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HIV-1 integration sites and their impact on HIV-1 pathogenesis

English title HIV-1 integration sites and their impact on HIV-1 pathogenesis
Applicant Metzner Karin
Number 141067
Funding scheme Project funding (Div. I-III)
Research institution Klinik für Infektionskrankheiten und Spitalhygiene Universitätsspital Zürich
Institution of higher education University of Zurich - ZH
Main discipline Medical Microbiology
Start/End 01.04.2012 - 30.06.2016
Approved amount 448'146.00
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All Disciplines (4)

Discipline
Medical Microbiology
Genetics
Molecular Biology
Experimental Microbiology

Keywords (4)

cell population; human immunodeficiency virus type 1; integration site; latency

Lay Summary (English)

Lead
Lay summary
Retroviral integration into the genome of the host cell is a very important step in the life cycle of a retrovirus. The integration site decides about the fate of the provirus. Integration into transcription-supporting units increases the chance of pursuing the retroviral life cycle and to produce the next generation of viruses. Integration into more silenced parts of the genome has the advantage that the virus can hide and persist, thus, establishing a latent reservoir. For human beings, this is particularly relevant in the context of infection with human immunodeficiency virus type 1 (HIV-1). HIV-1 can not only replicate to high levels, but it also establishes a life-long infection by generating a latent reservoir. It is still not known how HIV-1 achieves the state of latency. We will study changes in the frequencies and patterns of HIV-1 integration sites separately in its main target cell subpopulations from HIV-1 infected individuals followed over at least 5 years after primary HIV-1 infection. And we will investigate systematically chromosomal features surrounding HIV-1 integration sites and their influence on HIV-1 transcription by using a novel HIV-1 LTR-based reporter construct that will enable us to differentiate between (1) activated, (2) resting and inducible, (3) resting and non-inducible, and (4) silenced cells. These studies will help us understand how HIV-1 establishes and maintains a latent reservoir and which impact HIV-1 integration sites have on the pathogenesis of HIV-1. And it will enable us to obtain detailed insights into the regulation of HIV-1 transcription, thus, opening ways for novel therapeutic approaches to eradicate HIV-1.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Spontaneous reactivation of latent HIV-1 promoters is linked to the cell cycle as revealed by a genetic-insulators-containing dual-fluorescence HIV-1-based vector
Kok Yik Lim, Schmutz Stefan, Inderbitzin Anne, Neumann Kathrin, Kelley Audrey, Jörimann Lisa, Shilaih Mohaned, Vongrad Valentina, Kouyos Roger D., Günthard Huldrych F., Berens Christian, Metzner Karin J. (2018), Spontaneous reactivation of latent HIV-1 promoters is linked to the cell cycle as revealed by a genetic-insulators-containing dual-fluorescence HIV-1-based vector, in Scientific Reports, 8(1), 10204-10204.
Unravelling HIV-1 Latency, One Cell at a Time
Kok Yik Lim, Ciuffi Angela, Metzner Karin J. (2017), Unravelling HIV-1 Latency, One Cell at a Time, in Trends in Microbiology, 25(11), 932-941.
Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T cells.
Kok Yik Lim, Vongrad Valentina, Shilaih Mohaned, Di Giallonardo Francesca, Kuster Herbert, Kouyos Roger, Günthard Huldrych F, Metzner Karin J (2016), Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T cells., in Scientific reports, 6, 24157-24157.
HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages
Vongrad Valentina, Imig Jochen, Mohammadi Pejman, Kishore Shivendra, Jaskiewicz Lukasz, Hall Jonathan, Günthard Huldrych F., Beerenwinkel Niko, Metzner Karin J. (2015), HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages, in PLOS ONE, 10(7), e0132127-e0132127.
Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination
Di Giallonardo Francesca, Zagordi Osvaldo, Duport Yannick, Leemann Christine, Joos Beda, Künzli-Gontarczyk Marzanna, Bruggmann Rémy, Beerenwinkel Niko, Günthard Huldrych F., Metzner Karin J. (2013), Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination, in PLoS ONE, 8(9), e74249-e74249.

Collaboration

Group / person Country
Types of collaboration
Christian Berens/Friedrich-Loeffler-Institute Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Roger Kouyos/University of Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Alexandra Trkola/University of Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Keystone Symposium: HIV Persistence: Pathogenesis and Eradication Talk given at a conference A Novel HIV-1-based Vector that Reproduces Features of Productive and Latent HIV-1 Infections 20.03.2016 Olympic Valley, California, United States of America Günthard Huldrych Fritz; Vongrad Valentina; Kok Yik Lim; Metzner Karin;
Keystone Symposium: Mechanisms of HIV Persistence: Implications for a Cure Talk given at a conference Longitudinal patterns of HIV-1 integration sites (IS) in CD4+ T cell subsets in vivo 26.04.2015 Boston, MA, United States of America Metzner Karin; Kok Yik Lim; Günthard Huldrych Fritz; Vongrad Valentina;
Conference on Retroviruses and Opportunistic Infections (CROI) Poster HIV-1 Integration Sites in Macrophages and CD4+ T Cells Are Distinct 23.02.2015 Seattle, Washington, United States of America Kok Yik Lim; Metzner Karin; Günthard Huldrych Fritz; Vongrad Valentina;


Awards

Title Year
Young Investigator Award 2015

Associated projects

Number Title Start Funding scheme
148522 Swiss HIV Cohort Study (SHCS) 01.01.2014 Cohort Studies Large

Abstract

Retroviral integration into the genome of the host cell is a very important step in the life cycle of a retrovirus. The integration site decides about the fate of the provirus. Integration into transcription-supporting units increases the chance of pursuing the retroviral life cycle and to produce the next generation of viruses. Integration into more silenced parts of the genome has the advantage that the virus can hide and persist, thus, establishing a latent reservoir. For human beings, this is particularly relevant in the context of infection with human immunodeficiency virus type 1 (HIV-1). HIV-1 can not only replicate to high levels, but it also establishes a life-long infection by generating a latent reservoir. It is still not known how HIV-1 achieves the state of latency. It is conceivable that chromosomal features surrounding the HIV-1 integration site have a major impact on the transcription activity of the provirus. HIV-1 integration sites have been extensively studied in in vitro experiments using pseudotyped viruses and T cell lines. However, to date, knowledge of in vivo integration in HIV-1 infected individuals is very limited. For the first time, we will study changes in the frequencies and patterns of HIV-1 integration sites separately in its main target cell subpopulations from 10 HIV-1 infected individuals followed over at least 5 years after primary HIV-1 infection (subproject A). This study will help us understand how HIV-1 establishes and maintains a latent reservoir and which impact HIV-1 integration sites have on the pathogenesis of HIV-1.In subproject B, we will investigate systematically chromosomal features surrounding HIV-1 integration sites and their influence on HIV-1 transcription. So far, HIV-1 integration sites were studied in (1) activated and (2) resting and inducible cells in vitro using HIV-1 LTR-based reporter constructs in T cell lines. We will develop a novel system enabling us to study HIV-1 transcription and its dependence on surrounding chromosomal features also in (3) resting and non-inducible cells and, if possible, even in (4) silenced cells, which are important cell subpopulations not studied so far. To achieve this, we will insert an HIV-1 LTR-independent, EF1a promoter-controlled, second fluorescent marker, flanked by two potent insulators, into an HIV-1 LTR-based reporter construct. Using this novel approach, we will study patterns of HIV-1 transcription sites in primary CD4+ T lymphocytes and transcription pathways in stably transduced, monoclonal T cell lines from all 4 varieties of cell subpopulations described above. This will enable us to obtain detailed insights into the regulation of HIV-1 transcription, thus, opening ways for novel therapeutic approaches to eradicate HIV-1.
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