1
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Kisaka JK, Rauch D, Griffith M, Kyei GB. A macrophage-cell model of HIV latency reveals the unusual importance of the bromodomain axis. Virol J 2024; 21:80. [PMID: 38581045 PMCID: PMC10996205 DOI: 10.1186/s12985-024-02343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Although macrophages are now recognized as an essential part of the HIV latent reservoir, whether and how viral latency is established and reactivated in these cell types is poorly understood. To understand the fundamental mechanisms of viral latency in macrophages, there is an urgent need to develop latency models amenable to genetic manipulations and screening for appropriate latency-reversing agents (LRAs). Given that differentiated THP-1 cells resemble monocyte-derived macrophages in HIV replication mechanisms, we set out to establish a macrophage cell model for HIV latency using THP-1 cells. METHODS We created single-cell clones of THP-1 cells infected with a single copy of the dual-labeled HIVGKO in which a codon switched eGFP (csGFP) is under the control of the HIV-1 5' LTR promoter, and a monomeric Kusabira orange 2 (mKO2) under the control of cellular elongation factor one alpha promoter (EF1α). Latently infected cells are csGFP-, mKO2+, while cells with actively replicating HIV (or reactivated virus) are csGFP+,mKO2+. After sorting for latently infected cells, each of the THP-1 clones with unique integration sites for HIV was differentiated into macrophage-like cells with phorbol 12-myristate 13-acetate (PMA) and treated with established LRAs to stimulate HIV reactivation. Monocyte-derived macrophages (MDMs) harboring single copies of HIVGKO were used to confirm our findings. RESULTS We obtained clones of THP-1 cells with latently infected HIV with unique integration sites. When the differentiated THP-1 or primary MDMs cells were treated with various LRAs, the bromodomain inhibitors JQ1 and I-BET151 were the most potent compounds. Knockdown of BRD4, the target of JQ1, resulted in increased reactivation, thus confirming the pharmacological effect. The DYRK1A inhibitor Harmine and lipopolysaccharide (LPS) also showed significant reactivation across all three MDM donors. Remarkably, LRAs like PMA/ionomycin, bryostatin-1, and histone deacetylase inhibitors known to potently reactivate latent HIV in CD4 + T cells showed little activity in macrophages. CONCLUSIONS Our results indicate that this model could be used to screen for appropriate LRAs for macrophages and show that HIV latency and reactivation mechanisms in macrophages may be distinct from those of CD4 + T cells.
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Affiliation(s)
- Javan K Kisaka
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Daniel Rauch
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO, 63108, USA
| | - George B Kyei
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Department of Virology, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
- Medical and Scientific Research Center, University of Ghana Medical Center, Accra, Ghana.
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2
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Tahtouh T, Durieu E, Villiers B, Bruyère C, Nguyen TL, Fant X, Ahn KH, Khurana L, Deau E, Lindberg MF, Sévère E, Miege F, Roche D, Limanton E, L'Helgoual'ch JM, Burgy G, Guiheneuf S, Herault Y, Kendall DA, Carreaux F, Bazureau JP, Meijer L. Structure-Activity Relationship in the Leucettine Family of Kinase Inhibitors. J Med Chem 2021; 65:1396-1417. [PMID: 34928152 DOI: 10.1021/acs.jmedchem.1c01141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The protein kinase DYRK1A is involved in Alzheimer's disease, Down syndrome, diabetes, viral infections, and leukemia. Leucettines, a family of 2-aminoimidazolin-4-ones derived from the marine sponge alkaloid Leucettamine B, have been developed as pharmacological inhibitors of DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases). We report here on the synthesis and structure-activity relationship (SAR) of 68 Leucettines. Leucettines were tested on 11 purified kinases and in 5 cellular assays: (1) CLK1 pre-mRNA splicing, (2) Threonine-212-Tau phosphorylation, (3) glutamate-induced cell death, (4) autophagy and (5) antagonism of ligand-activated cannabinoid receptor CB1. The Leucettine SAR observed for DYRK1A is essentially identical for CLK1, CLK4, DYRK1B, and DYRK2. DYRK3 and CLK3 are less sensitive to Leucettines. In contrast, the cellular SAR highlights correlations between inhibition of specific kinase targets and some but not all cellular effects. Leucettines deserve further development as potential therapeutics against various diseases on the basis of their molecular targets and cellular effects.
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Affiliation(s)
- Tania Tahtouh
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,CNRS, 'Protein Phosphorylation and Human Disease' Group, Station Biologique De Roscoff, Place G. Teissier, Bp 74, 29682 Roscoff, Bretagne, France.,College Of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Emilie Durieu
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,CNRS, 'Protein Phosphorylation and Human Disease' Group, Station Biologique De Roscoff, Place G. Teissier, Bp 74, 29682 Roscoff, Bretagne, France
| | - Benoît Villiers
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Céline Bruyère
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Thu Lan Nguyen
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,Institut De Génétique Et De Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, Université de Strasbourg, CNRS UMR7104 & INSERM U964, 67400 Illkirch, France.,Laboratory of Molecular & Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, New York 10021-6399, United States
| | - Xavier Fant
- CNRS, 'Protein Phosphorylation and Human Disease' Group, Station Biologique De Roscoff, Place G. Teissier, Bp 74, 29682 Roscoff, Bretagne, France
| | - Kwang H Ahn
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, Connecticut 06269, United States
| | - Leepakshi Khurana
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, Connecticut 06269, United States
| | - Emmanuel Deau
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Mattias F Lindberg
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Elodie Sévère
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Frédéric Miege
- Edelris, Bâtiment Bioserra 1, 60 avenue Rockefeller, 69008 Lyon, France
| | - Didier Roche
- Edelris, Bâtiment Bioserra 1, 60 avenue Rockefeller, 69008 Lyon, France
| | - Emmanuelle Limanton
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Jean-Martial L'Helgoual'ch
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Guillaume Burgy
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Solène Guiheneuf
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Yann Herault
- Institut De Génétique Et De Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, Université de Strasbourg, CNRS UMR7104 & INSERM U964, 67400 Illkirch, France
| | - Debra A Kendall
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, Connecticut 06269, United States
| | - François Carreaux
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Jean-Pierre Bazureau
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Laurent Meijer
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
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3
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Lindberg MF, Meijer L. Dual-Specificity, Tyrosine Phosphorylation-Regulated Kinases (DYRKs) and cdc2-Like Kinases (CLKs) in Human Disease, an Overview. Int J Mol Sci 2021; 22:6047. [PMID: 34205123 PMCID: PMC8199962 DOI: 10.3390/ijms22116047] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/09/2023] Open
Abstract
Dual-specificity tyrosine phosphorylation-regulated kinases (DYRK1A, 1B, 2-4) and cdc2-like kinases (CLK1-4) belong to the CMGC group of serine/threonine kinases. These protein kinases are involved in multiple cellular functions, including intracellular signaling, mRNA splicing, chromatin transcription, DNA damage repair, cell survival, cell cycle control, differentiation, homocysteine/methionine/folate regulation, body temperature regulation, endocytosis, neuronal development, synaptic plasticity, etc. Abnormal expression and/or activity of some of these kinases, DYRK1A in particular, is seen in many human nervous system diseases, such as cognitive deficits associated with Down syndrome, Alzheimer's disease and related diseases, tauopathies, dementia, Pick's disease, Parkinson's disease and other neurodegenerative diseases, Phelan-McDermid syndrome, autism, and CDKL5 deficiency disorder. DYRKs and CLKs are also involved in diabetes, abnormal folate/methionine metabolism, osteoarthritis, several solid cancers (glioblastoma, breast, and pancreatic cancers) and leukemias (acute lymphoblastic leukemia, acute megakaryoblastic leukemia), viral infections (influenza, HIV-1, HCMV, HCV, CMV, HPV), as well as infections caused by unicellular parasites (Leishmania, Trypanosoma, Plasmodium). This variety of pathological implications calls for (1) a better understanding of the regulations and substrates of DYRKs and CLKs and (2) the development of potent and selective inhibitors of these kinases and their evaluation as therapeutic drugs. This article briefly reviews the current knowledge about DYRK/CLK kinases and their implications in human disease.
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Affiliation(s)
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France;
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4
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Pastor F, Shkreta L, Chabot B, Durantel D, Salvetti A. Interplay Between CMGC Kinases Targeting SR Proteins and Viral Replication: Splicing and Beyond. Front Microbiol 2021; 12:658721. [PMID: 33854493 PMCID: PMC8040976 DOI: 10.3389/fmicb.2021.658721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/04/2021] [Indexed: 12/27/2022] Open
Abstract
Protein phosphorylation constitutes a major post-translational modification that critically regulates the half-life, intra-cellular distribution, and activity of proteins. Among the large number of kinases that compose the human kinome tree, those targeting RNA-binding proteins, in particular serine/arginine-rich (SR) proteins, play a major role in the regulation of gene expression by controlling constitutive and alternative splicing. In humans, these kinases belong to the CMGC [Cyclin-dependent kinases (CDKs), Mitogen-activated protein kinases (MAPKs), Glycogen synthase kinases (GSKs), and Cdc2-like kinases (CLKs)] group and several studies indicate that they also control viral replication via direct or indirect mechanisms. The aim of this review is to describe known and emerging activities of CMGC kinases that share the common property to phosphorylate SR proteins, as well as their interplay with different families of viruses, in order to advance toward a comprehensive knowledge of their pro- or anti-viral phenotype and better assess possible translational opportunities.
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Affiliation(s)
- Florentin Pastor
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
| | - Lulzim Shkreta
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - David Durantel
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
| | - Anna Salvetti
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
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5
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Gingras SN, Tang D, Tuff J, McLaren PJ. Minding the gap in HIV host genetics: opportunities and challenges. Hum Genet 2020; 139:865-875. [PMID: 32409920 PMCID: PMC7272494 DOI: 10.1007/s00439-020-02177-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/12/2020] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have been successful in identifying and confirming novel genetic variants that are associated with diverse HIV phenotypes. However, these studies have predominantly focused on European cohorts. HLA molecules have been consistently associated with HIV outcomes, some of which have been found to be population specific, underscoring the need for diversity in GWAS. Recently, there has been a concerted effort to address this gap that leads to health care (disease prevention, diagnosis, treatment) disparities with marginal improvement. As precision medicine becomes more utilized, non-European individuals will be more and more disadvantaged, as the genetic variants identified in genomic research based on European populations may not accurately reflect that of non-European individuals. Leveraging pre-existing, large, multiethnic cohorts, such as the UK Biobank, 23andMe, and the National Institute of Health's All of Us Research Program, can contribute in raising genomic research in non-European populations and ultimately lead to better health outcomes.
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Affiliation(s)
- Shanelle N. Gingras
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - David Tang
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeffrey Tuff
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Paul J. McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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6
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Kruize Z, Kootstra NA. The Role of Macrophages in HIV-1 Persistence and Pathogenesis. Front Microbiol 2019; 10:2828. [PMID: 31866988 PMCID: PMC6906147 DOI: 10.3389/fmicb.2019.02828] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/21/2019] [Indexed: 12/12/2022] Open
Abstract
Current antiretroviral therapy (ART) effectively suppresses Human Immunodeficiency Virus type 1 (HIV-1) in infected individuals. However, even long term ART does not eradicate HIV-1 infected cells and the virus persists in cellular reservoirs. Beside memory CD4+ T cells, cells of the myeloid lineage, especially macrophages, are believed to be an important sanctuary for HIV-1. Monocytes and macrophages are key players in the innate immune response to pathogens and are recruited to sites of infection and inflammation. Due to their long life span and ability to reside in virtually every tissue, macrophages have been proposed to play a critical role in the establishment and persistence of the HIV-1 reservoir. Current HIV-1 cure strategies mainly focus on the concept of “shock and kill” to purge the viral reservoir. This approach aims to reactivate viral protein production in latently infected cells, which subsequently are eliminated as a consequence of viral replication, or recognized and killed by the immune system. Macrophage susceptibility to HIV-1 infection is dependent on the local microenvironment, suggesting that molecular pathways directing differentiation and polarization are involved. Current latency reversing agents (LRA) are mainly designed to reactivate the HIV-1 provirus in CD4+ T cells, while their ability to abolish viral latency in macrophages is largely unknown. Moreover, the resistance of macrophages to HIV-1 mediated kill and the presence of infected macrophages in immune privileged regions including the central nervous system (CNS), may pose a barrier to elimination of infected cells by current “shock and kill” strategies. This review focusses on the role of monocytes/macrophages in HIV-1 persistence. We will discuss mechanisms of viral latency and persistence in monocytes/macrophages. Furthermore, the role of these cells in HIV-1 tissue distribution and pathogenesis will be discussed.
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Affiliation(s)
- Zita Kruize
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
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7
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Yao HL, Liu M, Wang WJ, Wang XL, Song J, Song QQ, Han J. Construction of miRNA-target networks using microRNA profiles of CVB3-infected HeLa cells. Sci Rep 2019; 9:17876. [PMID: 31784561 PMCID: PMC6884461 DOI: 10.1038/s41598-019-54188-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in regulating gene expression in multiple biological processes and diseases. Thus, to understand changes in miRNA during CVB3 infection, specific miRNA expression profiles were investigated at 3 h, 6 h, and 9 h postinfection in HeLa cells by small-RNA high-throughput sequencing. Biological implications of 68 differentially expressed miRNAs were analyzed through GO and KEGG pathways. Interaction networks between 34 known highly differentially expressed miRNAs and targets were constructed by mirDIP and Navigator. The predicted targets showed that FAM135A, IKZF2, PLAG1, ZNF148, PHC3, LCOR and DYRK1A, which are associated with cellular differentiation and transcriptional regulation, were recognized by 8 miRNAs or 9 miRNAs through interactional regulatory networks. Seven target genes were confirmed by RT-qPCR. The results showed that the expression of DYRK1A, FAM135A, PLAG1, ZNF148, and PHC3 were obviously inhibited at 3 h, 6 h, and 9 h postinfection. The expression of LCOR did not show a significant change, and the expression of IKZF2 increased gradually with prolonged infection time. Our findings improve the understanding of the pathogenic mechanism of CVB3 infection on cellular differentiation and development through miRNA regulation, which has implications for interventional approaches to CVB3-infection therapy. Our results also provide a new method for screening target genes of microRNA regulation in virus-infected cells.
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Affiliation(s)
- Hai Lan Yao
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics, 2 YaBao Rd, Beijing, 100020, China
| | - Mi Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Wen Jun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Xin Ling Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Juan Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Qin Qin Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China.
- Center for Biosafety Mega-Science, Chinese Academy of Science, 44 Xiao HongShan, Wuhan, Hubei, 430071, China.
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8
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Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet 2019; 10:799. [PMID: 31572435 PMCID: PMC6754074 DOI: 10.3389/fgene.2019.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
In this review, we present the main large-scale experimental studies that have been performed in the HIV/AIDS field. These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. After describing the major results obtained with these omics technologies—including some with a high relevance for HIV-1 treatment—we discuss the next steps that the community needs to embrace in order to derive new actionable therapeutic or diagnostic targets. Only integrative approaches that combine all big data results and consider their complex interactions will allow us to capture the global picture of HIV molecular pathogenesis. This novel challenge will require large collaborative efforts and represents a huge open field for innovative bioinformatics approaches.
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Affiliation(s)
- Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation en Urologie et Néphrologie (ITUN), CHU de Nantes, Nantes, France.,Computer Sciences and Mathematics Department, Ecole Centrale de Nantes, Nantes, France
| | - Jean-François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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9
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Abstract
Current antiretroviral therapy (ART) effectively suppresses Human Immunodeficiency Virus type 1 (HIV-1) in infected individuals. However, even long term ART does not eradicate HIV-1 infected cells and the virus persists in cellular reservoirs. Beside memory CD4+ T cells, cells of the myeloid lineage, especially macrophages, are believed to be an important sanctuary for HIV-1. Monocytes and macrophages are key players in the innate immune response to pathogens and are recruited to sites of infection and inflammation. Due to their long life span and ability to reside in virtually every tissue, macrophages have been proposed to play a critical role in the establishment and persistence of the HIV-1 reservoir. Current HIV-1 cure strategies mainly focus on the concept of "shock and kill" to purge the viral reservoir. This approach aims to reactivate viral protein production in latently infected cells, which subsequently are eliminated as a consequence of viral replication, or recognized and killed by the immune system. Macrophage susceptibility to HIV-1 infection is dependent on the local microenvironment, suggesting that molecular pathways directing differentiation and polarization are involved. Current latency reversing agents (LRA) are mainly designed to reactivate the HIV-1 provirus in CD4+ T cells, while their ability to abolish viral latency in macrophages is largely unknown. Moreover, the resistance of macrophages to HIV-1 mediated kill and the presence of infected macrophages in immune privileged regions including the central nervous system (CNS), may pose a barrier to elimination of infected cells by current "shock and kill" strategies. This review focusses on the role of monocytes/macrophages in HIV-1 persistence. We will discuss mechanisms of viral latency and persistence in monocytes/macrophages. Furthermore, the role of these cells in HIV-1 tissue distribution and pathogenesis will be discussed.
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Affiliation(s)
- Zita Kruize
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
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10
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Kim B. Hierarchical Association Coefficient Algorithm: New Method for Genome-Wide Association Study. Evol Bioinform Online 2017; 13:1176934317713004. [PMID: 28894352 PMCID: PMC5582720 DOI: 10.1177/1176934317713004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/09/2017] [Indexed: 11/16/2022] Open
Abstract
Hierarchical association coefficient algorithm calculates the degree of association between observations and categories into a value named hierarchical association coefficient (HA-coefficient) between 0 for the lower limit and 1 for the upper limit. The HA-coefficient algorithm can be operated with stratified ascending categories based on the average of observations in each category. The upper limit refers to a condition where observations are increasingly ordered into the stratified ascending categories, whereas the lower limit refers to a condition where observations are decreasingly ordered into the stratified ascending categories. An HA-coefficient represents how close an observed categorization is to the upper limit, or how distant an observed categorization is from the lower limit. To demonstrate robustness and reliability, the HA-coefficient algorithm was applied to 3 different simulated data sets with the same pattern in terms of the association between observations and categories. From all simulated data sets, the same result was obtained, indicating that the HA-coefficient algorithm is robust and reliable.
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Affiliation(s)
- Bongsong Kim
- Department of Agronomy, Iowa State University, Ames, IA, USA
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Wang P, Wang L, Chen L, Sun X. Dual-specificity tyrosine-phosphorylation regulated kinase 1A Gene Transcription is regulated by Myocyte Enhancer Factor 2D. Sci Rep 2017; 7:7240. [PMID: 28775333 PMCID: PMC5543054 DOI: 10.1038/s41598-017-07655-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/30/2017] [Indexed: 12/19/2022] Open
Abstract
Dual-specificity tyrosine-phosphorylation regulated kinase 1A (DYRK1A) is localized in the Down syndrome critical region of chromosome 21. As a candidate gene responsible for learning defects associated with Down syndrome and Alzheimer's disease (AD), DYRK1A has been implied to play pivotal roles in cell proliferation and brain development. MEF2D, a member of the myocyte-specific enhancer factor 2 (MEF2) family of transcription factors, was proved to be in control of neuronal cell differentiation and development. Here we demonstrated that MEF2D could upregulate DYRK1A gene expression through specific activation of DYRK1A isoform 5 gene transcription. A MEF2D responsive element from -268 to -254 bp on promoter region of DYRK1A isoform 5 was identified and confirmed by luciferase assay, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP). The coordinated expression of DYRK1A and MEF2D in mouse brain development indicated a possibility of the cross-interaction of these two genes during neurodevelopment. The DYRK1A kinase activity was also affected by MEF2D's transcriptional regulation of DYRK1A. Therefore, the molecular regulation of DYRK1A by MEF2D further supported their involvement in neurodevelopment.
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Affiliation(s)
- Pin Wang
- Otolaryngology Key Lab, Qilu Hospital of Shandong University, No. 107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Luanluan Wang
- Otolaryngology Key Lab, Qilu Hospital of Shandong University, No. 107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Long Chen
- Otolaryngology Key Lab, Qilu Hospital of Shandong University, No. 107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Xiulian Sun
- Brain Research Institute, Qilu Hospital of Shandong University, No. 107 West Wenhua Road, Jinan, 250012, Shandong Province, China.
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12
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Bustamante M, Standl M, Bassat Q, Vilor-Tejedor N, Medina-Gomez C, Bonilla C, Ahluwalia TS, Bacelis J, Bradfield JP, Tiesler CMT, Rivadeneira F, Ring S, Vissing NH, Fink NR, Jugessur A, Mentch FD, Ballester F, Kriebel J, Kiefte-de Jong JC, Wolsk HM, Llop S, Thiering E, Beth SA, Timpson NJ, Andersen J, Schulz H, Jaddoe VWV, Evans DM, Waage J, Hakonarson H, Grant SFA, Jacobsson B, Bønnelykke K, Bisgaard H, Davey Smith G, Moll HA, Heinrich J, Estivill X, Sunyer J. A genome-wide association meta-analysis of diarrhoeal disease in young children identifies FUT2 locus and provides plausible biological pathways. Hum Mol Genet 2016; 25:4127-4142. [PMID: 27559109 PMCID: PMC5291237 DOI: 10.1093/hmg/ddw264] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/21/2016] [Accepted: 07/28/2016] [Indexed: 02/02/2023] Open
Abstract
More than a million childhood diarrhoeal episodes occur worldwide each year, and in developed countries a considerable part of them are caused by viral infections. In this study, we aimed to search for genetic variants associated with diarrhoeal disease in young children by meta-analyzing genome-wide association studies, and to elucidate plausible biological mechanisms. The study was conducted in the context of the Early Genetics and Lifecourse Epidemiology (EAGLE) consortium. Data about diarrhoeal disease in two time windows (around 1 year of age and around 2 years of age) was obtained via parental questionnaires, doctor interviews or medical records. Standard quality control and statistical tests were applied to the 1000 Genomes imputed genotypic data. The meta-analysis (N = 5758) followed by replication (N = 3784) identified a genome-wide significant association between rs8111874 and diarrhoea at age 1 year. Conditional analysis suggested that the causal variant could be rs601338 (W154X) in the FUT2 gene. Children with the A allele, which results in a truncated FUT2 protein, had lower risk of diarrhoea. FUT2 participates in the production of histo-blood group antigens and has previously been implicated in the susceptibility to infections, including Rotavirus and Norovirus Gene-set enrichment analysis suggested pathways related to the histo-blood group antigen production, and the regulation of ion transport and blood pressure. Among others, the gastrointestinal tract, and the immune and neuro-secretory systems were detected as relevant organs. In summary, this genome-wide association meta-analysis suggests the implication of the FUT2 gene in diarrhoeal disease in young children from the general population.
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Affiliation(s)
- Mariona Bustamante
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Quique Bassat
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Natalia Vilor-Tejedor
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Carolina Bonilla
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carla M T Tiesler
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Susan Ring
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Nadja H Vissing
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nadia R Fink
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ferran Ballester
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jessica C Kiefte-de Jong
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
- Leiden University College, The Hague, The Netherlands
| | - Helene M Wolsk
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Llop
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Elisabeth Thiering
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Systke A Beth
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - Nicholas J Timpson
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Josefine Andersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - David M Evans
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - George Davey Smith
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital of Munich (LMU), Munich, Germany
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Experimental Genetics, Sidra Medical and Research Centre, Doha, Qatar
| | - Jordi Sunyer
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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13
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Kay LJ, Smulders-Srinivasan TK, Soundararajan M. Understanding the Multifaceted Role of Human Down Syndrome Kinase DYRK1A. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:127-71. [PMID: 27567487 DOI: 10.1016/bs.apcsb.2016.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The dual-specificity tyrosine (Y) phosphorylation-regulated kinase DYRK1A, also known as Down syndrome (DS) kinase, is a dosage-dependent signaling kinase that was originally shown to be highly expressed in DS patients as a consequence of trisomy 21. Although this was evident some time ago, it is only in recent investigations that the molecular roles of DYRK1A in a wide range of cellular processes are becoming increasingly apparent. Since initial knowledge on DYRK1A became evident through minibrain mnb, the Drosophila homolog of DYRK1A, this review will first summarize the scientific reports on minibrain and further expand on the well-established neuronal functions of mammalian and human DYRK1A. Recent investigations across the current decade have provided rather interesting and compelling evidence in establishing nonneuronal functions for DYRK1A, including its role in infection, immunity, cardiomyocyte biology, cancer, and cell cycle control. The latter part of this review will therefore focus in detail on the emerging nonneuronal functions of DYRK1A and summarize the regulatory role of DYRK1A in controlling Tau and α-synuclein. Finally, the emerging role of DYRK1A in Parkinson's disease will be outlined.
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Affiliation(s)
- L J Kay
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - T K Smulders-Srinivasan
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - M Soundararajan
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.
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14
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Booiman T, Loukachov VV, van Dort KA, van ’t Wout AB, Kootstra NA. DYRK1A Controls HIV-1 Replication at a Transcriptional Level in an NFAT Dependent Manner. PLoS One 2015; 10:e0144229. [PMID: 26641855 PMCID: PMC4979971 DOI: 10.1371/journal.pone.0144229] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 11/16/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Transcription of the HIV-1 provirus is regulated by both viral and host proteins and is very important in the context of viral latency. In latently infected cells, viral gene expression is inhibited as a result of the sequestration of host transcription factors and epigenetic modifications. RESULTS In our present study we analyzed the effect of host factor dual specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) on HIV-1 replication. We show that DYRK1A controls HIV-1 replication by regulating provirus transcription. Downregulation or inhibition of DYRK1A increased LTR-driven transcription and viral replication in cell lines and primary PBMC. Furthermore, inhibition of DYRK1A resulted in reactivation of latent HIV-1 provirus to a similar extent as two commonly used broad-spectrum HDAC inhibitors. We observed that DYRK1A regulates HIV-1 transcription via the Nuclear Factor of Activated T-cells (NFAT) by promoting its translocation from the nucleus to the cytoplasm. Therefore, inhibition of DYRK1A results in increased nuclear levels of NFAT and increased NFAT binding to the viral LTR and thus increasing viral transcription. CONCLUSIONS Our data indicate that host factor DYRK1A plays a role in the regulation of viral transcription and latency. Therefore, DYRK1A might be an attractive candidate for therapeutic strategies targeting the viral reservoir.
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Affiliation(s)
- Thijs Booiman
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Vladimir V. Loukachov
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Karel A. van Dort
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van ’t Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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15
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Jin N, Yin X, Gu J, Zhang X, Shi J, Qian W, Ji Y, Cao M, Gu X, Ding F, Iqbal K, Gong CX, Liu F. Truncation and Activation of Dual Specificity Tyrosine Phosphorylation-regulated Kinase 1A by Calpain I: A MOLECULAR MECHANISM LINKED TO TAU PATHOLOGY IN ALZHEIMER DISEASE. J Biol Chem 2015; 290:15219-37. [PMID: 25918155 PMCID: PMC4463463 DOI: 10.1074/jbc.m115.645507] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/14/2015] [Indexed: 11/06/2022] Open
Abstract
Hyperphosphorylation and dysregulation of exon 10 splicing of Tau are pivotally involved in pathogenesis of Alzheimer disease (AD) and/or other tauopathies. Alternative splicing of Tau exon 10, which encodes the second microtubule-binding repeat, generates Tau isoforms containing three and four microtubule-binding repeats, termed 3R-Taus and 4R-Taus, respectively. Dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) lies at the Down syndrome critical region of chromosome 21. Overexpression of this kinase may contribute to the early Tau pathology in Down syndrome via phosphorylation of Tau and dysregulation of Tau exon 10. Here, we report that Dyrk1A was truncated at the C terminus and was associated with overactivation of calpain I in AD brain. Calpain I proteolyzed Dyrk1A in vitro first at the C terminus and further at the N terminus and enhanced its kinase activity toward Tau via increased Vmax but not Km. C-terminal truncation of Dyrk1A resulted in stronger activity than its full-length protein in promotion of exon 10 exclusion and phosphorylation of Tau. Dyrk1A was truncated in kainic acid-induced excitotoxic mouse brains and coincided with an increase in 3R-Tau expression and phosphorylation of Tau via calpain activation. Moreover, truncation of Dyrk1A was correlated with an increase in the ratio of 3R-Tau/4R-Tau and Tau hyperphosphorylation in AD brain. Collectively, these findings suggest that truncation/activation of Dyrk1A by Ca(2+)/calpain I might contribute to Tau pathology via promotion of exon 10 exclusion and hyperphosphorylation of Tau in AD brain.
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Affiliation(s)
- Nana Jin
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China, the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314
| | - Xiaomin Yin
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China, the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, the Department of Biochemistry and Molecular Biology, School of Medicine Sciences, Nantong University, Nantong, Jiangsu 226001, China, and
| | - Jianlan Gu
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China, the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, the Department of Biochemistry and Molecular Biology, School of Medicine Sciences, Nantong University, Nantong, Jiangsu 226001, China, and
| | - Xinhua Zhang
- the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314
| | - Jianhua Shi
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China, the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, the Department of Biochemistry and Molecular Biology, School of Medicine Sciences, Nantong University, Nantong, Jiangsu 226001, China, and
| | - Wei Qian
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China, the Department of Biochemistry and Molecular Biology, School of Medicine Sciences, Nantong University, Nantong, Jiangsu 226001, China, and
| | - Yuhua Ji
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Maohong Cao
- the Department of Neurology, Hospital Affiliated with Nantong University, Nantong, Jiangsu 226001, China
| | - Xiaosong Gu
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Fei Ding
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Khalid Iqbal
- the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314
| | - Cheng-Xin Gong
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China, the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314
| | - Fei Liu
- From the Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China, the Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314,
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16
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Ako-Adjei D, Fu W, Wallin C, Katz KS, Song G, Darji D, Brister JR, Ptak RG, Pruitt KD. HIV-1, human interaction database: current status and new features. Nucleic Acids Res 2014; 43:D566-70. [PMID: 25378338 DOI: 10.1093/nar/gku1126] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database', available through the National Library of Medicine at http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions, serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. Each HIV-1 human protein interaction can be retrieved without restriction by web-based downloads and ftp protocols and includes: Reference Sequence (RefSeq) protein accession numbers, National Center for Biotechnology Information Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. In addition to specific HIV-1 protein-human protein interactions, included are interaction effects upon HIV-1 replication resulting when individual human gene expression is blocked using siRNA. A total of 3142 human genes are described participating in 12,786 protein-protein interactions, along with 1316 replication interactions described for each of 1250 human genes identified using small interfering RNA (siRNA). Together the data identifies 4006 human genes involved in 14,102 interactions. With the inclusion of siRNA interactions we introduce a redesigned web interface to enhance viewing, filtering and downloading of the combined data set.
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Affiliation(s)
- Danso Ako-Adjei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - William Fu
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kenneth S Katz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Guangfeng Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Dakshesh Darji
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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17
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Booiman T, Cobos Jiménez V, van Dort KA, van 't Wout AB, Kootstra NA. Phosphodiesterase 8a supports HIV-1 replication in macrophages at the level of reverse transcription. PLoS One 2014; 9:e109673. [PMID: 25295610 PMCID: PMC4190361 DOI: 10.1371/journal.pone.0109673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/02/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND HIV-1 infected macrophages play a key role in HIV-1 infection. Even during anti-retroviral treatment, macrophages keep producing virus due to suboptimal tissue penetration and reduced efficacy of antiretrovirals. It is therefore of major importance to understand which host factors are involved in HIV-1 replication in macrophages. Previously, we have shown that genetic polymorphisms in phosphodiesterase 8a (PDE8A) are strongly associated with HIV-1 replication in these cells. Here we analyzed the mechanism and regulation of PDE8A in HIV-1 replication in macrophages. RESULTS PDE8A mRNA expression strongly increases upon differentiation of monocytes into macrophages, which corresponds to the increased susceptibility of mature macrophages to HIV-1. In parallel, expression of microRNA miR-145-5p, predicted to target PDE8A mRNA, strongly decreased. The interaction of miR-145-5p with the 3' UTR of PDE8A mRNA could be experimentally validated, suggesting that indeed miR-145-5p can regulate PDE8A expression levels. Knockdown of PDE8A in macrophages resulted in a decrease in total HIV-1 replication and proviral DNA levels. These observations confirm that PDE8A regulates HIV-1 replication in macrophages and that this effect is mediated through early steps in the viral replication cycle. CONCLUSIONS PDE8A is highly expressed in macrophages, and its expression is regulated by miR-145-5p. Our findings strongly suggest that PDE8A supports HIV-1 replication in macrophages and that this effect is mediated at the level of reverse transcription.
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Affiliation(s)
- Thijs Booiman
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Viviana Cobos Jiménez
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Karel A. van Dort
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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18
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Abstract
The success of combination antiretroviral therapy (cART) in transforming the lives of HIV-infected individuals with access to these drugs is tempered by the increasing threat of HIV-associated neurocognitive disorders (HAND) to their overall health and quality of life. Intensive investigations over the past two decades have underscored the role of host immune responses, inflammation, and monocyte-derived macrophages in HAND, but the precise pathogenic mechanisms underlying HAND remain only partially delineated. Complicating research efforts and therapeutic drug development are the sheer complexity of HAND phenotypes, diagnostic imprecision, and the growing intersection of chronic immune activation with aging-related comorbidities. Yet, genetic studies still offer a powerful means of advancing individualized care for HIV-infected individuals at risk. There is an urgent need for 1) longitudinal studies using consistent phenotypic definitions of HAND in HIV-infected subpopulations at very high risk of being adversely impacted, such as children, 2) tissue studies that correlate neuropathological changes in multiple brain regions with genomic markers in affected individuals and with changes at the RNA, epigenomic, and/or protein levels, and 3) genetic association studies using more sensitive subphenotypes of HAND. The NIH Brain Initiative and Human Connectome Project, coupled with rapidly evolving systems biology and machine learning approaches for analyzing high-throughput genetic, transcriptomic and epigenetic data, hold promise for identifying actionable biological processes and gene networks that underlie HAND. This review summarizes the current state of understanding of host genetic factors predisposing to HAND in light of past challenges and suggests some priorities for future research to advance the understanding and clinical management of HAND in the cART era.
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Affiliation(s)
- Asha R Kallianpur
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue/Mail Code NE50, Cleveland, OH, 44195, USA,
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19
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Abstract
While the role of viral variants has long been known to play a key role in causing variation in disease severity, it is also clear that host genetic variation plays a critical role in determining virus-induced disease responses. However, a variety of factors, including confounding environmental variables, rare genetic variants requiring extremely large cohorts, the temporal dynamics of infections, and ethical limitation on human studies, have made the identification and dissection of variant host genes and pathways difficult within human populations. This difficulty has led to the development of a variety of experimental approaches used to identify host genetic contributions to disease responses. In this chapter, we describe the history of genetic associations within the human population, the development of experimentally tractable systems, and the insights these specific approaches provide. We conclude with a discussion of recent advances that allow for the investigation of the role of complex genetic networks that underlie host responses to infection, with the goal of drawing connections to human infections. In particular, we highlight the need for robust animal models with which to directly control and assess the role of host genetics on viral infection outcomes.
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20
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Genetic, transcriptomic, and epigenetic studies of HIV-associated neurocognitive disorder. J Acquir Immune Defic Syndr 2014; 65:481-503. [PMID: 24583618 DOI: 10.1097/qai.0000000000000069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Human Genome Project, coupled with rapidly evolving high-throughput technologies, has opened the possibility of identifying heretofore unknown biological processes underlying human disease. Because of the opaque nature of HIV-associated neurocognitive disorder (HAND) neuropathogenesis, the utility of such methods has gained notice among NeuroAIDS researchers. Furthermore, the merging of genetics with other research areas has also allowed for application of relatively nascent fields, such as neuroimaging genomics, and pharmacogenetics, to the context of HAND. In this review, we detail the development of genetic, transcriptomic, and epigenetic studies of HAND, beginning with early candidate gene association studies and culminating in current "omics" approaches that incorporate methods from systems biology to interpret data from multiple levels of biological functioning. Challenges with this line of investigation are discussed, including the difficulty of defining a valid phenotype for HAND. We propose that leveraging known associations between biology and pathology across multiple levels will lead to a more reliable and valid phenotype. We also discuss the difficulties of interpreting the massive and multitiered mountains of data produced by current high-throughput omics assays and explore the utility of systems biology approaches in this regard.
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21
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Biasin M, De Luca M, Gnudi F, Clerici M. The genetic basis of resistance to HIV infection and disease progression. Expert Rev Clin Immunol 2013; 9:319-34. [PMID: 23557268 DOI: 10.1586/eci.13.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Susceptibility to HIV infection and the modulation of disease progression are strictly dependent on inter-individual variability, much of which is secondary to host genetic heterogeneity. The study of host factors that control these phenomena relies not only on candidate gene approaches but also on unbiased genome-wide genetic and functional analyses. Additional new insights stem from the study of mechanisms that control the expression of host and viral genes, such as miRNA. The genetic host factors that have been suggested to be associated either with resistance to HIV-1 infection or with absent/delayed progression to AIDS are nevertheless unable to fully justify the phenomenon of differential susceptibility to HIV. Multidisciplinary approaches are needed to further analyze individuals who deviate from the expected response to HIV exposure/infection. Results of these analyses will facilitate the identification of novel targets that could be exploited in the setting up of innovative therapeutic or vaccine approaches.
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Affiliation(s)
- Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via GB Grassi 74, 20157 Milan, Italy.
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22
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Dahiya S, Irish BP, Nonnemacher MR, Wigdahl B. Genetic variation and HIV-associated neurologic disease. Adv Virus Res 2013; 87:183-240. [PMID: 23809924 DOI: 10.1016/b978-0-12-407698-3.00006-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-associated neurologic disease continues to be a significant complication in the era of highly active antiretroviral therapy. A substantial subset of the HIV-infected population shows impaired neuropsychological performance as a result of HIV-mediated neuroinflammation and eventual central nervous system (CNS) injury. CNS compartmentalization of HIV, coupled with the evolution of genetically isolated populations in the CNS, is responsible for poor prognosis in patients with AIDS, warranting further investigation and possible additions to the current therapeutic strategy. This chapter reviews key advances in the field of neuropathogenesis and studies that have highlighted how molecular diversity within the HIV genome may impact HIV-associated neurologic disease. We also discuss the possible functional implications of genetic variation within the viral promoter and possibly other regions of the viral genome, especially in the cells of monocyte-macrophage lineage, which are arguably key cellular players in HIV-associated CNS disease.
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Affiliation(s)
- Satinder Dahiya
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Bryan P Irish
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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23
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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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24
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Abstract
Host genetic factors are a major contributing factor to the inter-individual variation observed in response to human immunodeficiency virus (HIV) infection and are linked to resistance to HIV infection among exposed individuals, as well as rate of disease progression and the likelihood of viral transmission. Of the genetic variants that have been shown to affect the natural history of HIV infection, the human leukocyte antigen (HLA) class I genes exhibit the strongest and most consistent association, underscoring a central role for CD8(+) T cells in resistance to the virus. HLA proteins play important roles in T-cell-mediated adaptive immunity by presenting immunodominant HIV epitopes to cytotoxic T lymphocytes (CTLs) and CD4(+) T cells. Genetic and functional data also indicate a function for HLA in natural killer cell-mediated innate immunity against HIV by interacting with killer cell immunoglobulin-like receptors (KIR). We review the HLA and KIR associations with HIV disease and discuss the mechanisms underlying these associations.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
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25
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Rinaldo CR. HIV-1 Trans Infection of CD4(+) T Cells by Professional Antigen Presenting Cells. SCIENTIFICA 2013; 2013:164203. [PMID: 24278768 PMCID: PMC3820354 DOI: 10.1155/2013/164203] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
Since the 1990s we have known of the fascinating ability of a complex set of professional antigen presenting cells (APCs; dendritic cells, monocytes/macrophages, and B lymphocytes) to mediate HIV-1 trans infection of CD4(+) T cells. This results in a burst of virus replication in the T cells that is much greater than that resulting from direct, cis infection of either APC or T cells, or trans infection between T cells. Such APC-to-T cell trans infection first involves a complex set of virus subtype, attachment, entry, and replication patterns that have many similarities among APC, as well as distinct differences related to virus receptors, intracellular trafficking, and productive and nonproductive replication pathways. The end result is that HIV-1 can sequester within the APC for several days and be transmitted via membrane extensions intracellularly and extracellularly to T cells across the virologic synapse. Virus replication requires activated T cells that can develop concurrently with the events of virus transmission. Further research is essential to fill the many gaps in our understanding of these trans infection processes and their role in natural HIV-1 infection.
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Affiliation(s)
- Charles R. Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
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26
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Zhao K, Ishida Y, Oleksyk TK, Winkler CA, Roca AL. Evidence for selection at HIV host susceptibility genes in a West Central African human population. BMC Evol Biol 2012; 12:237. [PMID: 23217182 PMCID: PMC3537702 DOI: 10.1186/1471-2148-12-237] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 11/27/2012] [Indexed: 01/14/2023] Open
Abstract
Background HIV-1 derives from multiple independent transfers of simian immunodeficiency virus (SIV) strains from chimpanzees to human populations. We hypothesized that human populations in west central Africa may have been exposed to SIV prior to the pandemic, and that previous outbreaks may have selected for genetic resistance to immunodeficiency viruses. To test this hypothesis, we examined the genomes of Biaka Western Pygmies, who historically resided in communities within the geographic range of the central African chimpanzee subspecies (Pan troglodytes troglodytes) that carries strains of SIV ancestral to HIV-1. Results SNP genotypes of the Biaka were compared to those of African human populations who historically resided outside the range of P. t. troglodytes, including the Mbuti Eastern Pygmies. Genomic regions showing signatures of selection were compared to the genomic locations of genes reported to be associated with HIV infection or pathogenesis. In the Biaka, a strong signal of selection was detected at CUL5, which codes for a component of the vif-mediated APOBEC3 degradation pathway. A CUL5 allele protective against AIDS progression was fixed in the Biaka. A signal of selection was detected at TRIM5, which codes for an HIV post-entry restriction factor. A protective mis-sense mutation in TRIM5 had the highest frequency in Biaka compared to other African populations, as did a protective allele for APOBEC3G, which codes for an anti-HIV-1 restriction factor. Alleles protective against HIV-1 for APOBEC3H, CXCR6 and HLA-C were at higher frequencies in the Biaka than in the Mbuti. Biaka genomes showed a strong signal of selection at TSG101, an inhibitor of HIV-1 viral budding. Conclusions We found protective alleles or evidence for selection in the Biaka at a number of genes associated with HIV-1 infection or progression. Pygmies have also been reported to carry genotypes protective against HIV-1 for the genes CCR5 and CCL3L1. Our hypothesis that HIV-1 may have shaped the genomes of some human populations in West Central Africa appears to merit further investigation.
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Affiliation(s)
- Kai Zhao
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Il 61801, USA
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27
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van Manen D, van 't Wout AB, Schuitemaker H. Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics. Retrovirology 2012; 9:70. [PMID: 22920050 PMCID: PMC3468375 DOI: 10.1186/1742-4690-9-70] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 07/31/2012] [Indexed: 11/22/2022] Open
Abstract
Susceptibility to HIV-1 and the clinical course after infection show a substantial heterogeneity between individuals. Part of this variability can be attributed to host genetic variation. Initial candidate gene studies have revealed interesting host factors that influence HIV infection, replication and pathogenesis. Recently, genome-wide association studies (GWAS) were utilized for unbiased searches at a genome-wide level to discover novel genetic factors and pathways involved in HIV-1 infection. This review gives an overview of findings from the GWAS performed on HIV infection, within different cohorts, with variable patient and phenotype selection. Furthermore, novel techniques and strategies in research that might contribute to the complete understanding of virus-host interactions and its role on the pathogenesis of HIV infection are discussed.
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Affiliation(s)
- Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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28
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Bol SM, Booiman T, van Manen D, Bunnik EM, van Sighem AI, Sieberer M, Boeser-Nunnink B, de Wolf F, Schuitemaker H, Portegies P, Kootstra NA, van 't Wout AB. Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia. PLoS One 2012; 7:e30990. [PMID: 22347417 PMCID: PMC3274517 DOI: 10.1371/journal.pone.0030990] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/29/2011] [Indexed: 11/18/2022] Open
Abstract
Background Infection with HIV-1 may result in severe cognitive and motor impairment, referred to as HIV-1-associated dementia (HAD). While its prevalence has dropped significantly in the era of combination antiretroviral therapy, milder neurocognitive disorders persist with a high prevalence. To identify additional therapeutic targets for treating HIV-associated neurocognitive disorders, several candidate gene polymorphisms have been evaluated, but few have been replicated across multiple studies. Methods We here tested 7 candidate gene polymorphisms for association with HAD in a case-control study consisting of 86 HAD cases and 246 non-HAD AIDS patients as controls. Since infected monocytes and macrophages are thought to play an important role in the infection of the brain, 5 recently identified single nucleotide polymorphisms (SNPs) affecting HIV-1 replication in macrophages in vitro were also tested. Results The CCR5 wt/Δ32 genotype was only associated with HAD in individuals who developed AIDS prior to 1991, in agreement with the observed fading effect of this genotype on viral load set point. A significant difference in genotype distribution among all cases and controls irrespective of year of AIDS diagnosis was found only for a SNP in candidate gene PREP1 (p = 1.2×10−5). Prep1 has recently been identified as a transcription factor preferentially binding the −2,518 G allele in the promoter of the gene encoding MCP-1, a protein with a well established role in the etiology of HAD. Conclusion These results support previous findings suggesting an important role for MCP-1 in the onset of HIV-1-associated neurocognitive disorders.
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Affiliation(s)
- Sebastiaan M. Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Thijs Booiman
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Evelien M. Bunnik
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ard I. van Sighem
- HIV Monitoring Foundation, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Margit Sieberer
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte Boeser-Nunnink
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Frank de Wolf
- HIV Monitoring Foundation, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Portegies
- Department of Neurology at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Department of Neurology at the OLVG Hospital, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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29
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Abstract
PURPOSE OF REVIEW Macrophages play an important role in HIV-1 pathogenesis and contribute to the establishment of the viral reservoir responsible for continuous virus production. This review will discuss new insights into HIV-1 infection in macrophages and the effect of infection on immune function and pathology. RECENT FINDINGS New cellular factors interacting with various steps of the HIV-1 replication cycle, such as entry, integration, transcription, and assembly of new viral progeny, have been identified. Cellular and viral microRNAs have been shown to regulate virus replication, promote viral latency, and prolong cell survival. Interference with innate immune functions, like phagocytosis, autophagy, cytokine production, and T-cell activation by HIV-1 has been found to contribute to virus replication and latency. Growing evidence indicates an important role of infected macrophages in a variety of HIV-1-associated diseases, including neurocognitive disorders. SUMMARY Under combined antiretroviral therapy (cART), HIV-1 continues to persist in macrophages. Better understanding of HIV-1 infection in macrophages may lead to new adjunctive therapies to improve cART, specifically targeting the viral reservoir and ameliorating tissue-specific diseases.
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Bol SM, Booiman T, Bunnik EM, Moerland PD, van Dort K, Strauss JF, Sieberer M, Schuitemaker H, Kootstra NA, van 't Wout AB. Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages. Virology 2011; 420:32-42. [PMID: 21920574 DOI: 10.1016/j.virol.2011.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 04/27/2011] [Accepted: 08/18/2011] [Indexed: 12/29/2022]
Abstract
Four genome-wide RNAi screens have recently identified hundreds of HIV-1 dependency factors (HDFs). Previously, we reported a large variation in the ability of HIV-1 to replicate in monocyte-derived macrophages (MDM) derived from >400 healthy seronegative blood donors. Here we determined whether SNPs in genes encoding newly identified HDFs were associated with this variation in HIV-1 replication. We found a significant association between the minor allele of SNP rs2304418 in phosphodiesterase 8A (PDE8A) and lower HIV-1 replication (p=2.4×10(-6)). The minor allele of SNP rs2304418 was also significantly associated with lower PDE8A mRNA levels in MDM (p=8.3×10(-5)). In accordance with this, overexpression of PDE8A in HEK293T cells resulted in increased HIV-1 replication, while subsequent knock-down of PDE8A decreased replication. This study links host genetic variation in a newly identified HDF to variation in HIV-1 replication in a relevant primary target cell for HIV-1 and may provide new leads for treatment of this infection.
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Affiliation(s)
- Sebastiaan M Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infection and Immunity at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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