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