35 results on '"Angélique B. van 't Wout"'
Search Results
2. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity
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Xue-Song Zhang, Jackie Li, Kimberly A Krautkramer, Michelle Badri, Thomas Battaglia, Timothy C Borbet, Hyunwook Koh, Sandy Ng, Rachel A Sibley, Yuanyuan Li, Wimal Pathmasiri, Shawn Jindal, Robin R Shields-Cutler, Ben Hillmann, Gabriel A Al-Ghalith, Victoria E Ruiz, Alexandra Livanos, Angélique B van ‘t Wout, Nabeetha Nagalingam, Arlin B Rogers, Susan Jenkins Sumner, Dan Knights, John M Denu, Huilin Li, Kelly V Ruggles, Richard Bonneau, R Anthony Williamson, Marcus Rauch, and Martin J Blaser
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microbiome ,autoimmune ,NOD mice ,animal models ,immune maturation ,gene expression ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated type 1 diabetes (T1D) development in male NOD mice. The single course had deep and persistent effects on the intestinal microbiome, leading to altered cecal, hepatic, and serum metabolites. The exposure elicited sex-specific effects on chromatin states in the ileum and liver and perturbed ileal gene expression, altering normal maturational patterns. The global signature changes included specific genes controlling both innate and adaptive immunity. Microbiome analysis revealed four taxa each that potentially protect against or accelerate T1D onset, that were linked in a network model to specific differences in ileal gene expression. This simplified animal model reveals multiple potential pathways to understand pathogenesis by which early-life gut microbiome perturbations alter a global suite of intestinal responses, contributing to the accelerated and enhanced T1D development.
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- 2018
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3. Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia.
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Sebastiaan M Bol, Thijs Booiman, Daniëlle van Manen, Evelien M Bunnik, Ard I van Sighem, Margit Sieberer, Brigitte Boeser-Nunnink, Frank de Wolf, Hanneke Schuitemaker, Peter Portegies, Neeltje A Kootstra, and Angélique B van 't Wout
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Medicine ,Science - 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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- 2012
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4. Development of reliable, valid and responsive scoring systems for endoscopy and histology in animal models for inflammatory bowel disease
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Michael Vieth, Pim J. Koelink, Larry Stitt, Brian G. Feagan, Suzanne Duijst, Geert R. D'Haens, Angélique B van ‘t Wout, Raja Atreya, Johannan F. Brandse, Anje A. te Velde, Martin Koldijk, Gijs R. van den Brink, Manon E. Wildenberg, Barrett G. Levesque, AII - Inflammatory diseases, Gastroenterology and Hepatology, AGEM - Re-generation and cancer of the digestive system, AGEM - Digestive immunity, and Tytgat Institute for Liver and Intestinal Research
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0301 basic medicine ,medicine.medical_specialty ,Intraclass correlation ,Basic science ,Mice, SCID ,Severity of Illness Index ,Gastroenterology ,Spearman's rank correlation coefficient ,Inflammatory bowel disease ,Endoscopy, Gastrointestinal ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Severity of illness ,medicine ,Animals ,Colitis ,Observer Variation ,Mice, Inbred BALB C ,medicine.diagnostic_test ,Tumor Necrosis Factor-alpha ,business.industry ,Antibodies, Monoclonal ,Reproducibility of Results ,Histology ,Original Articles ,General Medicine ,medicine.disease ,experimental pathophysiology ,Endoscopy ,Disease Models, Animal ,Inter-rater reliability ,030104 developmental biology ,Female ,030211 gastroenterology & hepatology ,business - Abstract
Background and Aims Although several endoscopic and histopathologic indices are available for evaluating the severity of inflammation in mouse models of colitis, the reliability of these scoring instruments is unknown. Our aim was to evaluate the reliability of the individual items in the existing indices and develop new scoring systems by selection of the most reliable index items. Methods Two observers scored the histological slides [n = 224] and endoscopy videos [n = 201] from treated and untreated Interleukin[IL]-10 knock-out and T-cell transferred SCID mice. Intra-rater and inter-rater reliability for endoscopy and histology scores, and each individual item, were measured using intraclass correlation coefficients [ICCs]. The Mouse Colitis Histology Index [MCHI] and Mouse Colitis Endoscopy Index [MCEI] were developed using the most reliable items. Both were correlated to the colon density and to each other and were evaluated for their ability to detect changes in pathobiology. Results The intraclass correlation coefficients (ICCs) for inter-rater agreement (95% CIs) for the total histology and endoscopy scores were 0.90 [0.87–0.92] and 0.80 [0.76–0.84], respectively. The MCHI and MCEI were highly correlated with colon density, with a Spearman Rho = 0.81[0.75–0.85] and 0.73 [0.66–0.79], respectively, and with each other, Spearman Rho = 0.71 [0.63–0.77]. The MCHI and MCEI were able to distinguish between the experimental groups within the models, with pairwise differences between the treated and untreated groups being statistically significant [p < 0.001]. Conclusions These histological and endoscopic indices are valid and reliable measures of intestinal inflammation in mice, and they are responsive to treatment effects in pre-clinical studies.
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- 2018
5. Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages.
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Sebastiaan M Bol, Perry D Moerland, Sophie Limou, Yvonne van Remmerden, Cédric Coulonges, Daniëlle van Manen, Joshua T Herbeck, Jacques Fellay, Margit Sieberer, Jantine G Sietzema, Ruben van 't Slot, Jeremy Martinson, Jean-François Zagury, Hanneke Schuitemaker, and Angélique B van 't Wout
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Medicine ,Science - Abstract
HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages.Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16 × 10(-5)). While the association was not genome-wide significant (p
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- 2011
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6. Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies
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Angélique B. van ‘t Wout, Jason S. McLellan, R. Anthony Williamson, Elissa Keogh, Tina Ritschel, Harrison G. Jones, Just P. J. Brakenhoff, Dirk Roymans, Ellen Lanckacker, Gabriel Pascual, Jehangir Wadia, Polina Furmanova-Hollenstein, Johannes P. M. Langedijk, and Morgan S.A. Gilman
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0301 basic medicine ,Male ,Pulmonology ,Protein Conformation ,Physiology ,viruses ,Respiratory System ,Glycobiology ,Antibodies, Viral ,Crystallography, X-Ray ,Biochemistry ,Epitope ,Epithelium ,Epitopes ,Protein structure ,Animal Cells ,Immune Physiology ,CX3CR1 ,Medicine and Health Sciences ,Public and Occupational Health ,Enzyme-Linked Immunoassays ,lcsh:QH301-705.5 ,Cells, Cultured ,chemistry.chemical_classification ,Immune System Proteins ,Crystallography ,biology ,Physics ,virus diseases ,respiratory system ,Condensed Matter Physics ,3. Good health ,Physical Sciences ,Crystal Structure ,Antibody ,Cellular Types ,Anatomy ,Research Article ,lcsh:Immunologic diseases. Allergy ,030106 microbiology ,Immunology ,Bronchi ,Respiratory Syncytial Virus Infections ,Research and Analysis Methods ,Microbiology ,Viral Attachment ,Virus ,Antibodies ,03 medical and health sciences ,Immune system ,Virology ,Genetics ,Respiratory Syncytial Virus Vaccines ,Animals ,Humans ,Solid State Physics ,Sigmodontinae ,CX3CL1 ,Immunoassays ,Molecular Biology ,Glycoproteins ,Virus Glycoproteins ,Chemokine CX3CL1 ,Prophylaxis ,Biology and Life Sciences ,Proteins ,Epithelial Cells ,Cell Biology ,Antibodies, Neutralizing ,Rats ,030104 developmental biology ,Biological Tissue ,chemistry ,lcsh:Biology (General) ,Respiratory Syncytial Virus, Human ,Respiratory Infections ,biology.protein ,Immunologic Techniques ,Parasitology ,Preventive Medicine ,Glycoprotein ,lcsh:RC581-607 ,Viral Fusion Proteins ,Viral Transmission and Infection - Abstract
Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and the elderly, and yet there remains no effective treatment or vaccine. The surface of the virion is decorated with the fusion glycoprotein (RSV F) and the attachment glycoprotein (RSV G), which binds to CX3CR1 on human airway epithelial cells to mediate viral attachment and subsequent infection. RSV G is a major target of the humoral immune response, and antibodies that target the central conserved region of G have been shown to neutralize both subtypes of RSV and to protect against severe RSV disease in animal models. However, the molecular underpinnings for antibody recognition of this region have remained unknown. Therefore, we isolated two human antibodies directed against the central conserved region of RSV G and demonstrated that they neutralize RSV infection of human bronchial epithelial cell cultures in the absence of complement. Moreover, the antibodies protected cotton rats from severe RSV disease. Both antibodies bound with high affinity to a secreted form of RSV G as well as to a peptide corresponding to the unglycosylated central conserved region. High-resolution crystal structures of each antibody in complex with the G peptide revealed two distinct conformational epitopes that require proper folding of the cystine noose located in the C-terminal part of the central conserved region. Comparison of these structures with the structure of fractalkine (CX3CL1) alone or in complex with a viral homolog of CX3CR1 (US28) suggests that RSV G would bind to CX3CR1 in a mode that is distinct from that of fractalkine. Collectively, these results build on recent studies demonstrating the importance of RSV G in antibody-mediated protection from severe RSV disease, and the structural information presented here should guide the development of new vaccines and antibody-based therapies for RSV., Author summary Respiratory syncytial virus (RSV) is a common cause of bronchiolitis and pneumonia, and is a leading cause of infant deaths globally due to infectious disease. Despite decades of research, there is still no vaccine or widespread treatment for RSV. In this study, we isolated two antibodies that bind to the central conserved region of the viral attachment glycoprotein, RSV G. The antibodies effectively neutralize both subtypes of RSV and protect RSV-challenged animals from severe disease. We also determined high-resolution crystal structures of each antibody in complex with the central conserved region of RSV G to gain a better understanding of how these antibodies bind to RSV G and how they neutralize the virus. Because RSV G is a small folded domain bounded by unstructured mucin-like domains, structural elucidation of the central conserved region provides atomic-level information for the complete folded portion of RSV G. The results presented here will help develop effective antibodies for passive prophylaxis as well as guide efforts to design vaccines that elicit broadly neutralizing antibodies against RSV G.
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- 2018
7. Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intra-host evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models
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Hanneke Schuitemaker, Jennifer Tom, Agnes E. van den Blink, Diana Edo-Matas, Cèlia Serna-Bolea, Philippe Lemey, Marc A. Suchard, Angélique B. van 't Wout, Department of Experimental Immunology, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA), Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Department of Biostatistics, University of California [Los Angeles] (UCLA), University of California-University of California, Universtitat de Barcelona, Barcelona Centre for International Health Research, Departments of Biomathematics and Human Genetics, Amsterdam institute for Infection and Immunity, and Experimental Immunology
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Male ,Heterozygote ,Genotype ,Receptors, CCR5 ,HIV Infections ,Sequence alignment ,HIV Envelope Protein gp120 ,Biology ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,Genetics ,Humans ,Evolutionary dynamics ,Molecular Biology ,Research Articles ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) ,030304 developmental biology ,Acquired Immunodeficiency Syndrome ,0303 health sciences ,Polymorphism, Genetic ,Models, Genetic ,Phylogenetic tree ,030306 microbiology ,Life Sciences ,Bayes Theorem ,Sequence Analysis, DNA ,CD4 Lymphocyte Count ,3. Good health ,Fixation (population genetics) ,Viral evolution ,Host-Pathogen Interactions ,Disease Progression ,HIV-1 ,Sequence Alignment ,Gene Deletion - Abstract
The interplay between C-C chemokine receptor type 5 (CCR5) host genetic background, disease progression, and intrahost HIV-1 evolutionary dynamics remains unclear because differences in viral evolution between hosts limit the ability to draw conclusions across hosts stratified into clinically relevant populations. Similar inference problems are proliferating across many measurably evolving pathogens for which intrahost sequence samples are readily available. To this end, we propose novel hierarchical phylogenetic models (HPMs) that incorporate fixed effects to test for differences in dynamics across host populations in a formal statistical framework employing stochastic search variable selection and model averaging. To clarify the role of CCR5 host genetic background and disease progression on viral evolutionary patterns, we obtain gp120 envelope sequences from clonal HIV-1 variants isolated at multiple time points in the course of infection from populations of HIV-1-infected individuals who only harbored CCR5-using HIV-1 variants at all time points. Presence or absence of a CCR5 wt/delta 32 genotype and progressive or long-term nonprogressive course of infection stratify the clinical populations in a two-way design. As compared with the standard approach of analyzing sequences from each patient independently, the HPM provides more efficient estimation of evolutionary parameters such as nucleotide substitution rates and d(N)/d(S) rate ratios, as shown by significant shrinkage of the estimator variance. The fixed effects also correct for nonindependence of data between populations and results in even further shrinkage of individual patient estimates. Model selection suggests an association between nucleotide substitution rate and disease progression, but a role for CCR5 genotype remains elusive. Given the absence of clear d(N)/d(S) differences between patient groups, delayed onset of AIDS symptoms appears to be solely associated with lower viral replication rates rather than with differences in selection on amino acid fixation
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- 2011
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8. Rising HIV-1 viral load set point at a population level coincides with a fading impact of host genetic factors on HIV-1 control
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Jan M. Prins, Frank de Wolf, Luuk Gras, Radjin Steingrover, Agnes M. Harskamp, Irma Maurer, Marga M. Mangas Ruiz, Angélique B. van 't Wout, Brigitte Boeser-Nunnink, Ard van Sighem, Daniëlle van Manen, Hanneke Schuitemaker, Other departments, Amsterdam institute for Infection and Immunity, Experimental Immunology, and Infectious diseases
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Male ,RNA, Untranslated ,Time Factors ,Receptors, CCR5 ,Immunology ,HLA-C Antigens ,Biology ,Polymorphism, Single Nucleotide ,Loss of heterozygosity ,Cohort Studies ,Major Histocompatibility Complex ,Polymorphism (computer science) ,Genotype ,HIV Seropositivity ,Immunology and Allergy ,Humans ,Allele ,Gene ,Netherlands ,Ecology ,HCP5 ,Viral Load ,Virology ,Infectious Diseases ,Genetic marker ,Disease Progression ,HIV-1 ,Female ,RNA, Long Noncoding ,Viral load - Abstract
Objective: Heterozygosity for a 32 base pair deletion in the CCR5 gene (CCR5wt/Δ32) and the minor alleles of a single-nucleotide polymorphism in the HCP5 gene (rs2395029) and in the HLA-C gene region (−35HLA-C; rs9264942) has been associated with a lower viral load set point. Recent studies have shown that over calendar time, viral load set point has significantly increased at a population level. Here we studied whether this increase coincides with a fading impact of above-mentioned host genetic markers on HIV-1 control. Methods: We compared the association between viral load set point and HCP5 rs2395029, −35HLA-C rs9264942, and the CCR5wt/Δ32 genotype in HIV-1-infected individuals in the Netherlands who had seroconverted between 1982 and 2002 (pre-2003 seroconverters, n = 459) or between 2003 and 2009 (post-2003 seroconverters, n = 231). Results: Viral load set point in post-2003 seroconverters was significantly higher than in pre-2003 seroconverters (P = 4.5 × 10−5). The minor alleles for HCP5 rs2395029, −35HLA-C rs9264942 and CCR5wt/Δ32 had a similar prevalence in both groups and were all individually associated with a significantly lower viral load set point in pre-2003 seroconverters. In post-2003 seroconverters, this association was no longer observed for HCP5 rs2395029 and CCR5wt/Δ32. The association between viral load set point and HCP5 rs2395029 had significantly changed over time, whereas the change in impact of the CCR5wt/Δ32 genotype over calendar time was not independent from the other markers under study. Conclusion: The increased viral load set point at a population level coincides with a lost impact of certain host genetic factors on HIV-1 control.
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- 2011
9. HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study
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Lisa P. Jacobson, Benjamin Jacobs, Surafel Gezahegne, James I. Mullins, Joseph B. Margolick, Angélique B. van 't Wout, Geoffrey S. Gottlieb, Kim G. Wong, Laura Heath, Stephanie E Leach, David C. Nickle, Amsterdam institute for Infection and Immunity, and Experimental Immunology
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Adult ,Male ,Glycosylation ,Time Factors ,Adolescent ,Genotype ,Receptors, CCR5 ,Multicenter AIDS Cohort Study ,Sequence Homology ,HIV Infections ,Article ,Men who have sex with men ,Cohort Studies ,Acquired immunodeficiency syndrome (AIDS) ,medicine ,Immunology and Allergy ,Cluster Analysis ,Humans ,Seroconversion ,Phylogeny ,Polymorphism, Genetic ,biology ,env Gene Products, Human Immunodeficiency Virus ,Homosexuality ,Sequence Analysis, DNA ,Middle Aged ,biology.organism_classification ,medicine.disease ,Virology ,CD4 Lymphocyte Count ,Infectious Diseases ,Cohort ,Lentivirus ,HIV-1 ,RNA, Viral ,Viral disease ,Cohort study - Abstract
Understanding the characteristics of human immunodeficiency virus (HIV) necessary for infection in a new host is a critical goal for acquired immunodeficiency syndrome (AIDS) research. We studied the characteristics of HIV-1 envelope genes in 38 men in the Multicenter AIDS Cohort Study cohort before seroconversion. We found a range of diversity (0.2%-5.6% [median, 0.86%]), V1-V2 loop length (58-93 aa), and potential N-linked glycosylation sites (n = 2-9). However, at least 46% of the men had replicating virus that appeared to have been derived from a single viral variant. Nearly all variants were predicted to be CCR5 tropic. We found no correlation between these viral characteristics and the HIV outcomes of time to clinical AIDS or death and/or a CD4 cell count
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- 2008
10. Isolation and propagation of HIV-1 on peripheral blood mononuclear cells
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Neeltje A. Kootstra, Hanneke Schuitemaker, Angélique B. van 't Wout, Amsterdam institute for Infection and Immunity, and Experimental Immunology
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Virus Cultivation ,HIV Infections ,Viral quasispecies ,Biology ,Virus Replication ,Peripheral blood mononuclear cell ,Virology ,Phenotype ,General Biochemistry, Genetics and Molecular Biology ,Reverse transcriptase ,Virus ,In vitro ,Viral replication ,HIV-1 ,Leukocytes, Mononuclear ,Humans ,Function (biology) - Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is characterized by a gradual loss of CD4+ T cells and T-cell function and an ongoing high level of virus replication. The high replication rate and the error-prone nature of HIV-1 reverse transcriptase create a diverse viral quasispecies throughout infection. To study biological properties of HIV-1 quasispecies in relation to the clinical course of infection, the in vitro preservation of phenotypical characteristics of the virus is essential. Here, we describe the method for bulk isolation of the HIV-1 quasispecies and a limiting dilution virus isolation protocol by which single coexisting HIV-1 variants can be obtained using peripheral blood mononuclear cells from a healthy donor as target cells. In addition, methods for propagation and titration of HIV-1 are provided.
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- 2008
11. DYRK1A Controls HIV-1 Replication at a Transcriptional Level in an NFAT Dependent Manner
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Angélique B. van 't Wout, Karel A. van Dort, Neeltje A. Kootstra, Thijs Booiman, Vladimir V. Loukachov, Other departments, AII - Amsterdam institute for Infection and Immunity, and Experimental Immunology
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Transcription, Genetic ,viruses ,lcsh:Medicine ,Protein Serine-Threonine Kinases ,Biology ,Virus Replication ,Transcription (biology) ,Humans ,lcsh:Science ,Transcription factor ,HIV Long Terminal Repeat ,Host factor ,Multidisciplinary ,NFATC Transcription Factors ,lcsh:R ,NFAT ,Protein-Tyrosine Kinases ,Provirus ,Molecular biology ,Cell biology ,HEK293 Cells ,Viral replication ,HIV-1 ,lcsh:Q ,Protein Binding ,Research Article - 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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- 2015
12. Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data
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Diana Edo-Matas, Art F. Y. Poon, Hanneke Schuitemaker, Evelien M. Bunnik, P. Richard Harrigan, Angélique B. van 't Wout, Luke C. Swenson, Amsterdam institute for Infection and Immunity, and Experimental Immunology
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0106 biological sciences ,Viral Diseases ,HIV Infections ,01 natural sciences ,Genotype ,Biology (General) ,Molecular clock ,Phylogeny ,Genetics ,0303 health sciences ,Ecology ,Phylogenetic tree ,virus diseases ,High-Throughput Nucleotide Sequencing ,3. Good health ,Infectious Diseases ,Phenotype ,Computational Theory and Mathematics ,Modeling and Simulation ,Viral evolution ,Host-Pathogen Interactions ,Medicine ,RNA, Viral ,Sequence Analysis ,Algorithms ,Research Article ,Ancestral reconstruction ,Receptors, CXCR4 ,Receptors, CCR5 ,QH301-705.5 ,Molecular Sequence Data ,Biology ,010603 evolutionary biology ,Evolution, Molecular ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Acquired immunodeficiency syndrome (AIDS) ,Phylogenetics ,Evolutionary Modeling ,medicine ,Humans ,Amino Acid Sequence ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Human evolutionary genetics ,Computational Biology ,HIV ,medicine.disease ,Mutation ,HIV-1 ,Genetic Fitness ,Population Genetics - Abstract
At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a ‘fitness valley’ separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant., Author Summary At the start of infection, human immunodeficiency virus (HIV) generally requires a specific protein receptor (CCR5) on the cell surface to bind and enter the cell. In roughly half of all HIV infections, the virus population eventually switches to using a different receptor (CXCR4). This ‘HIV coreceptor switch’ is associated with an accelerated rate of progression to AIDS. Although it is not known why this switch occurs in some infections and not others, it is thought to be shaped by constraints on how HIV can evolve from one mode to another. In this study, we test this hypothesis by reconstructing the evolutionary histories of HIV within 8 patients known to have undergone an HIV coreceptor switch. Each history is recreated from samples of HIV genetic sequences that were derived from repeated blood samples by next-generation sequencing, an emerging technology that is rapidly becoming an essential tool in the study of rapidly-evolving populations such as viruses or cancerous cells. Because we have samples from different points in time, we can use models of evolution to extrapolate back in time to the ancestors of each infection. Our analysis reveals patient-specific dynamics in HIV evolution that sheds new light on the determinants of the coreceptor switch.
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- 2012
13. Low Incidence of HIV-1 Superinfection Even After Episodes of Unsafe Sexual Behavior of Homosexual Men in the Amsterdam Cohort Studies on HIV Infection and AIDS
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Ineke G. Stolte, Maria Prins, Andrea Rachinger, Judith A. Burger, Tom Derks van de Ven, Angélique B. van 't Wout, Precious Manyenga, Hanneke Schuitemaker, Amsterdam institute for Infection and Immunity, Medical Microbiology and Infection Prevention, Amsterdam Public Health, Infectious diseases, and Experimental Immunology
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Male ,Maximum likelihood ,viruses ,Human immunodeficiency virus (HIV) ,HIV Infections ,Biology ,medicine.disease_cause ,Genes, env ,Risk-Taking ,Acquired immunodeficiency syndrome (AIDS) ,medicine ,Immunology and Allergy ,Humans ,Prospective Studies ,Homosexuality, Male ,Phylogeny ,Netherlands ,Unsafe Sex ,Incidence (epidemiology) ,virus diseases ,Serum samples ,medicine.disease ,Genes, gag ,Infectious Diseases ,Sexual behavior ,Superinfection ,Immunology ,HIV-1 ,RNA, Viral ,Cohort study - Abstract
Background. Human immunodeficiency virus type 1 (HIV-1) superinfection is infection of an HIV-1 seropositive individual with another HIV-1 strain. The rate at which HIV-1 superinfection occurs might be influenced by sexual behavior. Superinfection might be detected more often by analyzing longitudinal samples collected from time periods of unsafe sexual behavior. Methods. Envelope C2-C4 and gag sequences were generated from HIV-1 RNA from longitudinal serum samples that were obtained around self-reported sexual risk periods from 15 homosexual therapy-naive men who participated in the Amsterdam Cohort Studies on HIV Infection and AIDS. Maximum likelihood phylogenetic analysis was used to determine whether HIV-1 superinfection had occurred. Results. We studied a total of 124 serum samples from 15 patients with a median of 8 samples and of 5.8 person-years of follow-up per patient. Phylogenetic analysis on 907 C2-C4 env and 672 gag sequences revealed no case of HIV-1 superinfection, resulting in a superinfection incidence rate of 0 per 100 person-years [95% CI: 0 - -4.2]. Conclusions. We conclude that HIV-1 superinfection incidence is low in this subgroup of homosexual men who reported unsafe sexual behavior. Additional studies are required to estimate the impact of also other factors, which may determine the risk to acquire HIV-1 superinfection
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- 2011
14. Genome-Wide Association Study Identifies Single Nucleotide Polymorphism in DYRK1A Associated with Replication of HIV-1 in Monocyte-Derived Macrophages
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Perry D. Moerland, Jean-François Zagury, Cédric Coulonges, Margit Sieberer, Daniëlle van Manen, Jeremy J. Martinson, Sophie Limou, Jacques Fellay, Ruben van 't Slot, Hanneke Schuitemaker, Joshua T. Herbeck, Jantine G. Sietzema, Yvonne van Remmerden, Sebastiaan Bol, Angélique B. van 't Wout, Faculteit der Geneeskunde, Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA)-Center for Infection and Immunity Amsterdam (CINIMA), Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, University of Amsterdam [Amsterdam] (UvA)-University of Amsterdam [Amsterdam] (UvA), Netherlands Bioinformatics Center (NBIC), Netherlands Bioinformatics Center, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Department of Microbiology, University of Washington School of Medicine, Center for Human Genome Variation, Duke University [Durham], Complex Genetics Section, Department of Biomedical Genetics, University Medical Center [Utrecht], Department of Human Genetics, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), The authors acknowledge funding from the Landsteiner Foundation Blood Research (registration number 0526) and the European Union (Marie Curie International Reintegration Grant 029167). The MACS is funded by the National Institute of Allergy and Infectious Diseases, with additional supplemental funding from the National Cancer Institute. UO1-AI-35042, UL1-RR025005 (GCRC), UO1-AI-35043, UO1-AI-35039, UO1-AI-35040, UO1-AI-35041., Guellaen, Georges, University of Amsterdam [Amsterdam] (UvA)-Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA)-Center for Infection and Immunity Amsterdam (CINIMA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10, Amsterdam institute for Infection and Immunity, Amsterdam Public Health, Epidemiology and Data Science, Other departments, and Experimental Immunology
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Male ,lcsh:Medicine ,HIV Infections ,Genome-wide association study ,Virus Replication ,Linkage Disequilibrium ,Monocytes ,0302 clinical medicine ,MESH: Animals ,lcsh:Science ,Cells, Cultured ,0303 health sciences ,Multidisciplinary ,MESH: Enzyme-Linked Immunosorbent Assay ,MESH: Feces ,Genomics ,Middle Aged ,Protein-Tyrosine Kinases ,3. Good health ,SNP genotyping ,Host-Pathogen Interaction ,MESH: Entamoebiasis ,Medicine ,Infectious diseases ,Female ,Research Article ,Adult ,medicine.medical_specialty ,Immune Cells ,Immunology ,Retrovirology and HIV immunopathogenesis ,Single-nucleotide polymorphism ,Viral diseases ,Protein Serine-Threonine Kinases ,Biology ,Polymorphism, Single Nucleotide ,Microbiology ,Virus ,03 medical and health sciences ,Genome Analysis Tools ,In vivo ,Virology ,Molecular genetics ,Genome-Wide Association Studies ,Genetics ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,medicine ,Humans ,MESH: Antibodies, Protozoan ,Genetic Predisposition to Disease ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,030304 developmental biology ,Macrophages ,Host Cells ,lcsh:R ,DNA replication ,Computational Biology ,HIV ,Human Genetics ,MESH: Entamoeba histolytica ,MESH: Liver Abscess, Amebic ,Viral Replication ,Viral replication ,HIV-1 ,Clinical Immunology ,lcsh:Q ,Viral Transmission and Infection ,030217 neurology & neurosurgery ,Genome-Wide Association Study ,MESH: Antigens, Protozoan - Abstract
International audience; Background: HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages. Methodology/Principal Findings: Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.1661025). While the association was not genome-wide significant (p,161027), we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034). Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.8461026). In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048). Conclusions/Significance: These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo.
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- 2011
15. Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing
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Angélique B. van 't Wout, Arne Frantzell, Christos J. Petropoulos, Eoin Coakley, Winnie Dong, Evelien M. Bunnik, P. Richard Harrigan, Hanneke Schuitemaker, Diana Edo-Matas, Wei Huang, Luke C. Swenson, Faculteit der Geneeskunde, AII - Amsterdam institute for Infection and Immunity, and Experimental Immunology
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lcsh:Immunologic diseases. Allergy ,Receptors, CXCR4 ,Viral Diseases ,Time Factors ,Receptors, CCR5 ,Sequence analysis ,Immunology ,HIV Infections ,V3 loop ,Biology ,Microbiology ,CXCR4 ,Viral Evolution ,03 medical and health sciences ,Immunodeficiency Viruses ,Viral envelope ,Virology ,Genetic variation ,Genetics ,Humans ,lcsh:QH301-705.5 ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Transition (genetics) ,Sequence Analysis, RNA ,030306 microbiology ,env Gene Products, Human Immunodeficiency Virus ,Genetic Variation ,Computational Biology ,HIV ,RNA ,virus diseases ,Biological Evolution ,Phenotype ,3. Good health ,Infectious Diseases ,lcsh:Biology (General) ,HIV-1 ,RNA, Viral ,Medicine ,Parasitology ,lcsh:RC581-607 ,Sequence Analysis ,Research Article - Abstract
The emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants is associated with accelerated disease progression. CXCR4-using variants are believed to evolve from CCR5-using variants, but due to the extremely low frequency at which transitional intermediate variants are often present, the kinetics and mutational pathways involved in this process have been difficult to study and are therefore poorly understood. Here, we used ultra-deep sequencing of the V3 loop of the viral envelope in combination with the V3-based coreceptor prediction tools PSSMNSI/SI and geno2pheno[coreceptor] to detect HIV-1 variants during the transition from CCR5- to CXCR4-usage. We analyzed PBMC and serum samples obtained from eight HIV-1-infected individuals at three-month intervals up to one year prior to the first phenotypic detection of CXCR4-using variants in the MT-2 assay. Between 3,482 and 10,521 reads were generated from each sample. In all individuals, V3 sequences of predicted CXCR4-using HIV-1 were detected at least three months prior to phenotypic detection of CXCR4-using variants in the MT-2 assay. Subsequent analysis of the genetic relationships of these V3 sequences using minimum spanning trees revealed that the transition in coreceptor usage followed a stepwise mutational pathway involving sequential intermediate variants, which were generally present at relatively low frequencies compared to the major predicted CCR5- and CXCR4-using variants. In addition, we observed differences between individuals with respect to the number of predicted CXCR4-using variants, the diversity among major predicted CCR5-using variants, and the presence or absence of intermediate variants with discordant phenotype predictions. These results provide the first detailed description of the mutational pathways in V3 during the transition from CCR5- to CXCR4-usage in natural HIV-1 infection., Author Summary The first step in the infection of a target cell by human immunodeficiency virus type 1 (HIV-1) is binding of the envelope spike to its receptor CD4 and a coreceptor on the cellular surface. HIV-1 variants present early in the course of infection mainly use the coreceptor CCR5, while virus variants that use CXCR4 can appear later in infection. This change in coreceptor usage is associated with mutations in the third variable (V3) loop of the envelope spike, but has been difficult to study due to the low presence of intermediate variants. Using ultra-deep sequencing, we obtained thousands of sequences of the V3 loop from HIV-1 infected individuals in the year before CXCR4-using variants were first detected, including sequences from almost all intermediate variants. We show that mutations are introduced sequentially in the V3 loop during the evolution from CCR5- to CXCR4-usage. Furthermore, we describe differences and similarities between HIV-1-infected individuals that are related to this change in coreceptor usage, which provides the first detailed overview of this evolutionary process during natural HIV-1 infection.
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- 2011
16. Comparison of Human Immunodeficiency Virus Type 1 Tropism Profiles in Clinical Samples by the Trofile and MT-2 Assays▿
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Wei Huang, Eoin Coakley, Yolanda Lie, Soumi Gupta, Irma Maurer, Agnes M. Harskamp, Christos J. Petropoulos, Marga Mangas-Ruiz, Jacqueline D. Reeves, Angélique B. van 't Wout, Hanneke Schuitemaker, Other departments, Amsterdam institute for Infection and Immunity, and Experimental Immunology
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Pharmacology ,Receptors, CXCR4 ,CCR5 receptor antagonist ,Biology ,biology.organism_classification ,Virology ,Antiviral Agents ,Virus ,Plasma ,Viral Tropism ,Infectious Diseases ,Lentivirus ,Immunology ,Tissue tropism ,HIV-1 ,Leukocytes, Mononuclear ,Humans ,Pharmacology (medical) ,Viral disease ,Seroconversion ,Tropism ,Trofile assay - Abstract
The recent availability of CCR5 antagonists as anti-human immunodeficiency virus (anti-HIV) therapeutics has highlighted the need to accurately identify CXCR4-using variants in patient samples when use of this new drug class is considered. The Trofile assay (Monogram Biosciences) has become the method that is the most widely used to define tropism in the clinic prior to the use of a CCR5 antagonist. By comparison, the MT-2 assay has been used since early in the HIV epidemic to define tropism in clinical specimens. Given that there are few data from direct comparisons of these two assays, we evaluated the performance of the plasma-based Trofile assay and the peripheral blood mononuclear cell (PBMC)-based MT-2 assay for the detection of CXCR4 use in defining the tropism of HIV isolates derived from clinical samples. The various samples used for this comparison were derived from participants of the Amsterdam Cohort Studies on HIV infection and AIDS who underwent consecutive MT-2 assay testing of their PBMCs at approximately 3-month intervals. This unique sample set was specifically selected because consecutive MT-2 assays had demonstrated a shift from negative to positive in PBMCs, reflecting the first emergence of CXCR4-using virus in PBMCs above the level of detection of the assay in these individuals. Trofile testing was performed with clonal HIV type 1 (HIV-1) variants (n= 21), MT-2 cell culture-derived cells (n= 20) and supernatants (n= 42), and plasma samples (n= 76). Among the clonal HIV-1 variants and MT-2 cell culture-derived samples, the results of the Trofile and MT-2 assays demonstrated a high degree of concordance (95% to 98%). Among consecutive plasma samples, detection of CXCR4-using virus was at or before the time of first detection by the MT-2 assay in 5/10 patients by the original Trofile assay and in 9/10 patients by the enhanced-sensitivity Trofile assay. Differences in the time to the first detection of CXCR4 use between the MT-2 assay (PBMCs) and the original Trofile assay (plasma) were greatly reduced by the enhanced-sensitivity Trofile assay, suggesting that sensitivity for the detection of minor CXCR4-using variants may be a more important determinant of discordant findings than compartmentalization. The similarities in performance of the enhanced-sensitivity Trofile and MT-2 assays suggest that either may be an appropriate methodology to define tropism in patient specimens.
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- 2009
17. Evidence for limited genetic compartmentalization of HIV-1 between lung and blood
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Laura Heath, Angélique B. van 't Wout, Jan McClure, Hong Zhao, Homer L. Twigg, John E. Mittler, Alan Fox, Jeffrey T. Schouten, David R. Park, Kurt Diem, Lawrence Corey, James I. Mullins, Amsterdam institute for Infection and Immunity, and Experimental Immunology
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Glycosylation ,T-Lymphocytes ,lcsh:Medicine ,HIV Infections ,Bronchoalveolar Lavage ,Polymerase Chain Reaction ,law.invention ,0302 clinical medicine ,law ,Genotype ,Blood plasma ,030212 general & internal medicine ,lcsh:Science ,Lung ,Polymerase chain reaction ,Phylogeny ,0303 health sciences ,Multidisciplinary ,medicine.diagnostic_test ,Compartmentalization (psychology) ,Infectious Diseases/HIV Infection and AIDS ,respiratory system ,Computational Biology/Evolutionary Modeling ,Virology/Virus Evolution and Symbiosis ,3. Good health ,medicine.anatomical_structure ,Evolutionary Biology/Microbial Evolution and Genomics ,Virology/Immunodeficiency Viruses ,Research Article ,Biology ,Peripheral blood mononuclear cell ,03 medical and health sciences ,Immune system ,Infectious Diseases/Viral Infections ,medicine ,Humans ,030304 developmental biology ,Models, Statistical ,Infectious Diseases/Respiratory Infections ,lcsh:R ,Virology/Persistence and Latency ,Genetic Variation ,Sequence Analysis, DNA ,Virology ,respiratory tract diseases ,Bronchoalveolar lavage ,Immunology ,HIV-1 ,Leukocytes, Mononuclear ,RNA ,lcsh:Q - Abstract
Background HIV-1 is frequently detected in the lungs of infected individuals and is likely important in the development of pulmonary opportunistic infections. The unique environment of the lung, rich in alveolar macrophages and with specialized local immune responses, may contribute to differential evolution or selection of HIV-1. Methodology and Findings We characterized HIV-1 in the lung in relation to contemporaneous viral populations in the blood. The C2-V5 region of HIV-1 env was sequenced from paired lung (induced sputum or bronchoalveolar lavage) and blood (plasma RNA and proviral DNA from sorted or unsorted PBMC) from 18 subjects. Compartmentalization between tissue pairs was assessed using 5 established tree or distance-based methods, including permutation tests to determine statistical significance. We found statistical evidence of compartmentalization between lung and blood in 10/18 subjects, although lung and blood sequences were intermingled on phylogenetic trees in all subjects. The subject showing the greatest compartmentalization contained many nearly identical sequences in BAL sample, suggesting clonal expansion may contribute to reduced viral diversity in the lung in some cases. However, HIV-1 sequences in lung were not more homogeneous overall, nor were we able to find a lung-specific genotype associated with macrophage tropism in V3. In all four subjects in whom predicted X4 genotypes were found in blood, predicted X4 genotypes were also found in lung. Conclusions Our results support a picture of continuous migration of HIV-1 between circulating blood and lung tissue, with perhaps a very limited degree of localized evolution or clonal replication.
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- 2009
18. Nef induces multiple genes involved in cholesterol synthesis and uptake in human immunodeficiency virus type 1-infected T cells
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Ushnal Rao, Michael Schindler, Frank Kirchhoff, Angélique B. van 't Wout, J. Victor Swain, James I. Mullins, Melissa S. Pathmajeyan, and Experimental Immunology
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T-Lymphocytes ,Immunology ,HIV Infections ,Biology ,Microbiology ,Jurkat cells ,Virus ,Cell Line ,Jurkat Cells ,chemistry.chemical_compound ,Virology ,Aspartic Acid Endopeptidases ,Humans ,Gene ,Oligonucleotide Array Sequence Analysis ,Microarray analysis techniques ,Cholesterol ,Gene Expression Profiling ,virus diseases ,Molecular biology ,Virus-Cell Interactions ,Gene expression profiling ,Viral replication ,chemistry ,Cell culture ,Insect Science ,HIV-1 - Abstract
Several recent reports indicate that cholesterol might play an important role in human immunodeficiency virus type 1 (HIV-1) replication. We investigated the effects of HIV-1 infection on cholesterol biosynthesis and uptake using microarrays. HIV-1 increased gene expression of cholesterol genes in both transformed T-cell lines and primary CD4 + T cells. Consistent with our microarray data, 14 C-labeled mevalonate and acetate incorporation was increased in HIV-1-infected cells. Our data also demonstrate that changes in cholesterol biosynthesis and uptake are only observed in the presence of functional Nef, suggesting that increased cholesterol synthesis may contribute to Nef-mediated enhancement of virion infectivity and viral replication.
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- 2005
19. Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines
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Gary K. Geiss, Svetlana A. Mikheeva, James I. Mullins, Ginger K. Lehrman, Angélique B. van 't Wout, Gemma C. O'Keeffe, Roger E. Bumgarner, Michael G. Katze, and Experimental Immunology
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CD4-Positive T-Lymphocytes ,Gene Expression Regulation, Viral ,Immunology ,Biology ,Microbiology ,Cell Line ,Interferon ,Virology ,Gene expression ,medicine ,Gene ,Transcription factor ,DNA Primers ,Regulation of gene expression ,Base Sequence ,Microarray analysis techniques ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Flow Cytometry ,Molecular biology ,Virus-Cell Interactions ,Gene expression profiling ,Insect Science ,HIV-1 ,Cell activation ,medicine.drug - Abstract
The expression levels of ∼4,600 cellular RNA transcripts were assessed in CD4+-T-cell lines at different times after infection with human immunodeficiency virus type 1 strain BRU (HIV-1BRU) using DNA microarrays. We found that several classes of genes were inhibited by HIV-1BRUinfection, consistent with the G2arrest of HIV-1-infected cells induced by Vpr. These included genes involved in cell division and transcription, a family of DEAD-box proteins (RNA helicases), and all genes involved in translation and splicing. However, the overall level of cell activation and signaling was increased in infected cells, consistent with strong virus production. These included a subgroup of transcription factors, including EGR1 and JUN, suggesting they play a specific role in the HIV-1 life cycle. Some regulatory changes were cell line specific; however, the majority, including enzymes involved in cholesterol biosynthesis, of changes were regulated in most infected cell lines. Compendium analysis comparing gene expression profiles of our HIV-1 infection experiments to those of cells exposed to heat shock, interferon, or influenza A virus indicated that HIV-1 infection largely induced specific changes rather than simply activating stress response or cytokine response pathways. Thus, microarray analysis confirmed several known HIV-1 host cell interactions and permitted identification of specific cellular pathways not previously implicated in HIV-1 infection. Continuing analyses are expected to suggest strategies for impacting HIV-1 replication in vivo by targeting these pathways.
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- 2003
20. Pathogenesis of primary R5 human immunodeficiency virus type 1 clones in SCID-hu mice
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Angélique B. van 't Wout, David Camerini, James T. Patrie, Hanneke Schuitemaker, Robert M. Scoggins, James R. Taylor, and Other departments
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Receptors, CCR5 ,Immunology ,Cell ,CD4-CD8 Ratio ,Clone (cell biology) ,HIV Infections ,Mice, SCID ,Thymus Gland ,Viral quasispecies ,Biology ,Virus Replication ,Microbiology ,Peripheral blood mononuclear cell ,Pathogenesis ,Mice ,Cytopathogenic Effect, Viral ,Virology ,medicine ,Animals ,Humans ,Homozygote ,Thymocyte ,medicine.anatomical_structure ,Liver ,Viral replication ,Insect Science ,HIV-1 ,Pathogenesis and Immunity - Abstract
We studied the replication and cytopathicity in SCID-hu mice of R5 human immunodeficiency virus type 1 (HIV-1) biological clones from early and late stages of infection of three patients who never developed MT-2 cell syncytium-inducing (SI; R5X4 or X4) viruses. Several of the late-stage non-MT-2 cell syncytium-inducing (NSI; R5) viruses from these patients depleted human CD4+thymocytes from SCID-hu mice. Earlier clones from the same patients did not deplete CD4+thymocytes from SCID-hu mice as well as later clones. We studied three R5 HIV-1 clones from patient ACH142 in greater detail. Two of these clones were obtained prior to the onset of AIDS; the third was obtained following the AIDS diagnosis. In GHOST cell infection assays, all three ACH142 R5 HIV-1 clones could infect GHOST cells expressing CCR5 but not GHOST cells expressing any of nine other HIV coreceptors tested. Furthermore, these patient clones efficiently infected stimulated peripheral blood mononuclear cells from a normal donor but not those from a homozygous CCR5Δ32 individual. Statistical analyses of data obtained from infection of SCID-hu mice with patient ACH142 R5 clones revealed that only the AIDS-associated clone significantly depleted CD4+thymocytes from SCID-hu mice. This clone also replicated to higher levels in SCID-hu mice than the two earlier clones, and a significant correlation between viral replication and CD4+thymocyte depletion was observed. Our results indicate that an intrinsic property of AIDS-associated R5 patient clones causes their increased replication and cytopathic effects in SCID-hu mice and likely contributes to the development of AIDS in patients who harbor only R5 quasispecies of HIV-1.
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- 2000
21. Interaction of pseudomonas aeruginosa with epithelial cells: identification of differentially regulated genes by expression microarray analysis of human cDNAs
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Stephen Lory, Jeffrey K. Ichikawa, Angélique B. van 't Wout, Gita Bangera, Gary K. Geiss, Roger E. Bumgarner, Anne Norris, and Other departments
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Lipopolysaccharides ,Biology ,medicine.disease_cause ,Bacterial Adhesion ,Interferon-gamma ,Gene expression ,medicine ,Tumor Cells, Cultured ,Humans ,RNA, Messenger ,Oligonucleotide Array Sequence Analysis ,Regulation of gene expression ,Multidisciplinary ,Microarray analysis techniques ,Pseudomonas aeruginosa ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Epithelial Cells ,Biological Sciences ,Phosphoproteins ,Molecular biology ,Up-Regulation ,Gene expression profiling ,Bacterial adhesin ,DNA-Binding Proteins ,Gene Expression Regulation ,Genes ,Gene chip analysis ,DNA microarray ,Interferon Regulatory Factor-1 - Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that plays a major role in lung function deterioration in cystic fibrosis patients. To identify critical host responses during infection, we have used high-density DNA microarrays, consisting of 1,506 human cDNA clones, to monitor gene expression in the A549 lung pneumocyte cell line during exposure to P. aeruginosa . We have identified host genes that are differentially expressed upon infection, several of which require interaction with P. aeruginosa and the expression of the major subunit of type IV pili, PilA. Differential expression of genes involved in various cellular functions was identified, and we selected the gene encoding the transcription factor interferon regulatory factor 1 (IRF-1) for further analysis. The levels of the IRF-1 transcript increased 3- to 4-fold in A549 cells after adherence by P. aeruginosa . A similar increase of IRF-1 mRNA was observed in A549 cells exposed to wild-type P. aeruginosa when compared to an isogenic, nonpiliated strain. However, this difference was abolished when serum was present during the incubation of bacteria. Exposure of A549 cells to purified P. aeruginosa lipopolysaccharide did not result in a significant increase in IRF-1 mRNA. Although the P. aeruginosa -induced increased IRF-1 expression depends on the presence of bacterial adhesin, our findings do not preclude the possibility that other bacterial products are responsible for IRF-1 activation, which is enhanced by bacterial adherence to cells. These data show that microarray technology can be an important tool for studying the complex interplay between bacterial pathogens and host.
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- 2000
22. In vivo HIV-1 infection of CD45RA(+)CD4(+) T cells is established primarily by syncytium-inducing variants and correlates with the rate of CD4(+) T cell decline
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Hanneke Schuitemaker, Egbert Hovenkamp, Angélique B. van 't Wout, Hetty Blaak, Berend Hooibrink, M.H.J. Brouwer, and Other departments
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CD4-Positive T-Lymphocytes ,Male ,Receptors, CXCR4 ,Receptors, CCR5 ,T cell ,Cell ,Biology ,Giant Cells ,CXCR4 ,Pathogenesis ,Cytopathogenic Effect, Viral ,T-Lymphocyte Subsets ,In vivo ,immune system diseases ,medicine ,Humans ,Tropism ,Protein Tyrosine Phosphatase, Non-Receptor Type 1 ,Syncytium ,Multidisciplinary ,Genetic Variation ,virus diseases ,Biological Sciences ,biochemical phenomena, metabolism, and nutrition ,Virology ,CD4 Lymphocyte Count ,medicine.anatomical_structure ,Giant cell ,HIV-1 ,Leukocyte Common Antigens - Abstract
Switch from non-syncytium-inducing (NSI) to syncytium-inducing (SI) HIV type 1 (HIV-1) is associated with accelerated CD4+T cell depletion, which might partially be explained by higher virulence of SI variants compared with NSI variants. Because NSI and SI variants use different coreceptors for entry of target cells, altered tropism might offer an explanation for increased pathogenesis associated with SI HIV-1 infection. To investigate whether SI and NSI HIV-1 variants infect different CD4+T cell subsetsin vivo, the distribution of SI and NSI variants over CD4+memory (CD45RA−RO+) and naive (CD45RA+RO−) cells was studied by using limiting dilution cultures. In contrast to NSI variants that were mainly present in CD45RO+cells, SI variants were equally distributed over CD45RO+and CD45RA+cells. Infection of memory cells by both NSI and SI HIV-1 and infection of naive cells primarily by SI HIV-1 corresponded closely with the differential cell surface expression of CXCR4 and CCR5. The frequency of SI-infected CD45RA+CD4+T cells, but not the frequency of NSI- or SI-infected CD45RO+CD4+T cells, correlated with the rate of CD4+T cell depletion. Infection of naive cells by SI HIV-1 may interfere with CD4+T cell production and thus account for rapid CD4+T cell depletion.
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- 2000
23. Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics
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Daniëlle van Manen, Angélique B. van 't Wout, and Hanneke Schuitemaker
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lcsh:Immunologic diseases. Allergy ,Candidate gene ,Genome-wide association study ,Single-nucleotide polymorphism ,HIV Infections ,Review ,Biology ,Genome-wide association studies ,Single-nucleotide polymorphisms ,Pathogenesis ,Virology ,Genetic variation ,HIV susceptibility ,Humans ,Genetic Predisposition to Disease ,Genetic association ,Genetics ,Phenotype ,Host genetics ,Infectious Diseases ,HIV pathogenesis ,Pharmacogenomics ,Host-Pathogen Interactions ,HIV-1 ,lcsh:RC581-607 ,Genome-Wide Association Study - 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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- 2012
24. Clinical significance of HIV-1 coreceptor usage
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Paolo Lusso, Hanneke Schuitemaker, Angélique B. van 't Wout, and Faculteit der Geneeskunde
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CD4-Positive T-Lymphocytes ,Receptors, CXCR4 ,Receptors, CCR5 ,Human immunodeficiency virus (HIV) ,lcsh:Medicine ,HIV Infections ,Disease ,Review ,Biology ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Virus ,Pathogenesis ,Evolution, Molecular ,Acquired immunodeficiency syndrome (AIDS) ,medicine ,Humans ,Clinical significance ,Medicine(all) ,Acquired Immunodeficiency Syndrome ,Biochemistry, Genetics and Molecular Biology(all) ,lcsh:R ,virus diseases ,Computational Biology ,General Medicine ,medicine.disease ,Phenotype ,Protein Structure, Tertiary ,Anti-Retroviral Agents ,Immunology ,HIV-1 ,Identification (biology) ,Chemokines ,Algorithms - Abstract
The identification of phenotypically distinct HIV-1 variants with different prevalence during the progression of the disease has been one of the earliest discoveries in HIV-1 biology, but its relevance to AIDS pathogenesis remains only partially understood. The physiological basis for the phenotypic variability of HIV-1 was elucidated with the discovery of distinct coreceptors employed by the virus to infect susceptible cells. The role of the viral phenotype in the variable clinical course and treatment outcome of HIV-1 infection has been extensively investigated over the past two decades. In this review, we summarize the major findings on the clinical significance of the HIV-1 coreceptor usage.
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- 2011
25. Donor variation in in vitro HIV-1 susceptibility of monocyte-derived macrophages
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Hanneke Schuitemaker, Angélique B. van 't Wout, Neeltje A. Kootstra, Jantine G. Sietzema, Yvonne van Remmerden, Sebastiaan Bol, AII - Amsterdam institute for Infection and Immunity, and Experimental Immunology
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Adult ,Male ,Receptors, CCR5 ,Macrophage ,Human immunodeficiency virus (HIV) ,Biology ,medicine.disease_cause ,Monocyte ,Genetic analysis ,Young Adult ,Virology ,Genotype ,medicine ,Humans ,Genetic Predisposition to Disease ,Cells, Cultured ,Sequence Deletion ,Macrophages ,Genetic Variation ,virus diseases ,Middle Aged ,Phenotype ,In vitro ,medicine.anatomical_structure ,Host genetic variation ,Monocyte-Derived Macrophages ,Immunology ,HIV-1 ,Female ,CCR5 - Abstract
Primary human cells from different donors vary in their susceptibility to in vitro infection with HIV-1. In order to perform genetic analysis to identify host factors that affect HIV-1 susceptibility, it is important that a clear phenotype is defined. Here, we report a standardized method to Study variation for in vitro HIV-1 infection in monocyte-derived macrophages (MDM) from large numbers of individuals. With this assay, HIV-1 susceptibility of MDM from 489 different donors shows more than 3 log variation and a good correlation with the 32 base pair deletion in the CCR5 co-receptor (ccr5 Delta 32 genotype) of the donors. However, in 7 of 12 donors completely resistant to infection with CCR5-using HIV-1, this was not explained by the ccr5 Delta 32 genotype, showing evidence that other host factors are likely to influence HIV-1 replication in MDM. Infections with VSV-G pseudotyped HIV-1 indeed confirmed the existence of post-entry level restrictions in MDM. (C) 2009 Elsevier Inc. All rights reserved
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26. Large-Scale Monitoring of Host Cell Gene Expression during HIV-1 Infection Using cDNA Microarrays
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Erick Hammersmark, Gary K. Geiss, Michael G. Katze, David Upchurch, Victoria S. Carter, Angélique B. van 't Wout, Mahru C. An, Michael B. Agy, Roger E. Bumgarner, James I. Mullins, and Other departments
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CD4-Positive T-Lymphocytes ,DNA, Complementary ,host cell ,Microarray ,Transcription, Genetic ,Biology ,Cell Line ,Complementary DNA ,Virology ,Gene expression ,Transcriptional regulation ,Image Processing, Computer-Assisted ,Humans ,RNA, Messenger ,Gene ,Oligonucleotide Array Sequence Analysis ,Regulation of gene expression ,Microarray analysis techniques ,Gene Expression Profiling ,Molecular biology ,Gene expression profiling ,Gene Expression Regulation ,gene expression ,HIV-1 ,cDNA ,microarray - Abstract
Human immunodeficiency virus type 1 (HIV-1) infection alters the expression of host cell genes at both the mRNA and protein levels. To obtain a more comprehensive view of the global effects of HIV infection of CD4-positive T-cells at the mRNA level, we performed cDNA microarray analysis on approximately 1500 cellular cDNAs at 2 and 3 days postinfection (p.i.) with HIV-1. Host cell gene expression changed little at 2 days p.i., but at 3 days p.i. 20 cellular genes were identified as differentially expressed. Genes involved in T-cell signaling, subcellular trafficking, and transcriptional regulation, as well as several uncharacterized genes, were among those whose mRNAs were differentially regulated. These results support the hypothesis that HIV-1 infection alters expression of a broad array of cellular genes and provides a framework for future functional studies on the differentially expressed mRNA products.
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27. HIV-1 infection in polarized primary macrophages
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Viviana Cobos-Jiménez, Angélique B. van 't Wout, Neeltje A. Kootstra, Karel A. van Dort, Jörg Hamann, Steven W de Taeve, and Thijs Booiman
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lcsh:Immunologic diseases. Allergy ,biology ,business.industry ,Human immunodeficiency virus (HIV) ,medicine.disease_cause ,Phenotype ,Virus ,Cell biology ,Mucosal transmission ,Infectious Diseases ,In vivo ,Virology ,Poster Presentation ,biology.protein ,medicine ,Antibody ,lcsh:RC581-607 ,business - Abstract
Background Macrophages are important targets for HIV-1 infection and are involved in mucosal transmission of the virus. Due to their ubiquitous distribution, macrophages play a crucial role in virus spread and can become reservoirs for HIV-1. In vivo, macrophages are exposed to a multiplicity of signals that can polarize them into a classically activated M1 (IFN-g, LPS and/or TNF-a) or into alternatively activated M2a (IL-4, IL-13) and M2c (IL-10, glucocorticoids) phenotype. Previous studies have shown that the susceptibility of macrophages to HIV-1 infection is regulated by type I interferons (IFN-a, IFN-b) and by the cytokines IL-4 and IL-10, however the mechanism underlying the latter has not been described yet. In this study, the expression levels of HIV-1 restricting cellular factors in the different types of polarized monocyte-derived macrophages (MDM) was analyzed and their role in HIV-1 susceptibility was investigated.
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28. Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies.
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Harrison G Jones, Tina Ritschel, Gabriel Pascual, Just P J Brakenhoff, Elissa Keogh, Polina Furmanova-Hollenstein, Ellen Lanckacker, Jehangir S Wadia, Morgan S A Gilman, R Anthony Williamson, Dirk Roymans, Angélique B van 't Wout, Johannes P Langedijk, and Jason S McLellan
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Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and the elderly, and yet there remains no effective treatment or vaccine. The surface of the virion is decorated with the fusion glycoprotein (RSV F) and the attachment glycoprotein (RSV G), which binds to CX3CR1 on human airway epithelial cells to mediate viral attachment and subsequent infection. RSV G is a major target of the humoral immune response, and antibodies that target the central conserved region of G have been shown to neutralize both subtypes of RSV and to protect against severe RSV disease in animal models. However, the molecular underpinnings for antibody recognition of this region have remained unknown. Therefore, we isolated two human antibodies directed against the central conserved region of RSV G and demonstrated that they neutralize RSV infection of human bronchial epithelial cell cultures in the absence of complement. Moreover, the antibodies protected cotton rats from severe RSV disease. Both antibodies bound with high affinity to a secreted form of RSV G as well as to a peptide corresponding to the unglycosylated central conserved region. High-resolution crystal structures of each antibody in complex with the G peptide revealed two distinct conformational epitopes that require proper folding of the cystine noose located in the C-terminal part of the central conserved region. Comparison of these structures with the structure of fractalkine (CX3CL1) alone or in complex with a viral homolog of CX3CR1 (US28) suggests that RSV G would bind to CX3CR1 in a mode that is distinct from that of fractalkine. Collectively, these results build on recent studies demonstrating the importance of RSV G in antibody-mediated protection from severe RSV disease, and the structural information presented here should guide the development of new vaccines and antibody-based therapies for RSV.
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- 2018
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29. DYRK1A Controls HIV-1 Replication at a Transcriptional Level in an NFAT Dependent Manner.
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Thijs Booiman, Vladimir V Loukachov, Karel A van Dort, Angélique B van 't Wout, and Neeltje A Kootstra
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Medicine ,Science - Abstract
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.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.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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- 2015
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30. Phosphodiesterase 8a supports HIV-1 replication in macrophages at the level of reverse transcription.
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Thijs Booiman, Viviana Cobos Jiménez, Karel A van Dort, Angélique B van 't Wout, and Neeltje A Kootstra
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Medicine ,Science - 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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- 2014
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31. The presence of CXCR4-using HIV-1 prior to start of antiretroviral therapy is an independent predictor of delayed viral suppression.
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Esther F Gijsbers, Ard van Sighem, Agnes M Harskamp, Matthijs R A Welkers, Frank de Wolf, Kees Brinkman, Jan M Prins, Hanneke Schuitemaker, Angélique B van 't Wout, and Neeltje A Kootstra
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Medicine ,Science - Abstract
The emergence of CXCR4-using HIV variants (X4-HIV) is associated with accelerated disease progression in the absence of antiretroviral therapy. However, the effect of X4-HIV variants on the treatment response remains unclear. Here we determined whether the presence of X4-HIV variants influenced the time to undetectable viral load and CD4+ T cell reconstitution after initiation of cART in 732 patients. The presence of X4-HIV variants was determined by MT-2 assay prior to cART initiation and viral load and CD4+ T cell counts were analyzed every 3 to 6 months during a three year follow-up period. Kaplan-Meier and Cox proportional hazard analyses were performed to compare time to viral suppression and the absolute CD4+ T cell counts and increases in CD4+ T cell counts during follow-up were compared for patients with and without X4-HIV at start of cART. Patients harboring X4-HIV variants at baseline showed a delay in time to achieve viral suppression below the viral load detection limit. This delay in viral suppression was independently associated with high viral load and the presence of X4-HIV variants. Furthermore, the absolute CD4+ T cell counts were significantly lower in patients harboring X4-HIV variants at all time points during follow-up. However, no differences were observed in the increase in absolute CD4+ T cell numbers after treatment initiation, indicating that the reconstitution of CD4+ T cells is independent of the presence of X4-HIV variants. The emergence of X4-HIV has been associated with an accelerated CD4+ T cell decline during the natural course of infection and therefore, patients who develop X4-HIV variants may benefit from earlier treatment initiation in order to obtain faster reconstitution of the CD4+ T cell population to normal levels.
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- 2013
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32. HIV-1 disease progression is associated with bile-salt stimulated lipase (BSSL) gene polymorphism.
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Martijn J Stax, Neeltje A Kootstra, Angélique B van 't Wout, Michael W T Tanck, Margreet Bakker, Georgios Pollakis, and William A Paxton
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Medicine ,Science - Abstract
BackgroundDC-SIGN expressed by dendritic cells captures HIV-1 resulting in trans-infection of CD4(+) T-lymphocytes. However, BSSL (bile-salt stimulated lipase) binding to DC-SIGN interferes with HIV-1 capture. DC-SIGN binding properties of BSSL associate with the polymorphic repeated motif of BSSL exon 11. Furthermore, BSSL binds to HIV-1 co-receptor CXCR4. We hypothesized that BSSL modulates HIV-1 disease progression and emergence of CXCR4 using HIV-1 (X4) variants.ResultsThe relation between BSSL genotype and HIV-1 disease progression and emergence of X4 variants was studied using Kaplan Meier and multivariate Cox proportional hazard analysis in a cohort of HIV-1 infected men having sex with men (n = 334, with n = 130 seroconverters). We analyzed the association of BSSL genotype with set-point viral load and CD4 cell count, both pre-infection and post-infection at viral set-point. The number of repeats in BSSL exon 11 were highly variable ranging from 10 to 18 in seropositive individuals and from 5-17 in HRSN with 16 repeats being dominant (>80% carry at least one allele with 16 repeats). We defined 16 to 18 repeats as high (H) and less than 16 repeats as low (L) repeat numbers. Homozygosity for the high (H) repeat number BSSL genotype (HH) correlated with high CD4 cell numbers prior to infection (p = 0.007). In HIV-1 patients, delayed disease progression was linked to the HH BSSL genotype (RH = 0.462 CI = 0.282-0.757, p = 0.002) as was delayed emergence of X4 variants (RH = 0.525, 95% CI = 0.290-0.953, p = 0.034). The LH BSSL genotype, previously found to be associated with enhanced DC-SIGN binding of human milk, was identified to correlate with accelerated disease progression in our cohort of HIV-1 infected MSM (RH = 0.517, 95% CI = 0.328-0.818, p = 0.005).ConclusionWe identify BSSL as a marker for HIV-1 disease progression and emergence of X4 variants. Additionally, we identified a relation between BSSL genotype and CD4 cell counts prior to infection.
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- 2012
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33. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.
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Art F Y Poon, Luke C Swenson, Evelien M Bunnik, Diana Edo-Matas, Hanneke Schuitemaker, Angélique B van 't Wout, and P Richard Harrigan
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Biology (General) ,QH301-705.5 - Abstract
At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a 'fitness valley' separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant.
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- 2012
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34. Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing.
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Evelien M Bunnik, Luke C Swenson, Diana Edo-Matas, Wei Huang, Winnie Dong, Arne Frantzell, Christos J Petropoulos, Eoin Coakley, Hanneke Schuitemaker, P Richard Harrigan, and Angélique B van 't Wout
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Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
The emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants is associated with accelerated disease progression. CXCR4-using variants are believed to evolve from CCR5-using variants, but due to the extremely low frequency at which transitional intermediate variants are often present, the kinetics and mutational pathways involved in this process have been difficult to study and are therefore poorly understood. Here, we used ultra-deep sequencing of the V3 loop of the viral envelope in combination with the V3-based coreceptor prediction tools PSSM(NSI/SI) and geno2pheno([coreceptor]) to detect HIV-1 variants during the transition from CCR5- to CXCR4-usage. We analyzed PBMC and serum samples obtained from eight HIV-1-infected individuals at three-month intervals up to one year prior to the first phenotypic detection of CXCR4-using variants in the MT-2 assay. Between 3,482 and 10,521 reads were generated from each sample. In all individuals, V3 sequences of predicted CXCR4-using HIV-1 were detected at least three months prior to phenotypic detection of CXCR4-using variants in the MT-2 assay. Subsequent analysis of the genetic relationships of these V3 sequences using minimum spanning trees revealed that the transition in coreceptor usage followed a stepwise mutational pathway involving sequential intermediate variants, which were generally present at relatively low frequencies compared to the major predicted CCR5- and CXCR4-using variants. In addition, we observed differences between individuals with respect to the number of predicted CXCR4-using variants, the diversity among major predicted CCR5-using variants, and the presence or absence of intermediate variants with discordant phenotype predictions. These results provide the first detailed description of the mutational pathways in V3 during the transition from CCR5- to CXCR4-usage in natural HIV-1 infection.
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- 2011
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35. Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course.
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Daniëlle van Manen, Olivier Delaneau, Neeltje A Kootstra, Brigitte D Boeser-Nunnink, Sophie Limou, Sebastiaan M Bol, Judith A Burger, Aeilko H Zwinderman, Perry D Moerland, Ruben van 't Slot, Jean-François Zagury, Angélique B van 't Wout, and Hanneke Schuitemaker
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Medicine ,Science - Abstract
BACKGROUND: AIDS develops typically after 7-11 years of untreated HIV-1 infection, with extremes of very rapid disease progression (15 years). To reveal additional host genetic factors that may impact on the clinical course of HIV-1 infection, we designed a genome-wide association study (GWAS) in 404 participants of the Amsterdam Cohort Studies on HIV-1 infection and AIDS. METHODS: The association of SNP genotypes with the clinical course of HIV-1 infection was tested in Cox regression survival analyses using AIDS-diagnosis and AIDS-related death as endpoints. RESULTS: Multiple, not previously identified SNPs, were identified to be strongly associated with disease progression after HIV-1 infection, albeit not genome-wide significant. However, three independent SNPs in the top ten associations between SNP genotypes and time between seroconversion and AIDS-diagnosis, and one from the top ten associations between SNP genotypes and time between seroconversion and AIDS-related death, had P-values smaller than 0.05 in the French Genomics of Resistance to Immunodeficiency Virus cohort on disease progression. CONCLUSIONS: Our study emphasizes that the use of different phenotypes in GWAS may be useful to unravel the full spectrum of host genetic factors that may be associated with the clinical course of HIV-1 infection.
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- 2011
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