA Profile in CD8+ T-Lymphocytes from HIV-Infected Individuals: Relationship with Antiviral Immune Response and Disease Progression. PLoS One 2016; 11:e0155245. [PMID: 27171002 PMCID: PMC4865051 DOI: 10.1371/journal.pone.0155245] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/26/2016] [Indexed: 12/02/2022] Open
Abstract
Background The relationship between host microRNAs (miRNA), viral control and immune response has not yet been elucidated in the field of HIV. The aim of this study was to assess the differential miRNA profile in CD8+ T-cells between HIV-infected individuals who differ in terms of viral replication control and immune response. Methods miRNA profile from resting and CD3/CD28-stimulated CD8+ T-cells from uninfected individuals (HIV-, n = 11), Elite Controllers (EC, n = 15), Viremic Controllers (VC, n = 15), Viremic Progressors (VP, n = 13) and HIV-infected patients on therapy (ART, n = 14) was assessed using Affymetrix miRNA 3.1 arrays. After background correction, quantile normalization and median polish summarization, normalized data were fit to a linear model. The analysis comprised: resting samples between groups; stimulated samples between groups; and stimulated versus resting samples within each group. Enrichment analyses of the putative target genes were perfomed using bioinformatic algorithms. Results A downregulated miRNA pattern was observed when resting samples from all infected groups were compared to HIV-. A miRNA downregulation was also observed when stimulated samples from EC, ART and HIV- groups were compared to VP, being hsa-miR-4492 the most downregulated. Although a preferential miRNA downregulation was observed when stimulated samples were compared to the respective resting samples, VP presented a differential miRNA expression pattern. In fact, hsa-miR-155 and hsa-miR-181a were downregulated in VP whereas in the other groups, either an upregulation or no differences were observed after stimulation, respectively. Overall, functional enrichment analysis revealed that the predicted target genes were involved in signal transduction pathways, metabolic regulation, apoptosis, and immune response. Conclusions Resting CD8+ T-cells do not exhibit a differential miRNA expression between HIV-infected individuals but they do differ from non-infected individuals. Moreover, a specific miRNA pattern is present in stimulated CD8+ T-cells from VP which could reflect a detrimental pattern in terms of CD8+ T-cell immune response.
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21
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Guha D, Mancini A, Sparks J, Ayyavoo V. HIV-1 Infection Dysregulates Cell Cycle Regulatory Protein p21 in CD4+ T Cells Through miR-20a and miR-106b Regulation. J Cell Biochem 2016; 117:1902-12. [PMID: 26755399 DOI: 10.1002/jcb.25489] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/07/2016] [Indexed: 12/15/2022]
Abstract
Both CD4+ T lymphocytes and macrophages are the major targets of human immunodeficiency virus type 1 (HIV-1); however, they respond differently to HIV-1 infection. We hypothesized that HIV-1 infection alters gene expression in CD4+ T cells and monocyte-derived macrophages (MDMs) in a cell specific manner and microRNAs (miRNAs) in part play a role in cell-specific gene expression. Results indicate that 183 and 31 genes were differentially regulated in HIV-1 infected CD4+ T cells and MDMs, respectively, compared to their mock-infected counterparts. Among the differentially expressed genes, cell cycle regulatory gene, p21 (CDKN1A) was upregulated in virus infected CD4+ T cells both at the mRNA and protein level in CD4+ T cells, whereas no consistent change was observed in MDMs. Productively infected CD4+ T cells express higher amount of p21 compared to bystander cells. In determining the mechanism(s) of cell type specific regulation of p21, we found that the miRNAs miR-106b and miR-20a that target p21 were specifically downregulated in HIV-1 infected CD4+ T cells. Overexpression of these two miRNAs reduced p21 expression significantly in HIV-1 infected CD4+ T cells. These findings provide a potential mechanism, by which, HIV-1 could exploit host cellular machineries to regulate selective gene expression in target cells. J. Cell. Biochem. 117: 1902-1912, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Debjani Guha
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Allison Mancini
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jessica Sparks
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Velpandi Ayyavoo
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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22
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Spadoni JL, Rucart P, Le Clerc S, van Manen D, Coulonges C, Ulveling D, Laville V, Labib T, Taing L, Delaneau O, Montes M, Schuitemaker H, Noirel J, Zagury JF. Identification of Genes Whose Expression Profile Is Associated with Non-Progression towards AIDS Using eQTLs. PLoS One 2015; 10:e0136989. [PMID: 26367535 PMCID: PMC4569262 DOI: 10.1371/journal.pone.0136989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/12/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Many genome-wide association studies have been performed on progression towards the acquired immune deficiency syndrome (AIDS) and they mainly identified associations within the HLA loci. In this study, we demonstrate that the integration of biological information, namely gene expression data, can enhance the sensitivity of genetic studies to unravel new genetic associations relevant to AIDS. METHODS We collated the biological information compiled from three databases of expression quantitative trait loci (eQTLs) involved in cells of the immune system. We derived a list of single nucleotide polymorphisms (SNPs) that are functional in that they correlate with differential expression of genes in at least two of the databases. We tested the association of those SNPs with AIDS progression in two cohorts, GRIV and ACS. Tests on permuted phenotypes of the GRIV and ACS cohorts or on randomised sets of equivalent SNPs allowed us to assess the statistical robustness of this method and to estimate the true positive rate. RESULTS Eight genes were identified with high confidence (p = 0.001, rate of true positives 75%). Some of those genes had previously been linked with HIV infection. Notably, ENTPD4 belongs to the same family as CD39, whose expression has already been associated with AIDS progression; while DNAJB12 is part of the HSP90 pathway, which is involved in the control of HIV latency. Our study also drew our attention to lesser-known functions such as mitochondrial ribosomal proteins and a zinc finger protein, ZFP57, which could be central to the effectiveness of HIV infection. Interestingly, for six out of those eight genes, down-regulation is associated with non-progression, which makes them appealing targets to develop drugs against HIV.
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Affiliation(s)
- Jean-Louis Spadoni
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Pierre Rucart
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Sigrid Le Clerc
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
- Crucell Holland B.V., Archimedesweg 4–6, 2333 CN, Leiden, The Netherlands
| | - Cédric Coulonges
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Damien Ulveling
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Vincent Laville
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Taoufik Labib
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Lieng Taing
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Olivier Delaneau
- Département de Génétique et Développement, Faculté de Médecine, Université de Genève, Switzerland
| | - Matthieu Montes
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
- Crucell Holland B.V., Archimedesweg 4–6, 2333 CN, Leiden, The Netherlands
| | - Josselin Noirel
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
| | - Jean-François Zagury
- Chaire de Bioinformatique; Laboratoire Génomique, Bioinformatique, et Applications (EA 4627), Conservatoire National des Arts et Métiers, Paris, France
- * E-mail:
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Cotugno N, De Armas L, Pallikkuth S, Rossi P, Palma P, Pahwa S. Paediatric HIV infection in the ‘omics era: defining transcriptional signatures of viral control and vaccine responses. J Virus Erad 2015. [DOI: 10.1016/s2055-6640(20)30507-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Cotugno N, De Armas L, Pallikkuth S, Rossi P, Palma P, Pahwa S. Paediatric HIV infection in the 'omics era: defining transcriptional signatures of viral control and vaccine responses. J Virus Erad 2015; 1:153-158. [PMID: 26807446 PMCID: PMC4721557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Modern technologies and their increased accessibility have shifted 'benchtop' medical research to the larger dimension of 'omics. The huge amount of data derived from gene expression and sequencing experiments has propelled physicians, basic scientists and bioinformaticians towards a common goal to transform 'big data' into predictive constructs that are readily available and will offer clinical utility. Although most of the studies available in the literature have been performed on healthy subjects and in peripheral blood mononuclear cells (PBMC), which are a heterogenous and extremely variable pool of cells, scientists are now trying to address mechanistic questions in purified cell subsets in pathological conditions. In the field of HIV, few attempts have been made to comprehensively evaluate gene-expression profiles of infected patients with different disease status. With the view of discovering a path towards remission or viral eradication, perinatally HIV-infected children represent a unique model. In fact the well-defined time of infection and the resulting opportunity to start early treatment, thereby generating a smaller size of viral reservoir and a more intact immune system, allow for investigation of therapeutic strategies to defeat the virus. In this scenario, 'transcriptomic' or gene expression technologies and supporting bioinformatics applications need to be strategically integrated to provide novel information about immune correlates of virus control following treatment interruption. Here we review modern techniques for gene expression analysis and discuss the best transcriptomic strategies applicable to the field of functional cure in paediatric HIV infection.
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Affiliation(s)
- Nicola Cotugno
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy,Department of Systems Medicine,
University of Rome,‘Tor Vergata’,
Italy
| | - Lesley De Armas
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA
| | - Suresh Pallikkuth
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA
| | - Paolo Rossi
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy,Department of Systems Medicine,
University of Rome,‘Tor Vergata’,
Italy
| | - Paolo Palma
- University Department of Pediatrics, DPUO, Unit of Immune and Infectious Diseases,
Bambino Gesù Children's Hospital,
Rome,
Italy
| | - Savita Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami,
Miami,
Florida,
USA,Corresponding author: Savita Pahwa,
Department of Microbiology and Immunology, Miller School of Medicine,
University of Miami1580 NW 10th Avenue,
Miami,
FL33136,
USA
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25
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de Goede AL, Andeweg AC, van den Ham HJ, Bijl MA, Zaaraoui-Boutahar F, van IJcken WFJ, Wilgenhof S, Aerts JL, Gruters RA, Osterhaus ADME. DC immunotherapy in HIV-1 infection induces a major blood transcriptome shift. Vaccine 2015; 33:2922-9. [PMID: 25913415 DOI: 10.1016/j.vaccine.2015.04.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 02/06/2015] [Accepted: 04/14/2015] [Indexed: 12/24/2022]
Abstract
OBJECTIVE This study aimed to evaluate the effect of dendritic cell (DC) vaccination against HIV-1 on host gene expression profiles. DESIGN Longitudinal PBMC samples were collected from participants of the DC-TRN trial for immunotherapy against HIV. Microarray-assisted gene expression profiling was performed to evaluate the effects of vaccination and subsequent interruption of antiretroviral therapy on host genome expression. Data from the DC-TRN trial were compared with results from other vaccination trials. METHODS We used Affymetrix GeneChips for microarray gene expression analysis. Data were analyzed by principal component analysis and differential gene expression was assessed using linear modeling. Gene ontology enrichment and gene set analysis were used to characterize differentially expressed genes. Transcriptome analysis included comparison with PBMCs obtained from DC-vaccinated melanoma patients and of healthy individuals who received seasonal influenza vaccination. RESULTS DC-TRN immunotherapy in HIV-infected individuals resulted in a major shift in the transcriptome. Longitudinal analysis demonstrated that changes in the transcriptome sustained also during interruption of antiretroviral therapy. After DC-vaccination, the transcriptome was enriched for cellular immunity associated genes that were also induced in healthy adults who received live attenuated influenza virus vaccination. These beneficial responses were accompanied by detrimental signals of general immune activation. CONCLUSIONS The DC-TRN induced changes in the transcriptome were profound, lasting, and consisted of both protective signals and signatures of inflammation and immune exhaustion, with a net result of decreased viral load, without clinical benefit. Thus transcriptome analysis provides useful information, dissecting both positive and negative effects, for the evaluation of safety and efficacy of immunotherapeutic strategies.
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Affiliation(s)
- Anna L de Goede
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Hospital Pharmacy, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Arno C Andeweg
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Henk-Jan van den Ham
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Maarten A Bijl
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Fatiha Zaaraoui-Boutahar
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Sofie Wilgenhof
- Department of Medical Oncology, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium; Laboratory of Molecular and Cellular Therapy, Department of Physiology and Immunology, Medical School of the Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
| | - Joeri L Aerts
- Laboratory of Molecular and Cellular Therapy, Department of Physiology and Immunology, Medical School of the Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
| | - Rob A Gruters
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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Wu JQ, Saksena MM, Soriano V, Vispo E, Saksena NK. Differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection identified by transcriptome profiling of PBMCs. Virol J 2015; 12:4. [PMID: 25623235 PMCID: PMC4312599 DOI: 10.1186/s12985-014-0236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/30/2014] [Indexed: 01/01/2023] Open
Abstract
Background Despite the easy accessibility and diagnostic utility of PBMCs and their potential to show distinct expression patterns associated with the accelerated disease progression in HIV/HCV co-infection, there has not been a systematic study focusing on the global dysregulations of the biological pathways in PBMCs from HIV, HCV mono- and co-infected individuals. This study aimed at identifying the transcriptome distinctions of PBMCs between these patient groups. Methods Genome-wide transcriptomes of PBMCs from 10 HIV/HCV co-infected patients, 7 HIV+ patients, 5 HCV+ patients, and 5 HIV/HCV sero-negative healthy controls were analyzed using Illumina microarray. Pairwise comparisons were performed to identify differentially expressed genes (DEGs), followed by gene set enrichment analysis (GSEA) to detect the global dysregulations of the biological pathways between HIV, HCV mono- and co-infection. Results Forty-one, 262, and 44 DEGs with fold change > 1.5 and FDR (false discovery rate) <0.05 for the comparisons of HCV versus co-infection, HIV versus co-infection, and HIV versus HCV were identified, respectively. Significantly altered pathways (FDR < 0.05), featured by those involved in immune system, signaling transduction, and cell cycle, were detected. Notably, the differential regulation of cytotoxicity pathway discriminated between HIV, HCV mono- and co-infection (up-regulated in the former versus the latter group: co-infection versus HIV or HCV, HIV versus HCV; FDR <0.001 ~ 0.019). Conversely, the cytokine-cytokine receptor interaction pathway was down-regulated in co-infection versus either HCV (FDR = 0.003) or HIV (FDR = 0.028). For the comparison of HIV versus HCV, the cell cycle (FDR = 0.016) and WNT signaling (FDR = 0.006) pathways were up- and down-regulated in HIV, respectively. Conclusions Our study is the first to identify the differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection, which may reflect the distinct patterns of virus-host cell interactions underlying disease progression. Further inspection of cytotoxicity pathway has pinned down to the expression of the KIR genes to be associated with specific patterns of particular virus-host interactions. Between HIV and HCV, the altered cell cycle and WNT signaling pathways may suggest the different impact of HIV and HCV on cell proliferation and differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12985-014-0236-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Qin Wu
- School of Biomedical Sciences and Pharmacy, Faculty of Health, The University of Newcastle, University Drive, Callaghan, Newcastle, NSW, 2308, Australia.
| | - Monica Miranda Saksena
- Herpes Virus Pathogenesis Lab, Center for Virus Research, Westmead Millennium Institute, University of Sydney, Westmead, Sydney, NSW, 2145, Australia.
| | - Vincent Soriano
- Department of Infectious Diseases, Hospital Carlos III, Sinesio Delgado 10, 28029, Madrid, Spain.
| | - Eugenia Vispo
- Department of Infectious Diseases, Hospital Carlos III, Sinesio Delgado 10, 28029, Madrid, Spain.
| | - Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute & Westmead Hospital, University of Sydney, Westmead, Sydney, NSW, 2145, Australia.
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Landi A, Vermeire J, Iannucci V, Vanderstraeten H, Naessens E, Bentahir M, Verhasselt B. Genome-wide shRNA screening identifies host factors involved in early endocytic events for HIV-1-induced CD4 down-regulation. Retrovirology 2014; 11:118. [PMID: 25496667 PMCID: PMC4269872 DOI: 10.1186/s12977-014-0118-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/01/2014] [Indexed: 12/28/2022] Open
Abstract
Background Down-modulation of the CD4 receptor is one of the hallmarks of HIV-1 infection and it is believed to confer a selective replicative advantage to the virus in vivo. This process is mainly mediated by three viral proteins: Env, Vpu and Nef. To date, the mechanisms that lead to CD4 depletion from the surface of infected cells during HIV-1 infection are still only partially characterized. In this study, we sought to identify and characterize cellular host factors in HIV-1-induced CD4 down-modulation. Results To identify host factors involved in CD4 down-regulation, we used a whole genome-targeting shRNA lentiviral library in HeLa CD4+ cells expressing Nef as an inducer of CD4 down-modulation. We identified 55 genes, mainly encoding for proteins involved in various steps of clathrin-mediated endocytosis. For confirmation and further selection of the hits we performed several rounds of validation, using individual shRNA lentiviral vectors with a different target sequence for gene knock-down in HIV-1-infected T cells. By this stringent validation set-up, we could demonstrate that the knock-down of DNM3 (dynamin 3), SNX22 (sorting nexin 22), ATP6AP1 (ATPase, H+ Transporting, Lysosomal Accessory Protein 1), HRBL (HIV-Rev binding protein Like), IDH3G (Isocitrate dehydrogenase), HSP90B1 (Heat shock protein 90 kDa beta member 1) and EPS15 (Epidermal Growth Factor Receptor Pathway Substrate 15) significantly increases CD4 levels in HIV-infected SupT1 T cells compared to the non-targeting shRNA control. Moreover, EPS15, DNM3, IDH3G and ATP6AP1 knock-down significantly decreases HIV-1 replication in T cells. Conclusions We identified seven genes as cellular co-factors for HIV-1-mediated CD4 down-regulation in T cells. The knock-down of four out of seven of these genes also significantly reduces HIV-1 replication in T cells. Next to a role in HIV-mediated CD4 down-regulation, these genes might however affect HIV-1 replication in another way. Our findings give insights in the HIV-1-mediated CD4 down-regulation at the level of the plasma membrane and early endosomes and identify four possible new HIV-1 replication co-factors. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0118-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessia Landi
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University and Ghent University Hospital, De Pintelaan 185, B-9000, Gent, Belgium.
| | - Jolien Vermeire
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University and Ghent University Hospital, De Pintelaan 185, B-9000, Gent, Belgium.
| | - Veronica Iannucci
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University and Ghent University Hospital, De Pintelaan 185, B-9000, Gent, Belgium. .,Present address: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Hanne Vanderstraeten
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University and Ghent University Hospital, De Pintelaan 185, B-9000, Gent, Belgium.
| | - Evelien Naessens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University and Ghent University Hospital, De Pintelaan 185, B-9000, Gent, Belgium.
| | - Mostafa Bentahir
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University and Ghent University Hospital, De Pintelaan 185, B-9000, Gent, Belgium. .,Present address: Centre de Technologies Moléculaires Appliquées, Ecole de Santé Publique, Brussels, Belgium.
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University and Ghent University Hospital, De Pintelaan 185, B-9000, Gent, Belgium.
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Gene expression profile in long-term non progressor HIV infected patients: In search of potential resistance factors. Mol Immunol 2014; 62:63-70. [DOI: 10.1016/j.molimm.2014.05.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 05/29/2014] [Indexed: 12/22/2022]
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Blimp-1 overexpression is associated with low HIV-1 reservoir and transcription levels in central memory CD4+ T cells from elite controllers. AIDS 2014; 28:1567-77. [PMID: 24804861 DOI: 10.1097/qad.0000000000000295] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The aim of the study was to determine the molecular mechanisms underlying the quasi-equilibrium between HIV and its host in the model of functional cure represented by elite controllers who spontaneously maintain exceptionally low levels of HIV reservoirs. DESIGN Whole-genome transcriptional study and quantification of the cell-associated HIV DNA and HIV RNA levels of the four major resting CD4 T-cell subsets in HIV-1-infected elite controllers, viremic long-term nonprogressors (vir-LTNPs), and uninfected individuals. METHODS We compared the whole-genome transcriptional profiles (ArrayExpress accession number E-MTAB-1480) of the four major resting CD4 T-cell subsets [naive (TN), central-memory (TCM), transitional-memory (TTM), and effector-memory (TEM)] from 14 HIV-1-infected individuals including seven elite controllers (E-LTNPs) and seven vir-LTNPs, and from seven uninfected individuals. The HIV-1 cellular DNA and mRNA levels were quantified in parallel in each sorted subset. RESULTS Host gene transcriptomes followed subset differentiation and viremia except in E-LTNPs wherein TCM, the main CD4 cell compartment, showed the highest activity with three specific signatures involving overexpression of T-cell receptor and costimulation signaling pathways, overexpression of the PRDM-1/Blimp-1 transcriptional repressor, and downmodulation of type-I IFN-related genes. Among subsets, the PRDM1/Blimp-1 upregulation was associated with lower levels of both cellular HIV-DNA and HIV mRNA levels. CONCLUSION This unique Blimp-1 transcriptional repressor signature and the contrast between host and virus transcriptional activities in TCM from elite controllers suggest Blimp-1 might be involved in controlling the HIV reservoirs in the key TCM subset.
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Pauls E, Ruiz A, Badia R, Permanyer M, Gubern A, Riveira-Muñoz E, Torres-Torronteras J, Alvarez M, Mothe B, Brander C, Crespo M, Menéndez-Arias L, Clotet B, Keppler OT, Martí R, Posas F, Ballana E, Esté JA. Cell cycle control and HIV-1 susceptibility are linked by CDK6-dependent CDK2 phosphorylation of SAMHD1 in myeloid and lymphoid cells. THE JOURNAL OF IMMUNOLOGY 2014; 193:1988-97. [PMID: 25015816 DOI: 10.4049/jimmunol.1400873] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Proliferating cells are preferentially susceptible to infection by retroviruses. Sterile α motif and HD domain-containing protein-1 (SAMHD1) is a recently described deoxynucleotide phosphohydrolase controlling the size of the intracellular deoxynucleotide triphosphate (dNTP) pool, a limiting factor for retroviral reverse transcription in noncycling cells. Proliferating (Ki67(+)) primary CD4(+) T cells or macrophages express a phosphorylated form of SAMHD1 that corresponds with susceptibility to infection in cell culture. We identified cyclin-dependent kinase (CDK) 6 as an upstream regulator of CDK2 controlling SAMHD1 phosphorylation in primary T cells and macrophages susceptible to infection by HIV-1. In turn, CDK2 was strongly linked to cell cycle progression and coordinated SAMHD1 phosphorylation and inactivation. CDK inhibitors specifically blocked HIV-1 infection at the reverse transcription step in a SAMHD1-dependent manner, reducing the intracellular dNTP pool. Our findings identify a direct relationship between control of the cell cycle by CDK6 and SAMHD1 activity, which is important for replication of lentiviruses, as well as other viruses whose replication may be regulated by intracellular dNTP availability.
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Affiliation(s)
- Eduardo Pauls
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - Alba Ruiz
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - Roger Badia
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - Marc Permanyer
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - Albert Gubern
- Cell Signaling Unit, Department of Experimental Science and Health, Pompeu Fabra University, Barcelona Biomedicine Research Park, 08003 Barcelona, Spain
| | - Eva Riveira-Muñoz
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - Javier Torres-Torronteras
- Vall d'Hebron Research Institute, Autonomous University of Barcelona and Biomedical Research Centre on Rare Diseases, Health Institute Carlos III, Spain
| | - Mar Alvarez
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), 28049 Madrid, Spain
| | - Beatriz Mothe
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - Christian Brander
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Manel Crespo
- Infectious Diseases Department, Vall d'Hebron University Hospital, 08035 Barcelona, Spain; and
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), 28049 Madrid, Spain
| | - Bonaventura Clotet
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - Oliver T Keppler
- Institute of Medical Virology, University of Frankfurt, 60596 Frankfurt, Germany
| | - Ramon Martí
- Vall d'Hebron Research Institute, Autonomous University of Barcelona and Biomedical Research Centre on Rare Diseases, Health Institute Carlos III, Spain
| | - Francesc Posas
- Cell Signaling Unit, Department of Experimental Science and Health, Pompeu Fabra University, Barcelona Biomedicine Research Park, 08003 Barcelona, Spain
| | - Ester Ballana
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain
| | - José A Esté
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Autonomous University of Barcelona, 08916 Badalona, Spain;
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da Conceicao VN, Dyer WB, Gandhi K, Gupta P, Saksena NK. Genome-wide analysis of primary peripheral blood mononuclear cells from HIV + patients-pre-and post- HAART show immune activation and inflammation the main drivers of host gene expression. MOLECULAR AND CELLULAR THERAPIES 2014; 2:11. [PMID: 26056580 PMCID: PMC4451969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/23/2014] [Indexed: 11/21/2023]
Abstract
BACKGROUND Although the host gene expression in the context of HIV has been explored by several studies, it remains unclear how HIV is able to manipulate and subvert host gene machinery before and after highly active antiretroviral therapy (HAART) in the same individual. In order to define the underlying pharmaco-genomic basis of HIV control during HAART and genomic basis of immune deterioration prior to HAART initiation, we performed a genome-wide expression analysis using primary peripheral blood mononuclear cells (PBMC) derived from 14 HIV + subjects pre-highly active antiretroviral therapy (HAART) (time point-1 or TP1) with detectable plasma viremia and post-HAART (time point-2 or TP2) with effective control of plasma viremia (<40 HIV RNA copies/mL of plasma). METHODS Genomic RNA extracted from the PBMCs was used in microarray analysis using HT-12V3 Illumina chips. Illumina®BeadStudio Software was used to obtain differentially expressed (DE) genes. Only the genes with p value <0.01 and FDR of <5% were considered for analysis. Pathway analysis was performed in MetaCore™ to derive functional annotations. Functionally significant genes were validated by qRT-PCR. RESULTS Between TP1 and TP2, 234 genes were differentially expressed (DE). During viremic phase (TP1), there was an orchestrated and coordinated up-regulation of immune, inflammation and antiviral genes, consistent with HIV infection and immune activation, which comprised of genes mainly involved in antiviral action of interferons and their signalling. In contrast, the therapy-mediated control phase (TP2) showed systematic down-regulation of these pathways, suggesting that the reduction in plasma viremia with HAART has a considerable influence on reducing the immune activation, thereby implying a definitive role of HIV in subverting the human gene machinery. CONCLUSIONS This is the first study to show the evidence for the differential regulation of gene expression between the untreated and treated time points, suggesting that gene expression is a consequence of cellular activation during plasma viremia. Affirmation to these observations comes from down-modulation of genes involved in cellular activation and inflammation upon initiation of HAART coinciding with below detectable levels of plasma viremia.
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Affiliation(s)
- Viviane N da Conceicao
- />Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Wayne B Dyer
- />Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Kaushal Gandhi
- />Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Priyanka Gupta
- />Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Nitin K Saksena
- />Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
- />Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Sydney, Westmead, NSW 2145 Australia
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da Conceicao VN, Dyer WB, Gandhi K, Gupta P, Saksena NK. Genome-wide analysis of primary peripheral blood mononuclear cells from HIV + patients-pre-and post- HAART show immune activation and inflammation the main drivers of host gene expression. MOLECULAR AND CELLULAR THERAPIES 2014; 2:11. [PMID: 26056580 PMCID: PMC4451969 DOI: 10.1186/2052-8426-2-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/23/2014] [Indexed: 01/09/2023]
Abstract
Background Although the host gene expression in the context of HIV has been explored by several studies, it remains unclear how HIV is able to manipulate and subvert host gene machinery before and after highly active antiretroviral therapy (HAART) in the same individual. In order to define the underlying pharmaco-genomic basis of HIV control during HAART and genomic basis of immune deterioration prior to HAART initiation, we performed a genome-wide expression analysis using primary peripheral blood mononuclear cells (PBMC) derived from 14 HIV + subjects pre-highly active antiretroviral therapy (HAART) (time point-1 or TP1) with detectable plasma viremia and post-HAART (time point-2 or TP2) with effective control of plasma viremia (<40 HIV RNA copies/mL of plasma). Methods Genomic RNA extracted from the PBMCs was used in microarray analysis using HT-12V3 Illumina chips. Illumina®BeadStudio Software was used to obtain differentially expressed (DE) genes. Only the genes with p value <0.01 and FDR of <5% were considered for analysis. Pathway analysis was performed in MetaCore™ to derive functional annotations. Functionally significant genes were validated by qRT-PCR. Results Between TP1 and TP2, 234 genes were differentially expressed (DE). During viremic phase (TP1), there was an orchestrated and coordinated up-regulation of immune, inflammation and antiviral genes, consistent with HIV infection and immune activation, which comprised of genes mainly involved in antiviral action of interferons and their signalling. In contrast, the therapy-mediated control phase (TP2) showed systematic down-regulation of these pathways, suggesting that the reduction in plasma viremia with HAART has a considerable influence on reducing the immune activation, thereby implying a definitive role of HIV in subverting the human gene machinery. Conclusions This is the first study to show the evidence for the differential regulation of gene expression between the untreated and treated time points, suggesting that gene expression is a consequence of cellular activation during plasma viremia. Affirmation to these observations comes from down-modulation of genes involved in cellular activation and inflammation upon initiation of HAART coinciding with below detectable levels of plasma viremia. Electronic supplementary material The online version of this article (doi:10.1186/2052-8426-2-11) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viviane N da Conceicao
- Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Wayne B Dyer
- Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Kaushal Gandhi
- Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Priyanka Gupta
- Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia
| | - Nitin K Saksena
- Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Darcy Road, Sydney, Westmead, NSW 2145 Australia ; Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute, Sydney, Westmead, NSW 2145 Australia
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ACSM4 polymorphisms are associated with rapid AIDS progression in HIV-infected patients. J Acquir Immune Defic Syndr 2014; 65:27-32. [PMID: 23982661 DOI: 10.1097/qai.0b013e3182a990e2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
: Our aim was to explore the association among ACSM4 and PECI polymorphisms and AIDS progression in 454 HIV-infected patients never treated with antiretroviral drugs (146 long-term nonprogressors, 228 moderate progressors, and 80 rapid progressors). For ACSM4 polymorphisms, rs7137120 AA/AG and rs7961991 CC/CT genotypes had higher odds of having a rapid AIDS progression [odds ratio (OR) = 3.21; 95% of confidence interval (95% CI) = 1.26 to 8.16; P = 0.014 and OR = 3.60; 95% CI = 1.38 to 9.36; P = 0.009, respectively]. Additionally, the ACSM4 haplotype integrated for both rs7961991 A and rs7137120 C alleles had higher odds of having a rapid AIDS progression (OR = 2.85; 95% CI = 1.28 to 6.25; P = 0.010). For PECI polymorphisms, no significant associations were found. In conclusion, ACSM4 polymorphisms might play a significant role in AIDS progression.
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Guzmán-Fulgencio M, Rallón N, Berenguer J, Fernández-Rodríguez A, Soriano V, Miralles P, Jiménez-Sousa MA, Restrepo C, López JC, García-Álvarez M, Aldámiz T, Benito JM, Resino S. European mitochondrial haplogroups are not associated with hepatitis C virus (HCV) treatment response in HIV/HCV-coinfected patients. HIV Med 2014; 15:425-30. [PMID: 24580757 DOI: 10.1111/hiv.12126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2013] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Mitochondria are multifunctional organelles with a key role in the innate immune response against viral infections. Mitochondrial DNA (mtDNA) haplogroups have been related to AIDS progression and CD4 T-cell recovery in HIV-infected patients, and to a delay in the development of liver fibrosis in HIV/hepatitis C virus (HCV)-coinfected patients. We performed a study to investigate whether mtDNA haplogroups may be associated with HCV treatment response in HIV/HCV-coinfected patients on pegylated interferon (pegIFN) plus ribavirin (RBV). METHODS We performed a retrospective study in 304 patients who completed a course of HCV therapy. mtDNA polymorphisms were genotyped using Sequenom's MassARRAY platform. The interleukin-28B (IL-28B) polymorphism (rs12980275) was genotyped using the GoldenGate® assay. Sustained virological response (SVR) was defined as an undetectable HCV viral load at week 24 after the end of treatment. The statistical analysis was carried out using on-treatment data. RESULTS The SVR rates were 52.6% (160 of 304) for all patients, and 37.8% (46 of 201) for patients with HCV genotype 1 or 4 vs. 81.4% (83 of 102) for patients with HCV genotype 2 or 3 (P < 0.001). No significant associations were found between mtDNA haplogroup and SVR when all patients were included in the analysis and when patients were stratified by HCV genotype (i.e. those with genotypes 1/4 and 2/3 analysed separately) or IL-28B rs12980275 genotype. CONCLUSIONS European mtDNA haplogroups were not related to HCV treatment response in HIV/HCV-coinfected patients on pegIFN-α/RBV therapy.
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Affiliation(s)
- M Guzmán-Fulgencio
- HIV/Hepatitis Coinfection Unit, Microbiology National Center, Carlos III Health Institute, Majadahonda, Madrid, Spain
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Yi L, Zhao J, Lu J, Chen Y, Chen L, Cheng J, Sun Y, Li Z, Men R, Yang L, Kung H, Yang Z, He ML. Gene expression profiling of CD4⁺ T cells in treatment-naive HIV, HCV mono- or co-infected Chinese. Virol J 2014; 11:27. [PMID: 24520951 PMCID: PMC3943807 DOI: 10.1186/1743-422x-11-27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/29/2014] [Indexed: 11/28/2022] Open
Abstract
Background Because of the shared transmission routes, co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HIV) is very common. Accumulated clinical evidence showed that one could alter the infectious course of the other virus in HIV and HCV co-infected individuals. However, little is known on the molecular basis of HIV/HCV interactions and their modulations on hosts. Methods In this study, treatment-naive HIV, HCV mono-/co-infected individuals with CD4+ T cell counts >300/μl were recruited and their gene expression profiles were investigated by microarray assays. The differentially expressed genes were identified and validated by quantitative real-time PCR (qRT-PCR). To further understand the biological meanings of the gene expression profiles in these three groups, GSEA analysis (version 2.0, Broad Institute
http://www.broad.mit.edu/gsea) was performed. Results By gene set enrichment analysis, we revealed that gene sets of cell cycle progression, innate immune response and some transcription factors in CD4+ T cells were mainly affected by HIV; while genes associated with GPCR signaling were the major targets of HCV. Metabolic pathways were modulated by both HCV and HIV viruses. Conclusions This study for the first time offers gene profiling basis for HCV/HIV mono-/co- infections in human beings. HIV infection displayed the great impact on transcription profile of CD4+ T cells in HIV/HCV co-infected individuals. Genes related to cell cycle arrest were significantly mediated by HIV which may lead to dysfunction of CD4+ T cells and acceleration of HCV-related disease progression in the co-infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Zhengrong Yang
- Stanley Ho Center for Emerging Infectious Diseases, and Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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Genome-wide mRNA and miRNA analysis of peripheral blood mononuclear cells (PBMC) reveals different miRNAs regulating HIV/HCV co-infection. Virology 2014; 450-451:336-49. [PMID: 24503097 DOI: 10.1016/j.virol.2013.12.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/24/2013] [Accepted: 12/19/2013] [Indexed: 12/12/2022]
Abstract
Co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) is common due to shared transmission routes. The genomic basis of HIV/HCV co-infection and its regulation by microRNA (miRNA) is unknown. Therefore, our objective was to investigate genome-wide mRNA expression and its regulation by miRNA in primary PBMCs derived from 27 patients (5 HCV - mono-infected, 5 HIV-mono-infected, 12 HCV/HIV co-infected, and 5 healthy controls). This revealed 27 miRNAs and 476 mRNAs as differentially expressed (DE) in HCV/HIV co-infection when compared to controls (adj p<0.05). Our study shows the first evidence of miRNAs specific for co-infection, several of which are correlated with key gene targets demonstrating functional relationships to pathways in cancer, immune-function, and metabolism. Notable was the up regulation of HCV-specific miR-122 in co-infection (FC>50, p=4.02E-06), which may have clinical/biological implications.
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Wu JQ, Sassé TR, Saksena MM, Saksena NK. Transcriptome analysis of primary monocytes from HIV-positive patients with differential responses to antiretroviral therapy. Virol J 2013; 10:361. [PMID: 24370116 PMCID: PMC3877975 DOI: 10.1186/1743-422x-10-361] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/18/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the significant contributions of monocytes to HIV persistence, the HIV-monocyte interaction remains elusive. For patients on antiretroviral therapy, previous studies observed a virological suppression rate of >70% and suggested complete viral suppression as the primary goal. Although some studies have reported genetic dysregulations associated with HIV disease progression, research on ex vivo-derived monocytic transcriptomes from HIV+ patients with differential responses to therapy is limited. This study investigated the monocytic transcriptome distinctions between patients with sustained virus suppression and those with virological failure during highly active antiretroviral therapy (HAART). METHODS Genome-wide transcriptomes of primary monocytes from five HIV+ patients on HAART who sustainably controlled HIV to below detection level (BDL), five HIV+ patients on HAART who consecutively experienced viremia, and four healthy HIV sero-negative controls were analyzed using Illumina microarray. Pairwise comparisons were performed to identify differentially expressed genes followed by quantitative PCR validation. Gene set enrichment analysis was used to check the consistency of our dataset with previous studies, as well as to detect the global dysregulations of the biological pathways in monocytes between viremic patients and BDLs. RESULTS Pairwise comparisons including viremic patients versus controls, BDL versus controls, and viremic patients versus BDLs identified 473, 76, and 59 differentially expressed genes (fold change > 2 and FDR < 0.05), respectively. The reliability of our dataset was confirmed by gene set enrichment analysis showing that 6 out of 10 published gene lists were significantly enriched (FDR < 0.01) in at least one of the three pairwise comparisons. In the comparison of viremic patients versus BDLs, gene set enrichment analysis revealed that the pathways characterizing the primary functions of monocytes including antigen processing and presentation, FcγR mediated phagocytosis, and chemokine signaling were significantly up-regulated in viremic patients. CONCLUSIONS This study revealed the first transcriptome distinctions in monocytes between viremic patients and BDLs on HAART. Our results reflected the outcome balanced between the subversion of the monocyte transcriptome by HIV and the compensatory effect adapted by host cells. The up-regulation of antigen presentation pathway in viremic patients particularly highlighted the role of the interface between innate and adaptive immunity in HIV disease progression.
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Affiliation(s)
| | | | | | - Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute & Westmead Hospital, University of Sydney, Westmead, Sydney, NSW, 2145, Australia.
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Ballana E, Esté JA. Insights from host genomics into HIV infection and disease: Identification of host targets for drug development. Antiviral Res 2013; 100:473-86. [PMID: 24084487 DOI: 10.1016/j.antiviral.2013.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 01/11/2023]
Abstract
HIV susceptibility and disease progression show a substantial degree of individual heterogeneity, ranging from fast progressors to long-term non progressors or elite controllers, that is, subjects that control infection in the absence of therapy. Recent years have seen a significant increase in understanding of the host genetic determinants of susceptibility to HIV infection and disease progression, driven in large part by candidate gene studies, genome-wide association studies, genome-wide transcriptome analyses, and large-scale functional screens. These studies have identified common variants in host loci that clearly influence disease progression, characterized the scale and dynamics of gene and protein expression changes in response to infection, and provided the first comprehensive catalogue of genes and pathways involved in viral replication. This review highlights the potential of host genomic influences in antiviral therapy by pointing to promising novel drug targets but also providing the basis of the identification and validation of host mechanisms that might be susceptible targets for novel antiviral therapies.
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Affiliation(s)
- Ester Ballana
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
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Barrero CA, Datta PK, Sen S, Deshmane S, Amini S, Khalili K, Merali S. HIV-1 Vpr modulates macrophage metabolic pathways: a SILAC-based quantitative analysis. PLoS One 2013; 8:e68376. [PMID: 23874603 PMCID: PMC3709966 DOI: 10.1371/journal.pone.0068376] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/29/2013] [Indexed: 01/09/2023] Open
Abstract
Human immunodeficiency virus type 1 encoded viral protein Vpr is essential for infection of macrophages by HIV-1. Furthermore, these macrophages are resistant to cell death and are viral reservoir. However, the impact of Vpr on the macrophage proteome is yet to be comprehended. The goal of the present study was to use a stable-isotope labeling by amino acids in cell culture (SILAC) coupled with mass spectrometry-based proteomics approach to characterize the Vpr response in macrophages. Cultured human monocytic cells, U937, were differentiated into macrophages and transduced with adenovirus construct harboring the Vpr gene. More than 600 proteins were quantified in SILAC coupled with LC-MS/MS approach, among which 136 were significantly altered upon Vpr overexpression in macrophages. Quantified proteins were selected and clustered by biological functions, pathway and network analysis using Ingenuity computational pathway analysis. The proteomic data illustrating increase in abundance of enzymes in the glycolytic pathway (pentose phosphate and pyruvate metabolism) was further validated by western blot analysis. In addition, the proteomic data demonstrate down regulation of some key mitochondrial enzymes such as glutamate dehydrogenase 2 (GLUD2), adenylate kinase 2 (AK2) and transketolase (TKT). Based on these observations we postulate that HIV-1 hijacks the macrophage glucose metabolism pathway via the Vpr-hypoxia inducible factor 1 alpha (HIF-1 alpha) axis to induce expression of hexokinase (HK), glucose-6-phosphate dehyrogenase (G6PD) and pyruvate kinase muscle type 2 (PKM2) that facilitates viral replication and biogenesis, and long-term survival of macrophages. Furthermore, dysregulation of mitochondrial glutamate metabolism in macrophages can contribute to neurodegeneration via neuroexcitotoxic mechanisms in the context of NeuroAIDS.
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Affiliation(s)
- Carlos A. Barrero
- Department of Biochemistry, Temple University School of Medicine, Fels Institute, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Prasun K. Datta
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Satarupa Sen
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Satish Deshmane
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Shohreh Amini
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Kamel Khalili
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Salim Merali
- Department of Biochemistry, Temple University School of Medicine, Fels Institute, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
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Shrivastav S, Zhang L, Okamoto K, Lee H, Lagranha C, Abe Y, Balasubramanyam A, Lopaschuk GD, Kino T, Kopp JB. HIV-1 Vpr enhances PPARβ/δ-mediated transcription, increases PDK4 expression, and reduces PDC activity. Mol Endocrinol 2013; 27:1564-76. [PMID: 23842279 DOI: 10.1210/me.2012-1370] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
HIV infection and its therapy are associated with disorders of lipid metabolism and bioenergetics. Previous work has suggested that viral protein R (Vpr) may contribute to the development of lipodystrophy and insulin resistance observed in HIV-1-infected patients. In adipocytes, Vpr suppresses mRNA expression of peroxisomal proliferator-activating receptor-γ (PPARγ)-responsive genes and inhibits differentiation. We investigated whether Vpr might interact with PPARβ/δ and influence its transcriptional activity. In the presence of PPARβ/δ, Vpr induced a 3.3-fold increase in PPAR response element-driven transcriptional activity, a 1.9-fold increase in pyruvate dehydrogenase kinase 4 (PDK4) protein expression, and a 1.6-fold increase in the phosphorylated pyruvate dehydrogenase subunit E1α leading to a 47% decrease in the activity of the pyruvate dehydrogenase complex in HepG2 cells. PPARβ/δ knockdown attenuated Vpr-induced enhancement of endogenous PPARβ/δ-responsive PDK4 mRNA expression. Vpr induced a 1.3-fold increase in mRNA expression of both carnitine palmitoyltransferase I (CPT1) and acetyl-coenzyme A acyltransferase 2 (ACAA2) and doubled the activity of β-hydroxylacyl coenzyme A dehydrogenase (HADH). Vpr physically interacted with the ligand-binding domain of PPARβ/δ in vitro and in vivo. Consistent with a role in energy expenditure, Vpr increased state-3 respiration in isolated mitochondria (1.16-fold) and basal oxygen consumption rate in intact HepG2 cells (1.2-fold) in an etomoxir-sensitive manner, indicating that the oxygen consumption rate increase is β-oxidation-dependent. The effects of Vpr on PPAR response element activation, pyruvate dehydrogenase complex activity, and β-oxidation were reversed by specific PPARβ/δ antagonists. These results support the hypothesis that Vpr contributes to impaired energy metabolism and increased energy expenditure in HIV patients.
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Affiliation(s)
- Shashi Shrivastav
- Kidney Disease Section, National Institute of Diabetes and Digestive andKidney Diseases, National Institutes of Health,Bethesda, Maryland 20892-1268, USA
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Jia B, Lu H, Liu Q, Yin J, Jiang N, Chen Q. Genome-wide comparative analysis revealed significant transcriptome changes in mice after Toxoplasma gondii infection. Parasit Vectors 2013; 6:161. [PMID: 23734932 PMCID: PMC3679772 DOI: 10.1186/1756-3305-6-161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 05/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Toxoplasma gondii is an intracellular parasite that can modulate host responses and presumably host behavior. Host responses as well as pathogenesis vary depending on the parasite strains that are responsible for infection. In immune competent individuals, T. gondii preferentially infects tissues of the central nervous systems (CNS), which might be an additional factor in certain psychiatric disorders. While in immune-compromised individuals and pregnant women, the parasite can cause life-threatening infections. With the availability of the genome-wide investigation platform, the global responses in gene expression of the host after T. gondii infection can be systematically investigated. METHODS Total RNA of brain tissues and peripheral lymphocytes of BALB/C mice infected with RH and ME 49 strain T. gondii as well as that of healthy mice were purified and converted to cRNA with incorporated Cy5-CTP (experimental samples), or Cy3-CTP (control samples). The labeled cRNA probes were hybridized to the Whole Mouse Genome Microarray. The impact of parasite infection on gene expression in both brain tissues and peripheral lymphocytes were analyzed. Differentially expressed genes were revalidated with real-time quantitative reverse transcriptase-polymerase chain reaction (Q-PCR). RESULTS Data indicated that the genes associated with immunity were up-regulated after infection by the two parasite strains, but significant up-regulation was observed in both brain tissues and peripheral lymphocytes of mice infected with ME49 strain compared to that infected by RH strain. The pathways related to pathogenesis of the nervous system were more significantly up-regulated in mice infected with RH strain. CONCLUSIONS Genetically distinct T. gondii strains showed clear differences in modulation of host pathophysiological and immunological responses in both brain tissue and peripheral lymphocytes. It was likely that some of the host responses to T. gondii infection were universal, but the immune response and CNS reaction were in a strain-specific manner.
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Affiliation(s)
- Boyin Jia
- Key Laboratory of Zoonosis, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Xi An Da Lu 5333, Changchun 130062, China.
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Zhou L, Miranda-Saksena M, Saksena NK. Viruses and neurodegeneration. Virol J 2013; 10:172. [PMID: 23724961 PMCID: PMC3679988 DOI: 10.1186/1743-422x-10-172] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 05/20/2013] [Indexed: 11/10/2022] Open
Abstract
Neurodegenerative diseases (NDs) are chronic degenerative diseases of the central nervous system (CNS), which affect 37 million people worldwide. As the lifespan increases, the NDs are the fourth leading cause of death in the developed countries and becoming increasingly prevalent in developing countries. Despite considerable research, the underlying mechanisms remain poorly understood. Although the large majority of studies do not show support for the involvement of pathogenic aetiology in classical NDs, a number of emerging studies show support for possible association of viruses with classical neurodegenerative diseases in humans. Space does not permit for extensive details to be discussed here on non-viral-induced neurodegenerative diseases in humans, as they are well described in literature.Viruses induce alterations and degenerations of neurons both directly and indirectly. Their ability to attack the host immune system, regions of nervous tissue implies that they can interfere with the same pathways involved in classical NDs in humans. Supporting this, many similarities between classical NDs and virus-mediated neurodegeneration (non-classical) have been shown at the anatomic, sub-cellular, genomic and proteomic levels suggesting that viruses can explain neurodegenerative disorders mechanistically. The main objective of this review is to provide readers a detailed snapshot of similarities viral and non-viral neurodegenerative diseases share, so that mechanistic pathways of neurodegeneration in human NDs can be clearly understood. Viruses can guide us to unveil these pathways in human NDs. This will further stimulate the birth of new concepts in the biological research, which is needed for gaining deeper insights into the treatment of human NDs and delineate mechanisms underlying neurodegeneration.
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Affiliation(s)
- Li Zhou
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead NSW 2145, Sydney Australia
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Duskova K, Nagilla P, Le HS, Iyer P, Thalamuthu A, Martinson J, Bar-Joseph Z, Buchanan W, Rinaldo C, Ayyavoo V. MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. BMC Infect Dis 2013; 13:250. [PMID: 23721325 PMCID: PMC3680326 DOI: 10.1186/1471-2334-13-250] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 05/16/2013] [Indexed: 12/13/2022] Open
Abstract
Background Disease progression in the absence of therapy varies significantly in HIV-1 infected individuals. Both viral and host cellular molecules are implicated; however, the exact role of these factors and/or the mechanism involved remains elusive. To understand how microRNAs (miRNAs), which are regulators of transcription and translation, influence host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative miRNA and mRNA microarray analysis using PBMCs obtained from infected individuals with distinct viral load and CD4 counts. Methods RNA isolated from PBMCs obtained from HIV-1 seronegative and HIV-1 positive individuals with distinct viral load and CD4 counts were assessed for miRNA and mRNA profile. Selected miRNA and mRNA transcripts were validated using in vivo and in vitro infection model. Results Our results indicate that HIV-1 positive individuals with high viral load (HVL) showed a dysregulation of 191 miRNAs and 309 mRNA transcripts compared to the uninfected age and sex matched controls. The miRNAs miR-19b, 146a, 615-3p, 382, 34a, 144 and 155, that are known to target innate and inflammatory factors, were significantly upregulated in PBMCs with high viral load, as were the inflammatory molecules CXCL5, CCL2, IL6 and IL8, whereas defensin, CD4, ALDH1, and Neurogranin (NRGN) were significantly downregulated. Using the transcriptome profile and predicted target genes, we constructed the regulatory networks of miRNA-mRNA pairs that were differentially expressed between control, LVL and HVL subjects. The regulatory network revealed an inverse correlation of several miRNA-mRNA pair expression patterns, suggesting HIV-1 mediated transcriptional regulation is in part likely through miRNA regulation. Conclusions Results from our studies indicate that gene expression is significantly altered in PBMCs in response to virus replication. It is interesting to note that the infected individuals with low or undetectable viral load exhibit a gene expression profile very similar to control or uninfected subjects. Importantly, we identified several new mRNA targets (Defensin, Neurogranin, AIF) as well as the miRNAs that could be involved in regulating their expression through the miRNA-mRNA interaction.
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Affiliation(s)
- Karolina Duskova
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 425 Parran Hall, 130 Desoto Street, Pittsburgh, PA 15261, USA
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Yang J, Yang Z, Lv H, Lou Y, Wang J, Wu N. Bridging HIV-1 cellular latency and clinical long-term non-progressor: an interactomic view. PLoS One 2013; 8:e55791. [PMID: 23451031 PMCID: PMC3581534 DOI: 10.1371/journal.pone.0055791] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 12/31/2012] [Indexed: 11/30/2022] Open
Abstract
Development of an effective HIV management is enticed by the fact that long-term non-progressors (LTNP) restrict viral replication spontaneously, but is hindered by HIV-1 latency. Given that the most overlapping characteristics found between HIV-1 LTNP and latency, detailed analysis of the difference would disclose the essentials of latency. In this study, microarray data from our previous study was combined with HIV-1 latency and LTNP data obtained from NCBI GEO database. Principal variance component analysis and hierarchical clustering verified the removal of batch effect across platform. The analysis revealed a total of 456 differential expressed genes with >2-fold change and B-statistic >0. Bayesian inference was used to reconstitute the transcriptional network of HIV-1 latency or LTNP, respectively. Gene regulation was reprogrammed under different disease condition. By network interference, KPNA2 and ATP5G3 were identified as the hubs in latency network which mediate nuclear export and RNA processing. These data offer comparative insights into HIV-1 latency, which will facilitate the understanding of the genetic basis of HIV-1 latency in vivo and serve as a clue for future treatment dealing with key targets in HIV-1 latency.
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Affiliation(s)
- Jin Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Institute of Infectious Diseases, The First Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Medicine, Blood Center of Zhejiang Province, Hangzhou, China
| | - Zongxing Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Institute of Infectious Diseases, The First Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hangjun Lv
- Department of Medicine, Blood Center of Zhejiang Province, Hangzhou, China
| | - Yi Lou
- Department of Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Juan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Institute of Infectious Diseases, The First Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Institute of Infectious Diseases, The First Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, China
- * E-mail:
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Gene array data relevant to immunological and virological monitoring of human immunodeficiency virus type 1 infection. Curr Opin HIV AIDS 2013; 8:132-9. [PMID: 23380654 DOI: 10.1097/coh.0b013e32835ccae1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Immunomonitoring technologies are not only fast changing, but also have already revolutionized the way we look at treatments, diagnosis, and prognosis of a given disease. The purpose of the review is to provide a recent update on the use or possible use of array-based data in immunomonitoring of HIV patients. RECENT FINDINGS Since the inception of gene arrays, there has been a rapid surge in the development of a variety of array-based technologies, which comprise of gene and protein expression platforms. These have been instrumental in studying various immunological and genomic aspects of HIV disease at the subcellular level. SUMMARY Gene and protein array technologies are ideal for a high-throughput multiplexing of large datasets in determining the difference between diseased and nondiseased and pretreatment and posttreatment stages of HIV patients. Therefore, these technologies have the potential to revolutionize HIV immunomonitoring, treatment, diagnosis and prognosis. Although the array-based technologies have not yet replaced conventional immunomonitoring, the data coming out from high-throughput transcriptomic and proteomic studies and its global integration will lead to developing new generation of candidates and tools for immunomonitoring of HIV disease.
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Jeang KT. Diversity matters in scientific publishing. Retrovirology 2012; 9:109. [PMID: 23253815 PMCID: PMC3542026 DOI: 10.1186/1742-4690-9-109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 12/18/2012] [Indexed: 11/10/2022] Open
Abstract
The importance of geographic diversity in publishing is emphasized in this editorial.
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Wu JQ, Sassé TR, Wolkenstein G, Conceicao V, Saksena MM, Soedjono M, Perera SS, Wang B, Dwyer DE, Saksena NK. Transcriptome analysis of primary monocytes shows global down-regulation of genetic networks in HIV viremic patients versus long-term non-progressors. Virology 2012; 435:308-19. [PMID: 23158100 DOI: 10.1016/j.virol.2012.10.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 09/23/2012] [Accepted: 10/16/2012] [Indexed: 01/09/2023]
Abstract
Despite significant contributions of monocytes to HIV persistence, the genomic basis of HIV-infection of monocytes and its association with plasma viremia remain elusive. To understand HIV interactions with monocytes during disease progression, monocytic transcriptomes from long-term non-progressors (LTNP), HIV+ patients with viral load <1000, with viral load >1000, and seronegative controls were analyzed using Illumina microarray. Differentially expressed genes were identified (fold change >2; adjusted p<0.05) and GSEA between HIV+ groups demonstrated that the down-regulation of the pathways including Toll-like receptor (TLR) signaling, cytokine-cytokine receptor interaction, cell cycle and apoptosis was significantly associated with the viremic groups, whereas their up-regulation with the LTNP group. The down-regulation of TLR pathway in the viremic patients was exemplified by the decreased expression of TLR with the subsequent tuning down of MAPK, NF-κB, JAK-STAT, and IRF cascades. These data provide the first transcriptomic distinction between HIV+ progressors and LTNPs based on primary monocytes.
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Affiliation(s)
- Jing Qin Wu
- School of Biomedical Sciences and Pharmacy, Faculty of Health, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
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Kramer G, Moerland PD, Jeeninga RE, Vlietstra WJ, Ringrose JH, Byrman C, Berkhout B, Speijer D. Proteomic analysis of HIV-T cell interaction: an update. Front Microbiol 2012; 3:240. [PMID: 22783244 PMCID: PMC3389432 DOI: 10.3389/fmicb.2012.00240] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 06/15/2012] [Indexed: 12/20/2022] Open
Abstract
This mini-review summarizes techniques applied in, and results obtained with, proteomic studies of human immunodeficiency virus type 1 (HIV-1)–T cell interaction. Our group previously reported on the use of two-dimensional differential gel electrophoresis (2D-DIGE) coupled to matrix assisted laser-desorption time of flight peptide mass fingerprint analysis, to study T cell responses upon HIV-1 infection. Only one in three differentially expressed proteins could be identified using this experimental setup. Here we report on our latest efforts to test models generated by this data set and extend its analysis by using novel bioinformatic algorithms. The 2D-DIGE results are compared with other studies including a pilot study using one-dimensional peptide separation coupled to MSE, a novel mass spectrometric approach. It can be concluded that although the latter method detects fewer proteins, it is much faster and less labor intensive. Last but not least, recent developments and remaining challenges in the field of proteomic studies of HIV-1 infection and proteomics in general are discussed.
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Affiliation(s)
- Gertjan Kramer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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Lee J, Bottje WG, Kong BW. Genome-wide host responses against infectious laryngotracheitis virus vaccine infection in chicken embryo lung cells. BMC Genomics 2012; 13:143. [PMID: 22530940 PMCID: PMC3353197 DOI: 10.1186/1471-2164-13-143] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 04/24/2012] [Indexed: 12/20/2022] Open
Abstract
Background Infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) infection causes high mortality and huge economic losses in the poultry industry. To protect chickens against ILTV infection, chicken-embryo origin (CEO) and tissue-culture origin (TCO) vaccines have been used. However, the transmission of vaccine ILTV from vaccinated- to unvaccinated chickens can cause severe respiratory disease. Previously, host cell responses against virulent ILTV infections were determined by microarray analysis. In this study, a microarray analysis was performed to understand host-vaccine ILTV interactions at the host gene transcription level. Results The 44 K chicken oligo microarrays were used, and the results were compared to those found in virulent ILTV infection. Total RNAs extracted from vaccine ILTV infected chicken embryo lung cells at 1, 2, 3 and 4 days post infection (dpi), compared to 0 dpi, were subjected to microarray assay using the two color hybridization method. Data analysis using JMP Genomics 5.0 and the Ingenuity Pathway Analysis (IPA) program showed that 213 differentially expressed genes could be grouped into a number of functional categories including tissue development, cellular growth and proliferation, cellular movement, and inflammatory responses. Moreover, 10 possible gene networks were created by the IPA program to show intermolecular connections. Interestingly, of 213 differentially expressed genes, BMP2, C8orf79, F10, and NPY were expressed distinctly in vaccine ILTV infection when compared to virulent ILTV infection. Conclusions Comprehensive knowledge of gene expression and biological functionalities of host factors during vaccine ILTV infection can provide insight into host cellular defense mechanisms compared to those of virulent ILTV.
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Affiliation(s)
- Jeongyoon Lee
- Department of Poultry Science, Division of Agriculture, POSC O-404, 1260 West Maple, Fayetteville, AR 72701, USA
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Abstract
PURPOSE OF REVIEW Several unique HIV-infected or HIV-resistant cohorts have been studied over the years to try and delineate the correlates of protection. Although several mechanisms have been put forward, studies aiming to integrate the different mechanisms into a comprehensive model are still lacking. Current systems biology approaches emphasize the importance of unifying independent datasets, provide tools that facilitate hypothesis formulation and testing, and direct us toward uncovering novel therapeutic targets by defining molecular networks perturbed during disease. This review will focus on the current findings that utilized systems biology techniques in order to identify correlates of protection from HIV disease progression and resistance to infection in unique cohorts of individuals as well as in nonhuman primate models of SIV infection. RECENT FINDINGS Using systems biology technologies and data analysis tools, the studies described herein have found that pathways implicated in survival, cell cycling, inflammation, and oxidative stress work in unison to limit pathology caused by chronic immune activation. This situation favors the survival of effector lymphocytes and limits the dissemination of viral particles in HIV elite controllers, exposed-uninfected individuals, and natural hosts of SIV infection. SUMMARY Systems and computational biology tools have clearly expanded our understanding of HIV pathogenesis by unifying independent observations and by giving us novel molecular targets to pursue. These molecular signatures have the potential to uncover correlates of protection in HIV disease and, in the era of personalized medicine, to determine predictive signatures of treatment efficacy and/or failure.
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