Identifying antiviral effector mechanisms that influence HIV-1 infection

The ability of an organism to detect a viral infection is critical for triggering host defence systems at the earliest possible moment and preventing development of a disease. Our current understanding of the way human immunodeficiency virus type 1 (HIV-1) infects human cells and activates the innate immune system is still incomplete and many of the key questions remain unanswered. In particular, we need to describe specific PAMP-PRR interactions and the pathways for interferon (IFN) induction following infection. In this respect, the early steps of infection, following fusion and reverse transcription seem as good candidates for being involved in both recognition and evasion of the innate immune system. The purpose of this project grant is to describe where and how the innate immune system recognise HIV in human macrophages.

The project
The pivotal sensor responsible for sensing HIV cDNA and dsDNA, and driving IFN induction was not discovered until recently when my group published a paper in PNAS. We reported that DNA-containing nucleic acid forms produced during RT induced IFN expression. We found that the protein IFI16 interacted directly with intracellular DNA and was responsible for the IFN responses observed. Importantly, IFI16 was recruited to cytosolic regions of HIV-DNA accumulation where IFI16 directly associated with viral DNA and knockdown of IFI16 in HIV non-permissive cells abolished IFN and ISG induction but enabled HIV to replicate. Collectively, our study concludes that IFI16 is a sensor for HIV RT products and restricts HIV-1 replication in human macrophages. Building upon this work, we now have preliminary results indicating that IFI16 also works as a restriction factor against HIV infection. Thus the first project is expected to describe in details how IFI16 may work as a restriction factor against HIV.

It is widely discussed whether HIV nucleic acids are protected by the capsid complex in the cytoplasm or whether the viral capsid needs to be destabilized for RT to initiate. Recently, it has been proposed that uncompleted RT lead to cytosolic accumulation of viral DNA fragments, which then trigger innate immune sensing. Thus the second part of our project is to investigate the interconnection of IFI16 with HIV capsid molecules.

Aims and hypothesis
It is our goal to add new evidence to which proteins are assembled in the innate immune complex that detects the release of HIV capsid into the cell and subsequently senses viral DNA. The project has two aims that fit into the general research theme of my group focusing on “viral-host interactions”.

Hypothesis: “HIV replication is controlled by intrinsic restriction factors, which individually exert blocking of viral replication. Removing one of these factors allows the virus to overproduce and exhaust the cell whereas overexpression of these factors may improve the antiviral functions.” Aim 1 is to describe the function of IFI16 as a restriction factor against HIV.

Hypothesis: “DNA products from retroviruses can be found at distinct foci in the cell cytoplasm where they bind to DNA-specific pathogen recognition receptors (PRRs). This complex traffics to the Endoplasmic Reticulum (ER) where it interacts with Stimulator of interferon genes (STING)”. Aim 2 is to describe where and how sensing complexes related to HIV DNA are formed.

Participants in the project

  • Martin Roelsgaard Jakobsen (PI, Grant licensee)
  • Karthiga Thavachelvam (expected PhD student)
  • Ane Kjeldsen (Lab technician)
  • Søren Riis Paludan (Collaborator)