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Zivanovic N, Öner D, Abraham Y, McGinley J, Drysdale SB, Wildenbeest JG, Crabbe M, Vanhoof G, Thys K, Thwaites RS, Robinson H, Bont L, Openshaw PJM, Martinón‐Torres F, Pollard AJ, Aerssens J. Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus disease in infants. Clin Transl Med 2023; 13:e1507. [PMID: 38115705 PMCID: PMC10731116 DOI: 10.1002/ctm2.1507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/31/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023] Open
Abstract
Whereas most infants infected with respiratory syncytial virus (RSV) show no or only mild symptoms, an estimated 3 million children under five are hospitalized annually due to RSV disease. This study aimed to investigate biological mechanisms and associated biomarkers underlying RSV disease heterogeneity in young infants, enabling the potential to objectively categorize RSV-infected infants according to their medical needs. Immunophenotypic and functional profiling demonstrated the emergence of immature and progenitor-like neutrophils, proliferative monocytes (HLA-DRLow , Ki67+), impaired antigen-presenting function, downregulation of T cell response and low abundance of HLA-DRLow B cells in severe RSV disease. HLA-DRLow monocytes were found as a hallmark of RSV-infected infants requiring hospitalization. Complementary transcriptomics identified genes associated with disease severity and pointed to the emergency myelopoiesis response. These results shed new light on mechanisms underlying the pathogenesis and development of severe RSV disease and identified potential new candidate biomarkers for patient stratification.
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Affiliation(s)
- Nevena Zivanovic
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Deniz Öner
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Yann Abraham
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Joseph McGinley
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Simon B. Drysdale
- Centre for Neonatal and Paediatric Infection, Institute for Infection and Immunity, St George's, University of LondonLondonUK
| | - Joanne G. Wildenbeest
- Department of Pediatric Infectious Diseases and ImmunologyWilhelmina Children's Hospital, University Medical Center UtrechtUtrechtThe Netherlands
| | - Marjolein Crabbe
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Greet Vanhoof
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Kim Thys
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Ryan S. Thwaites
- Department of Respiratory MedicineNational Heart and Lung Institute, Imperial College LondonLondonUK
| | - Hannah Robinson
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Louis Bont
- Department of Pediatric Infectious Diseases and ImmunologyWilhelmina Children's Hospital, University Medical Center UtrechtUtrechtThe Netherlands
| | - Peter J. M. Openshaw
- Department of Respiratory MedicineNational Heart and Lung Institute, Imperial College LondonLondonUK
| | - Federico Martinón‐Torres
- Pediatrics DepartmentTranslational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de CompostelaGaliciaSpain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de CompostelaGaliciaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadridSpain
| | | | - Andrew J. Pollard
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Jeroen Aerssens
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
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Goethals O, Kaptein SJF, Kesteleyn B, Bonfanti JF, Van Wesenbeeck L, Bardiot D, Verschoor EJ, Verstrepen BE, Fagrouch Z, Putnak JR, Kiemel D, Ackaert O, Straetemans R, Lachau-Durand S, Geluykens P, Crabbe M, Thys K, Stoops B, Lenz O, Tambuyzer L, De Meyer S, Dallmeier K, McCracken MK, Gromowski GD, Rutvisuttinunt W, Jarman RG, Karasavvas N, Touret F, Querat G, de Lamballerie X, Chatel-Chaix L, Milligan GN, Beasley DWC, Bourne N, Barrett ADT, Marchand A, Jonckers THM, Raboisson P, Simmen K, Chaltin P, Bartenschlager R, Bogers WM, Neyts J, Van Loock M. Blocking NS3-NS4B interaction inhibits dengue virus in non-human primates. Nature 2023; 615:678-686. [PMID: 36922586 PMCID: PMC10033419 DOI: 10.1038/s41586-023-05790-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Dengue is a major health threat and the number of symptomatic infections caused by the four dengue serotypes is estimated to be 96 million1 with annually around 10,000 deaths2. However, no antiviral drugs are available for the treatment or prophylaxis of dengue. We recently described the interaction between non-structural proteins NS3 and NS4B as a promising target for the development of pan-serotype dengue virus (DENV) inhibitors3. Here we present JNJ-1802-a highly potent DENV inhibitor that blocks the NS3-NS4B interaction within the viral replication complex. JNJ-1802 exerts picomolar to low nanomolar in vitro antiviral activity, a high barrier to resistance and potent in vivo efficacy in mice against infection with any of the four DENV serotypes. Finally, we demonstrate that the small-molecule inhibitor JNJ-1802 is highly effective against viral infection with DENV-1 or DENV-2 in non-human primates. JNJ-1802 has successfully completed a phase I first-in-human clinical study in healthy volunteers and was found to be safe and well tolerated4. These findings support the further clinical development of JNJ-1802, a first-in-class antiviral agent against dengue, which is now progressing in clinical studies for the prevention and treatment of dengue.
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Affiliation(s)
- Olivia Goethals
- Janssen Global Public Health, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Suzanne J F Kaptein
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Bart Kesteleyn
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Jean-François Bonfanti
- Janssen Infectious Diseases Discovery, Janssen-Cilag, Val de Reuil, France
- Galapagos, Romainville, France
| | | | | | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Babs E Verstrepen
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Zahra Fagrouch
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - J Robert Putnak
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Dominik Kiemel
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Oliver Ackaert
- Janssen Clinical Pharmacology and Pharmacometrics, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Roel Straetemans
- Statistics and Decision Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - Peggy Geluykens
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
- Discovery, Charles River Beerse, Beerse, Belgium
| | - Marjolein Crabbe
- Statistics and Decision Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Kim Thys
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Bart Stoops
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Oliver Lenz
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Lotke Tambuyzer
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Sandra De Meyer
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Kai Dallmeier
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Michael K McCracken
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nicos Karasavvas
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Franck Touret
- Unité des Virus Émergents, Aix-Marseille Université-IRD 190-Inserm 1207, Marseille, France
| | - Gilles Querat
- Unité des Virus Émergents, Aix-Marseille Université-IRD 190-Inserm 1207, Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents, Aix-Marseille Université-IRD 190-Inserm 1207, Marseille, France
| | - Laurent Chatel-Chaix
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Gregg N Milligan
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | - David W C Beasley
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | - Nigel Bourne
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | - Alan D T Barrett
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch Health, Galveston, TX, USA
| | | | - Tim H M Jonckers
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Pierre Raboisson
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse, Belgium
- Galapagos NV, Mechelen, Belgium
| | | | - Patrick Chaltin
- Cistim Leuven vzw, Leuven, Belgium
- Centre for Drug Design and Discovery (CD3), KU Leuven, Leuven, Belgium
| | - Ralf Bartenschlager
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
- German Centre for Infection Research, Heidelberg Partner Site, Heidelberg, Germany
| | - Willy M Bogers
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
- Global Virus Network (GVN), Baltimore, MD, USA
| | - Marnix Van Loock
- Janssen Global Public Health, Janssen Pharmaceutica NV, Beerse, Belgium.
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Vijgen L, Thys K, Vandebosch A, Van Remoortere P, Verloes R, De Meyer S. Virology analysis in HCV genotype 1-infected patients treated with the combination of simeprevir and TMC647055/ritonavir, with and without ribavirin, and JNJ-56914845. Virol J 2017; 14:101. [PMID: 28569206 PMCID: PMC5452362 DOI: 10.1186/s12985-017-0760-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/01/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In study TMC647055HPC2001, a 3-direct-acting-antiviral (DAA) regimen combining NS3/4A protease inhibitor simeprevir (SMV), non-nucleoside NS5B inhibitor TMC647055/ritonavir (RTV) and NS5A inhibitor JNJ-56914845 resulted in high sustained virologic response 12 weeks after actual end of treatment (SVR12) in chronic hepatitis C virus (HCV) genotype 1-infected patients. SVR12 rates were generally lower in the 2-DAA regimen SMV + TMC647055/RTV with or without ribavirin. The objective of this study was to identify and characterise pre-existing and emerging resistance-associated variants (RAVs) in patients enrolled in study TMC647055HPC2001. METHODS HCV population sequencing analyses were performed on baseline isolates from all patients (n = 90) and post-baseline isolates from patients with virologic failure (n = 22). In addition, deep sequencing and phenotypic analyses were performed on selected baseline and post-baseline isolates. RESULTS The majority of patients with virologic failure had emerging RAVs to all study drugs at the time of failure: in all 22 patients SMV RAVs emerged at NS3 positions 80, 155, 156 and/or 168, consistent with the known SMV resistance profile. Emerging TMC647055 RAVs at NS5B position 495 were detected in the majority of patients (16/22), and all 5 patients who failed the 3-DAA regimen had emerging JNJ-56914845 RAVs at NS5A positions 30 and/or 31. While at the end of study emerging SMV and TMC647055 RAVs were no longer observed by population sequencing in 40% (8/20) and 62.5% (10/16) of patients with follow-up data available, respectively, emerging JNJ-56914845 RAVs were still detected in all (5/5) patients. CONCLUSIONS Virologic failure in the 2- and 3-DAA combinations was, in the majority of patients, associated with the emergence of RAVs to all study drugs. While emerging SMV and TMC647055 RAVs became undetectable during follow-up, JNJ-56914845 RAVs in NS5A were still observed at end of study. TRIAL REGISTRATION NUMBER NCT01724086 (date of registration: September 26, 2012).
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Affiliation(s)
- Leen Vijgen
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Kim Thys
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - An Vandebosch
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pieter Van Remoortere
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - René Verloes
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Sandra De Meyer
- Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
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Thys K, Van Assche K, Nys H, Sterckx S, Borry P. Living Organ Donation by Minors: An Analysis of the Regulations in European Union Member States. Am J Transplant 2016; 16:3554-3561. [PMID: 27172349 DOI: 10.1111/ajt.13868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 04/18/2016] [Accepted: 05/07/2016] [Indexed: 01/25/2023]
Abstract
Living organ donation (LD) is an increasingly established practice. Whereas in the United States and Canada LD by minors has occasionally been reported, LD by minors seems to be largely absent in the European Union (EU). It is currently unclear whether this is the result of a different legal approach. This study is the first to systematically analyze the regulations of EU member states, Norway, and Iceland toward LD by minors. Relevant regulations were identified by searching government websites, translated, compared, and sent for verification to national legal experts. We identified five countries where LD by minors is allowed. In two of these (Belgium and the United Kingdom), some minors may be deemed sufficiently mature to make an autonomous decision regarding LD. In contrast, in the three other countries (Luxembourg, Norway, and Sweden), LD by minors is only allowed subject to parental permission and the assent (or absence of objection) of the donor. Where allowed, regulations differ significantly with regard to the substantive and procedural safeguards in place. In view of the controversial nature of the procedure, as illustrated by recent reports and surveys, we argue for a very cautious approach and greater harmonization in countries where LD by minors is allowed.
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Affiliation(s)
- K Thys
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.,University Colleges Leuven-Limburg, Faculty of Health and Social Work, Research Unit Healthy Living, Genk, Belgium
| | - K Van Assche
- Research Group Personal Rights and Property Rights, University of Antwerp, Antwerp, Belgium
| | - H Nys
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - S Sterckx
- Bioethics Institute Ghent, University of Ghent, Ghent, Belgium
| | - P Borry
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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Sénécal K, Thys K, Vears DF, Van Assche K, Knoppers BM, Borry P. Reply to Kranendonk et al. Eur J Hum Genet 2016; 25:166-167. [PMID: 27876816 DOI: 10.1038/ejhg.2016.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- K Sénécal
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - K Thys
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - D F Vears
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - K Van Assche
- Research Group on Personality Rights and Property Rights, Faculty of Law, University of Antwerp, Antwerp, Belgium
| | - B M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - P Borry
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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Van Damme E, Thys K, Tuefferd M, Van Hove C, Aerssens J, Van Loock M. HCMV Displays a Unique Transcriptome of Immunomodulatory Genes in Primary Monocyte-Derived Cell Types. PLoS One 2016; 11:e0164843. [PMID: 27760232 PMCID: PMC5070835 DOI: 10.1371/journal.pone.0164843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/01/2016] [Indexed: 12/17/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a betaherpesvirus which rarely presents problems in healthy individuals, yet may result in severe morbidity in immunocompromised patients and in immune-naïve neonates. HCMV has a large 235 kb genome with a coding capacity of at least 165 open reading frames (ORFs). This large genome allows complex gene regulation resulting in different sets of transcripts during lytic and latent infection. While latent virus mainly resides within monocytes and CD34+ progenitor cells, reactivation to lytic infection is driven by differentiation towards terminally differentiated myeloid dendritic cells and macrophages. Consequently, it has been suggested that macrophages and dendritic cells contribute to viral spread in vivo. Thus far only limited knowledge is available on the expression of HCMV genes in terminally differentiated myeloid primary cells and whether or not the virus exhibits a different set of lytic genes in primary cells compared with lytic infection in NHDF fibroblasts. To address these questions, we used Illumina next generation sequencing to determine the HCMV transcriptome in macrophages and dendritic cells during lytic infection and compared it to the transcriptome in NHDF fibroblasts. Here, we demonstrate unique expression profiles in macrophages and dendritic cells which significantly differ from the transcriptome in fibroblasts mainly by modulating the expression of viral transcripts involved in immune modulation, cell tropism and viral spread. In a head to head comparison between macrophages and dendritic cells, we observed that factors involved in viral spread and virion composition are differentially regulated suggesting that the plasticity of the virion facilitates the infection of surrounding cells. Taken together, this study provides the full transcript expression analysis of lytic HCMV genes in monocyte-derived type 1 and type 2 macrophages as well as in monocyte-derived dendritic cells. Thereby underlining the potential of HCMV to adapt to or influence different cellular environments to promote its own survival.
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Affiliation(s)
- Ellen Van Damme
- Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Kim Thys
- Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - Carl Van Hove
- Discovery Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Jeroen Aerssens
- Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Marnix Van Loock
- Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
- * E-mail:
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Fevery B, Thys K, Van Eygen V, Verbinnen T, Van Rossem E, Buelens A, Aerssens J, Witek J, Picchio G, De Meyer S, Lenz O. Pre-existence and Persistence of Resistant Minority Hepatitis C Virus Variants in Genotype 1-Infected Patients Treated With Simeprevir/Peginterferon/Ribavirin. Open Forum Infect Dis 2016; 3:ofw052. [PMID: 27186579 PMCID: PMC4866569 DOI: 10.1093/ofid/ofw052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/04/2016] [Indexed: 01/27/2023] Open
Abstract
Deep sequencing analyses in HCV genotype 1-infected patients treated with simeprevir/peginterferon/ribavirin showed that pre-existing minority HCV variants did not impact treatment outcome and emerging resistant variants in patients failing treatment were not persisting at minority levels Background. The pre-existence of minority hepatitis C virus (HCV) variants and their impact on treatment outcome, as well as the persistence of emerging resistant variants posttreatment in patients failing treatment with simeprevir/peginterferon/ribavirin (SMV/PR), were assessed by deep sequencing (DS). Methods. Population sequencing (PS) and Illumina DS were performed on HCV genotype 1 isolates from patients treated with SMV/PR in Phase 2b (PILLAR [NCT00882908] and ASPIRE [NCT00980330]) and Phase 3 (QUEST-1 [NCT01289782], QUEST-2 [NCT01290679], and PROMISE [NCT01281839]) trials. Results. Minority polymorphisms (ie, detected pretreatment by DS only) reducing SMV activity in vitro were uncommon (3.6%, 19 of 534 patients). These SMV-resistant minority polymorphisms were detected in similar proportions of patients achieving (3.7%) and not achieving (3.3%) sustained virologic response with SMV/PR and generally did not emerge as major variants at time of failure. SMV-resistant variants emerging at time of failure were no longer detected at end of study in 69.3% and 52.0% of the patients by PS and DS, respectively. Conclusions. Minority polymorphisms did not impact outcome of SMV/PR treatment. The majority of emerging variants that became undetectable at end of study by PS were also undetectable by DS. These results suggest no added value of DS for clinical usage of SMV.
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Affiliation(s)
| | - Kim Thys
- Janssen Discovery Sciences, Beerse , Belgium
| | | | | | | | | | | | - James Witek
- Janssen Research & Development , LLC , Titusville, New Jersey
| | - Gaston Picchio
- Janssen Research & Development , LLC , Titusville, New Jersey
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Tambuyzer L, Thys K, Hoogstoel A, Nijs S, Tomaka F, Opsomer M, De Meyer S, Vingerhoets J. Assessment of etravirine resistance in HIV-1-infected paediatric patients using population and deep sequencing: final results of the PIANO study. Antivir Ther 2015; 21:317-27. [PMID: 26566161 DOI: 10.3851/imp3011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND We assessed etravirine resistance in treatment-experienced, HIV-1-infected children (n=41)/adolescents (n=60) who received twice-daily etravirine 5.2 mg/kg and a background regimen (boosted protease inhibitor plus nucleoside/nucleotide reverse transcriptase inhibitors, optional enfuvirtide/raltegravir) in a Phase II, open-label, multicentre trial (PIANO). METHODS In addition to phenotypes, viral genotypes were assessed by population and deep sequencing (PS and DS) in virological failures (VFs; baseline and end point) and responders (baseline). Minority resistance-associated mutations (RAMs) were defined as those with frequencies above 1% and not detected with PS. RESULTS By week 48, 41/101 (40.6%) patients experienced VF; 17/41 (41.5%) VFs and 22/54 (40.8%) responders had ≥1 baseline etravirine RAM by PS, mainly A98G, K101E, V106I and G190A. Baseline minority etravirine RAMs (n) were detected in 8/40 VFs (V90I [2], A98G [1], L100I [1], V106I [1], E138G [1] and Y181C [2]) and 5/38 responders (V90I [3], A98G [1], V106I [1] and E138G [1]). The most frequent emerging non-nucleoside reverse transcriptase inhibitor RAMs detected by PS (≥3 VFs; n) were the etravirine RAMs Y181C (8), V90I (3), L100I (3) and E138A (3). In 15 of 29 (51.7%) VFs with baseline DS/PS and end point PS data, ≥1 emerging etravirine RAM was detected by PS, which was not detected at baseline by DS in most cases (12/15 [80.0%]). In 10/26 (38.5%) VFs with baseline/end point DS data, ≥1 additional emerging minority etravirine RAM was detected. CONCLUSIONS Patterns of etravirine resistance in adults, adolescents and children experiencing VF are similar. The presence of minority etravirine RAMs at baseline was not consistently associated with treatment failure. ClinicalTrials.gov: NCT00665847.
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Van der Borght K, Thys K, Wetzels Y, Clement L, Verbist B, Reumers J, van Vlijmen H, Aerssens J. QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles. BMC Bioinformatics 2015; 16:379. [PMID: 26554718 PMCID: PMC4641353 DOI: 10.1186/s12859-015-0812-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/31/2015] [Indexed: 12/03/2022] Open
Abstract
Background Next generation sequencing enables studying heterogeneous populations of viral infections. When the sequencing is done at high coverage depth (“deep sequencing”), low frequency variants can be detected. Here we present QQ-SNV (http://sourceforge.net/projects/qqsnv), a logistic regression classifier model developed for the Illumina sequencing platforms that uses the quantiles of the quality scores, to distinguish true single nucleotide variants from sequencing errors based on the estimated SNV probability. To train the model, we created a dataset of an in silico mixture of five HIV-1 plasmids. Testing of our method in comparison to the existing methods LoFreq, ShoRAH, and V-Phaser 2 was performed on two HIV and four HCV plasmid mixture datasets and one influenza H1N1 clinical dataset. Results For default application of QQ-SNV, variants were called using a SNV probability cutoff of 0.5 (QQ-SNVD). To improve the sensitivity we used a SNV probability cutoff of 0.0001 (QQ-SNVHS). To also increase specificity, SNVs called were overruled when their frequency was below the 80th percentile calculated on the distribution of error frequencies (QQ-SNVHS-P80). When comparing QQ-SNV versus the other methods on the plasmid mixture test sets, QQ-SNVD performed similarly to the existing approaches. QQ-SNVHS was more sensitive on all test sets but with more false positives. QQ-SNVHS-P80 was found to be the most accurate method over all test sets by balancing sensitivity and specificity. When applied to a paired-end HCV sequencing study, with lowest spiked-in true frequency of 0.5 %, QQ-SNVHS-P80 revealed a sensitivity of 100 % (vs. 40–60 % for the existing methods) and a specificity of 100 % (vs. 98.0–99.7 % for the existing methods). In addition, QQ-SNV required the least overall computation time to process the test sets. Finally, when testing on a clinical sample, four putative true variants with frequency below 0.5 % were consistently detected by QQ-SNVHS-P80 from different generations of Illumina sequencers. Conclusions We developed and successfully evaluated a novel method, called QQ-SNV, for highly efficient single nucleotide variant calling on Illumina deep sequencing virology data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0812-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Koen Van der Borght
- Janssen Infectious Diseases-Diagnostics BVBA, B-2340, Beerse, Belgium. .,Interuniversity Institute for Biostatistics and statistical Bioinformatics, Katholieke Universiteit Leuven, B-3000, Leuven, Belgium.
| | - Kim Thys
- Janssen Infectious Diseases-Diagnostics BVBA, B-2340, Beerse, Belgium.
| | - Yves Wetzels
- Janssen Infectious Diseases-Diagnostics BVBA, B-2340, Beerse, Belgium.
| | - Lieven Clement
- Ghent University, Applied Mathematics, Informatics and Statistics, B-9000, Ghent, Belgium.
| | - Bie Verbist
- Janssen Infectious Diseases-Diagnostics BVBA, B-2340, Beerse, Belgium.
| | - Joke Reumers
- Janssen Infectious Diseases-Diagnostics BVBA, B-2340, Beerse, Belgium.
| | | | - Jeroen Aerssens
- Janssen Infectious Diseases-Diagnostics BVBA, B-2340, Beerse, Belgium.
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10
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Van Eygen V, Thys K, Van Hove C, Rimsky LT, De Meyer S, Aerssens J, Picchio G, Vingerhoets J. Deep sequencing analysis of HIV-1 reverse transcriptase at baseline and time of failure in patients receiving rilpivirine in the phase III studies ECHO and THRIVE. J Med Virol 2015; 88:798-806. [PMID: 26412111 DOI: 10.1002/jmv.24395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 11/10/2022]
Abstract
Minority variants (1.0-25.0%) were evaluated by deep sequencing (DS) at baseline and virological failure (VF) in a selection of antiretroviral treatment-naïve, HIV-1-infected patients from the rilpivirine ECHO/THRIVE phase III studies. Linkage between frequently emerging resistance-associated mutations (RAMs) was determined. DS (llIumina®) and population sequencing (PS) results were available at baseline for 47 VFs and time of failure for 48 VFs; and at baseline for 49 responders matched for baseline characteristics. Minority mutations were accurately detected at frequencies down to 1.2% of the HIV-1 quasispecies. No baseline minority rilpivirine RAMs were detected in VFs; one responder carried 1.9% F227C. Baseline minority mutations associated with resistance to other non-nucleoside reverse transcriptase inhibitors (NNRTIs) were detected in 8/47 VFs (17.0%) and 7/49 responders (14.3%). Baseline minority nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) RAMs M184V and L210W were each detected in one VF (none in responders). At failure, two patients without NNRTI RAMs by PS carried minority rilpivirine RAMs K101E and/or E138K; and five additional patients carried other minority NNRTI RAMs V90I, V106I, V179I, V189I, and Y188H. Overall at failure, minority NNRTI RAMs and NRTI RAMs were found in 29/48 (60.4%) and 16/48 VFs (33.3%), respectively. Linkage analysis showed that E138K and K101E were usually not observed on the same viral genome. In conclusion, baseline minority rilpivirine RAMs and other NNRTI/NRTI RAMs were uncommon in the rilpivirine arm of the ECHO and THRIVE studies. DS at failure showed emerging NNRTI resistant minority variants in seven rilpivirine VFs who had no detectable NNRTI RAMs by PS.
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Affiliation(s)
| | - Kim Thys
- Janssen Infectious Diseases BVBA, Beerse, Belgium
| | | | | | | | | | - Gaston Picchio
- Janssen Research and Development, Titusville, New Jersey
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Thys K, Verhasselt P, Reumers J, Verbist BMP, Maes B, Aerssens J. Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants. J Virol Methods 2015; 221:29-38. [PMID: 25917877 DOI: 10.1016/j.jviromet.2015.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 03/21/2015] [Accepted: 04/16/2015] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) technology has opened new avenues to study viral dynamics and treatment-induced resistance mechanisms of infections such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Whereas the Roche/454 platform has been used widely for the detection of low-frequent drug resistant variants, more recently developed short-read MPS technologies have the advantage of delivering a higher sequencing depth at a lower cost per sequenced base. This study assesses the performance characteristics of Illumina MPS technology for the characterization of genetic variability in viral populations by deep sequencing. The reported results from MPS experiments comprising HIV and HCV plasmids demonstrate that a 0.5-1% lower limit of detection can be achieved readily with Illumina MPS while retaining good accuracy also at low frequencies. Deep sequencing of a set of clinical samples (12 HIV and 9 HCV patients), designed at a similar budget for both MPS platforms, reveals a comparable lower limit of detection for Illumina and Roche/454. Finally, this study shows the possibility to apply Illumina's paired-end sequencing as a strategy to assess linkage between different mutations identified in individual viral subspecies. These results support the use of Illumina as another MPS platform of choice for deep sequencing of viral minority species.
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Affiliation(s)
- Kim Thys
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Peter Verhasselt
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Joke Reumers
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Bie M P Verbist
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
| | - Bart Maes
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Jeroen Aerssens
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
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12
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Verbist B, Clement L, Reumers J, Thys K, Vapirev A, Talloen W, Wetzels Y, Meys J, Aerssens J, Bijnens L, Thas O. ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering. BMC Bioinformatics 2015; 16:59. [PMID: 25887734 PMCID: PMC4369097 DOI: 10.1186/s12859-015-0458-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022] Open
Abstract
Background Deep-sequencing allows for an in-depth characterization of sequence variation in complex populations. However, technology associated errors may impede a powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores which are derived from a quadruplet of intensities, one channel for each nucleotide type for Illumina sequencing. The highest intensity of the four channels determines the base that is called. Mismatch bases can often be corrected by the second best base, i.e. the base with the second highest intensity in the quadruplet. A virus variant model-based clustering method, ViVaMBC, is presented that explores quality scores and second best base calls for identifying and quantifying viral variants. ViVaMBC is optimized to call variants at the codon level (nucleotide triplets) which enables immediate biological interpretation of the variants with respect to their antiviral drug responses. Results Using mixtures of HCV plasmids we show that our method accurately estimates frequencies down to 0.5%. The estimates are unbiased when average coverages of 25,000 are reached. A comparison with the SNP-callers V-Phaser2, ShoRAH, and LoFreq shows that ViVaMBC has a superb sensitivity and specificity for variants with frequencies above 0.4%. Unlike the competitors, ViVaMBC reports a higher number of false-positive findings with frequencies below 0.4% which might partially originate from picking up artificial variants introduced by errors in the sample and library preparation step. Conclusions ViVaMBC is the first method to call viral variants directly at the codon level. The strength of the approach lies in modeling the error probabilities based on the quality scores. Although the use of second best base calls appeared very promising in our data exploration phase, their utility was limited. They provided a slight increase in sensitivity, which however does not warrant the additional computational cost of running the offline base caller. Apparently a lot of information is already contained in the quality scores enabling the model based clustering procedure to adjust the majority of the sequencing errors. Overall the sensitivity of ViVaMBC is such that technical constraints like PCR errors start to form the bottleneck for low frequency variant detection. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0458-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bie Verbist
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Gent, 9000, Belgium.
| | - Lieven Clement
- Department of Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, Gent, 9000, Belgium.
| | - Joke Reumers
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium.
| | - Kim Thys
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium.
| | - Alexander Vapirev
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium. .,ExaScience Life Lab, Kapeldreef 75, Leuven, 3001, Belgium.
| | - Willem Talloen
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium.
| | - Yves Wetzels
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium.
| | - Joris Meys
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Gent, 9000, Belgium.
| | - Jeroen Aerssens
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium.
| | - Luc Bijnens
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium.
| | - Olivier Thas
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Gent, 9000, Belgium. .,University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW, 2522, Australia.
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13
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Verbist BMP, Thys K, Reumers J, Wetzels Y, Van der Borght K, Talloen W, Aerssens J, Clement L, Thas O. VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering. ACTA ACUST UNITED AC 2014; 31:94-101. [PMID: 25178459 DOI: 10.1093/bioinformatics/btu587] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
MOTIVATION In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations. RESULTS A variant calling tool, Q-cpileup, is proposed, which exploits the Qs of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open-source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical samples, we show that Q-cpileup is able to reduce the number of false-positive findings. The filtering strategy is adaptive and provides an optimized threshold for individual samples in each sequencing run. Additionally, linkage information is kept between single-nucleotide polymorphisms as variants are called at the codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their antiviral drug responses. A comparison with existing SNP caller tools reveals that calling variants at the codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%. AVAILABILITY The VirVarSeq is available, together with a user's guide and test data, at sourceforge: http://sourceforge.net/projects/virtools/?source=directory.
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Affiliation(s)
- Bie M P Verbist
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Kim Thys
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Joke Reumers
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Yves Wetzels
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Koen Van der Borght
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Willem Talloen
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Jeroen Aerssens
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Lieven Clement
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
| | - Olivier Thas
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Janssen R&D, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Applied Mathematics, Informatics and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Gent, Belgium and University of Wollongong, National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, NSW 2522, Australia
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14
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Andries K, Villellas C, Coeck N, Thys K, Gevers T, Vranckx L, Lounis N, de Jong BC, Koul A. Acquired resistance of Mycobacterium tuberculosis to bedaquiline. PLoS One 2014; 9:e102135. [PMID: 25010492 PMCID: PMC4092087 DOI: 10.1371/journal.pone.0102135] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/16/2014] [Indexed: 11/18/2022] Open
Abstract
Bedaquiline (BDQ), an ATP synthase inhibitor, is the first drug to be approved for treatment of multi-drug resistant tuberculosis in decades. In vitro resistance to BDQ was previously shown to be due to target-based mutations. Here we report that non-target based resistance to BDQ, and cross-resistance to clofazimine (CFZ), is due to mutations in Rv0678, a transcriptional repressor of the genes encoding the MmpS5-MmpL5 efflux pump. Efflux-based resistance was identified in paired isolates from patients treated with BDQ, as well as in mice, in which it was confirmed to decrease bactericidal efficacy. The efflux inhibitors verapamil and reserpine decreased the minimum inhibitory concentrations of BDQ and CFZ in vitro, but verapamil failed to increase the bactericidal effect of BDQ in mice and was unable to reverse efflux-based resistance in vivo. Cross-resistance between BDQ and CFZ may have important clinical implications.
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Affiliation(s)
- Koen Andries
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
- * E-mail:
| | - Cristina Villellas
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
| | - Nele Coeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kim Thys
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
| | - Tom Gevers
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
| | - Luc Vranckx
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
| | - Nacer Lounis
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
| | - Bouke C. de Jong
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anil Koul
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
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15
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Dierynck I, Thys K, Ghys A, Sullivan JC, Kieffer TL, Aerssens J, Picchio G, De Meyer S. Deep-sequencing analysis of the gene encoding the hepatitis C virus nonstructural 3-4A protease confirms a low prevalence of telaprevir-resistant variants at baseline and the end of the REALIZE study. J Infect Dis 2014; 210:1871-80. [PMID: 24943725 DOI: 10.1093/infdis/jiu340] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Population sequencing (PS) has shown that telaprevir-resistant variants are not typically detectable at baseline (prevalence, ≤5% of patients), and most variants present at the time of treatment failure are no longer detectable at the end of the study. METHODS To gain insight into the evolution of telaprevir-resistant variants, their baseline prevalence and persistence after treatment was investigated using a more sensitive, deep-sequencing (DS) technique in a large number of treatment-experienced patients from the REALIZE study who were infected with hepatitis C virus genotype 1. RESULTS Before treatment initiation, telaprevir-resistant variants (T54A, T54S, or R155K in 1%-2% of the viral population) were detected by DS in a fraction (2%) of patients for whom PS failed to detect resistance; these variants were not necessarily detected at the time of treatment failure. Of 49 patients in whom telaprevir-resistant variants were detected by PS at the time of treatment failure but not at the end of the study, DS revealed the presence of variants (V36A/L/M, T54S, or R155K in 1%-36% of the viral population) in 16 patients (33%) at the end of the study. CONCLUSIONS Similar to PS findings, DS analysis revealed that the frequency of telaprevir-resistant variants before treatment was also low, and variants detected at the time of treatment failure were no longer detectable in the majority of patients during follow-up.
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Affiliation(s)
| | - Kim Thys
- Janssen Infectious Diseases, Beerse, Belgium
| | - Anne Ghys
- Janssen Infectious Diseases, Beerse, Belgium
| | | | | | | | - Gaston Picchio
- Janssen Research and Development, Titusville, New Jersey
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16
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Sijmons S, Thys K, Corthout M, Van Damme E, Van Loock M, Bollen S, Baguet S, Aerssens J, Van Ranst M, Maes P. A method enabling high-throughput sequencing of human cytomegalovirus complete genomes from clinical isolates. PLoS One 2014; 9:e95501. [PMID: 24755734 PMCID: PMC3995935 DOI: 10.1371/journal.pone.0095501] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/26/2014] [Indexed: 12/20/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous virus that can cause serious sequelae in immunocompromised patients and in the developing fetus. The coding capacity of the 235 kbp genome is still incompletely understood, and there is a pressing need to characterize genomic contents in clinical isolates. In this study, a procedure for the high-throughput generation of full genome consensus sequences from clinical HCMV isolates is presented. This method relies on low number passaging of clinical isolates on human fibroblasts, followed by digestion of cellular DNA and purification of viral DNA. After multiple displacement amplification, highly pure viral DNA is generated. These extracts are suitable for high-throughput next-generation sequencing and assembly of consensus sequences. Throughout a series of validation experiments, we showed that the workflow reproducibly generated consensus sequences representative for the virus population present in the original clinical material. Additionally, the performance of 454 GS FLX and/or Illumina Genome Analyzer datasets in consensus sequence deduction was evaluated. Based on assembly performance data, the Illumina Genome Analyzer was the platform of choice in the presented workflow. Analysis of the consensus sequences derived in this study confirmed the presence of gene-disrupting mutations in clinical HCMV isolates independent from in vitro passaging. These mutations were identified in genes RL5A, UL1, UL9, UL111A and UL150. In conclusion, the presented workflow provides opportunities for high-throughput characterization of complete HCMV genomes that could deliver new insights into HCMV coding capacity and genetic determinants of viral tropism and pathogenicity.
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Affiliation(s)
- Steven Sijmons
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- * E-mail:
| | - Kim Thys
- Janssen Infectious Diseases BVBA, Beerse, Belgium
| | - Michaël Corthout
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Stefanie Bollen
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sylvie Baguet
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Marc Van Ranst
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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Swennenhuis JF, Reumers J, Thys K, Aerssens J, Terstappen LW. Efficiency of whole genome amplification of single circulating tumor cells enriched by CellSearch and sorted by FACS. Genome Med 2013; 5:106. [PMID: 24286536 PMCID: PMC3978840 DOI: 10.1186/gm510] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 11/04/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tumor cells in the blood of patients with metastatic carcinomas are associated with poor survival. Knowledge of the cells' genetic make-up can help to guide targeted therapy. We evaluated the efficiency and quality of isolation and amplification of DNA from single circulating tumor cells (CTC). METHODS The efficiency of the procedure was determined by spiking blood with SKBR-3 cells, enrichment with the CellSearch system, followed by single cell sorting by fluorescence-activated cell sorting (FACS) and whole genome amplification. A selection of single cell DNA from fixed and unfixed SKBR-3 cells was exome sequenced and the DNA quality analyzed. Single CTC from patients with lung cancer were used to demonstrate the potential of single CTC molecular characterization. RESULTS The overall efficiency of the procedure from spiked cell to amplified DNA was approximately 20%. Losses attributed to the CellSearch system were around 20%, transfer to FACS around 25%, sorting around 5% and DNA amplification around 25%. Exome sequencing revealed that the quality of the DNA was affected by the fixation of the cells, amplification, and the low starting quantity of DNA. A single fixed cell had an average coverage at 20× depth of 30% when sequencing to an average of 40× depth, whereas a single unfixed cell had 45% coverage. GenomiPhi-amplified genomic DNA had a coverage of 72% versus a coverage of 87% of genomic DNA. Twenty-one percent of the CTC from patients with lung cancer identified by the CellSearch system could be isolated individually and amplified. CONCLUSIONS CTC enriched by the CellSearch system were sorted by FACS, and DNA retrieved and amplified with an overall efficiency of 20%. Analysis of the sequencing data showed that this DNA could be used for variant calling, but not for quantitative measurements such as copy number detection. Close to 55% of the exome of single SKBR-3 cells were successfully sequenced to 20× depth making it possible to call 72% of the variants. The overall coverage was reduced to 30% at 20× depth, making it possible to call 56% of the variants in CellSave-fixed cells.
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Affiliation(s)
- Joost F Swennenhuis
- Department of Medical Cell BioPhysics, MIRA Institute, University of Twente, Carre Room C4437, Hallenweg 23, 7522 NH Enschede, The Netherlands
| | - Joke Reumers
- Janssen Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Kim Thys
- Janssen Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Jeroen Aerssens
- Janssen Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Leon Wmm Terstappen
- Department of Medical Cell BioPhysics, MIRA Institute, University of Twente, Carre Room C4437, Hallenweg 23, 7522 NH Enschede, The Netherlands
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18
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Geretti AM, Conibear T, Hill A, Johnson JA, Tambuyzer L, Thys K, Vingerhoets J, Van Delft Y, Rieger A, Vetter N, Greil R, Pedersen C, Storgaard M, Morlat P, Katlama C, Durant J, Cotte L, Duvivier C, Rey D, Esser S, Stellbrink C, Schmidt W, Stoll M, Stephan C, Fatkenheuer G, Stoehr A, Rockstroh J, Banhegyi D, Itzchak L, Shahar E, Maayan S, Turner D, Lazzarin A, Antinori A, Carosi G, Minoli L, di Perri G, Filice G, Andreoni M, Duiculescu D, Rugina S, Erscoiu S, Streinu A, Pronin A, Pokrovsky V, Gruzdev B, Yakovlev A, Voronin E, Clotet B, Gatell J, Arribas J, Podzamczer D, Domingo P, Alvarez CM, Quero JH, Furrer H, Feher J, Johnson M, Fox J, Nelson M, Fisher M, Orkin C. Sensitive testing of plasma HIV-1 RNA and Sanger sequencing of cellular HIV-1 DNA for the detection of drug resistance prior to starting first-line antiretroviral therapy with etravirine or efavirenz. J Antimicrob Chemother 2013; 69:1090-7. [DOI: 10.1093/jac/dkt474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Messiaen P, Verhofstede C, Vandenbroucke I, Dinakis S, Van Eygen V, Thys K, Winters B, Aerssens J, Vogelaers D, Stuyver LJ, Vandekerckhove L. Ultra-deep sequencing of HIV-1 reverse transcriptase before start of an NNRTI-based regimen in treatment-naive patients. Virology 2012; 426:7-11. [PMID: 22305619 DOI: 10.1016/j.virol.2012.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/09/2011] [Accepted: 01/04/2012] [Indexed: 10/14/2022]
Abstract
There are conflicting data on the impact of low frequency HIV-1 drug-resistant mutants on the response of first-line highly active antiretroviral therapy (HAART), more specifically containing a NNRTI. As population sequencing does not detect resistant viruses representing less than 15-25% of the viral population, more sensitive techniques have been developed but still need clinical validation. We evaluated ultra-deep sequencing (UDPS), recently more available and affordable, as a tool for the detection of HIV-1 minority species carrying drug resistant mutation (DRM) in a clinical setting. A retrospective analysis of the reverse transcriptase (RT) gene of plasma HIV-1 from 70 patients starting a NNRTI based regimen was performed. Minority populations were defined as representing > 1% and < 20% of the total viral population. Using UDPS, we could not confirm an association between the presence of low minority variants harbouring RT mutations at the start of therapy and primary or secondary therapeutic failure.
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Affiliation(s)
- Peter Messiaen
- AIDS Reference Laboratory, Ghent University, De Pintelaan 185-9000 Gent, Belgium
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20
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De Wolf H, Van Marck H, Mostmans W, Thys K, Vandenbroucke I, Van Eygen V, Pattery T, Verhasselt P, Aerssens J. HIV-1 nucleotide mixture detection in the virco(®)TYPE HIV-1 genotyping assay: a comparison between Sanger sequencing and 454 pyrosequencing. J Virol Methods 2011; 175:129-32. [PMID: 21549149 DOI: 10.1016/j.jviromet.2011.04.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 04/19/2011] [Accepted: 04/20/2011] [Indexed: 02/06/2023]
Abstract
HIV-1 Protease (PR) and Reverse Transcriptase (RT) genotyping is well established for the management of antiretroviral (ARV) drug therapy, as it is able to detect gene mutations encoding resistance to ARV compounds or drug classes, that are associated with reduced drug susceptibility (i.e. phenotype). A correct phenotypic interpretation from the derived PR-RT genotype (i.e. virtual phenotype), requires a well characterized geno-phenotype correlative database and appropriate statistical predictive models. The applicability of the virtual phenotype for the patient, will, however, not only depend on the accuracy of the statistical models and the database they rely on, but also depend largely on the sequence information that is provided. Since HIV-1 evolves as a complex of closely related but non-identical viral genomes (i.e. quasispecies) it is crucial that the sequencing method used, is able to characterize most of the genetic mixtures that make up the different quasispecies within a single patient. US regulatory agencies require that developers of HIV-1 genotyping assays, determine and report the HIV-1 mixture detection level of their assay. Hence, the mixture scoring sensitivity of the population-based Sanger sequencing method, along with the defined mixture scoring rules, used to drive the virco(®)TYPE HIV-1 virtual phenotype, was investigated by comparing it to the 454 pyrosequencing technique, which is able to generate the complete viral population sequence. To this end the PR-RT coding sequence of 20 clinical isolates was determined by both sequencing methodologies. The genotyping assay which feeds the virco(®)TYPE HIV-1 virtual phenotype was able to call automatically 97.5% (i.e. 268 mixtures) and 95.3% (i.e. 326 mixtures) of the mixtures that were present between 25 and 75% and between 20 and 80% in the viral population, as detected by 454. From the not called mixtures, all but one did present a mixture sequence in the Sanger DNA chromatograms, however, with a peak surface area for the second peak that was below the threshold setting for automatic mixture calling in the basecaller software (i.e. 25%). Viral loads ranged from 470 to 629,000 copies/mL and exerted no effect on the mixture calling relationship between both sequencing methodologies (R(2)=0.92). In some occasions (i.e. 55 mixtures) the genotyping assay would detect automatically mixtures that were present below 20% in the viral population, when measured by 454. Hence, the mixture scoring sensitivity of the automated high throughput virco(®)TYPE HIV-1 genotyping assay is currently set at 97.5% and 95.3%, for mixtures present at 25 and 20% in the viral population and may identify occasionally mutations that are present at lower frequencies. These findings were not influenced by the viral load of the examined samples.
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Affiliation(s)
- Hans De Wolf
- Virco BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
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21
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Vandenbroucke I, Van Marck H, Mostmans W, Van Eygen V, Rondelez E, Thys K, Van Baelen K, Fransen K, Vaira D, Kabeya K, De Wit S, Florence E, Moutschen M, Vandekerckhove L, Verhofstede C, Stuyver LJ. HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays. AIDS Res Ther 2010; 7:4. [PMID: 20804564 PMCID: PMC2834596 DOI: 10.1186/1742-6405-7-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 02/15/2010] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 infected patients for whom standard gp160 phenotypic tropism testing failed are currently excluded from co-receptor antagonist treatment. To provide patients with maximal treatment options, massively parallel sequencing of the envelope V3 domain, in combination with tropism prediction tools, was evaluated as an alternative tropism determination strategy. Plasma samples from twelve HIV-1 infected individuals with failing phenotyping results were available. The samples were submitted to massive parallel sequencing and to confirmatory recombinant phenotyping using a fraction of the gp120 domain. Results A cut-off for sequence reads interpretation of 5 to10 times the sequencing error rate (0.2%) was implemented. On average, each sample contained 7 different V3 haplotypes. V3 haplotypes were submitted to tropism prediction algorithms, and 4/14 samples returned with presence of a dual/mixed (D/M) tropic virus, respectively at 3%, 10%, 11%, and 95% of the viral quasispecies. V3 tropism prediction was confirmed by gp120 phenotyping, except for two out of 4 D/M predicted viruses (with 3 and 95%) which were phenotypically R5-tropic. In the first case, the result was discordant due to the limit of detection for the phenotyping technology, while in the latter case the prediction algorithms were not computing the viral tropism correctly. Conclusions Although only demonstrated on a limited set of samples, the potential of the combined use of "deep sequencing + prediction algorithms" in cases where routine gp160 phenotype testing cannot be employed was illustrated. While good concordance was observed between gp120 phenotyping and prediction of R5-tropic virus, the results suggest that accurate prediction of X4-tropic virus would require further algorithm development.
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Arts GJ, Langemeijer E, Tissingh R, Ma L, Pavliska H, Dokic K, Dooijes R, Mesić E, Clasen R, Michiels F, van der Schueren J, Lambrecht M, Herman S, Brys R, Thys K, Hoffmann M, Tomme P, van Es H. Adenoviral vectors expressing siRNAs for discovery and validation of gene function. Genome Res 2003; 13:2325-32. [PMID: 12975310 PMCID: PMC403715 DOI: 10.1101/gr.1332603] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA interference is a powerful tool for studying gene function and for drug target discovery in diverse organisms and cell types. In mammalian systems, small interfering RNAs (siRNAs), or DNA plasmids expressing these siRNAs, have been used to down-modulate gene expression. However, inefficient transfection protocols, in particular, for primary cell types, have hampered the use of these tools in disease-relevant cellular assays. To be able to use this technology for genome-wide function screening, a more robust transduction protocol, resulting in a longer duration of the knock-down effect, is required. Here, we describe the validation of adenoviral vectors that express hairpin RNAs that are further processed to siRNAs. Infection of cell lines, or primary human cells, with these viruses leads to an efficient, sequence-specific, and prolonged reduction of the corresponding target mRNA, resulting in a reduction of the encoded protein level in the cell. For knock-down of one of the targets, GalphaS, we have measured inhibition of ligand-dependent, G-protein-coupled signaling. It is expected that this technology will prove to be of great value in target validation and target discovery efforts.
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Affiliation(s)
- Gert-Jan Arts
- Galapagos Genomics BV, 2333 CN Leiden, The Netherlands
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23
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Taghon T, Thys K, De Smedt M, Weerkamp F, Staal FJT, Plum J, Leclercq G. Homeobox gene expression profile in human hematopoietic multipotent stem cells and T-cell progenitors: implications for human T-cell development. Leukemia 2003; 17:1157-63. [PMID: 12764384 DOI: 10.1038/sj.leu.2402947] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Class I homeobox (HOX) genes comprise a large family of transcription factors that have been implicated in normal and malignant hematopoiesis. However, data on their expression or function during T-cell development is limited. Using degenerated RT-PCR and Affymetrix microarray analysis, we analyzed the expression pattern of this gene family in human multipotent stem cells from fetal liver (FL) and adult bone marrow (ABM), and in T-cell progenitors from child thymus. We show that FL and ABM stem cells are similar in terms of HOX gene expression, but significant differences were observed between these two cell types and child thymocytes. As the most immature thymocytes are derived from immigrated FL and ABM stem cells, this indicates a drastic change in HOX gene expression upon entry into the thymus. Further analysis of HOX-A7, HOX-A9, HOX-A10, and HOX-A11 expression with specific RT-PCR in all thymocyte differentiation stages showed a sequential loss of 3' region HOX-A cluster genes during intrathymic T-cell development and an unexpected expression of HOX-A11, previously not recognized to play a role in hematopoiesis. Also HOX-B3 and HOX-C4 were expressed throughout thymocyte development. Overall, these data provide novel evidence for an important role of certain HOX genes in human T-cell development.
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Affiliation(s)
- T Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, Ghent B-9000, Belgium
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