(47b) Stochastic Effects in Viral Gene Expression Contribute to HIV-1 Latency

HIV, the retrovirus that causes AIDS, can establish rare, latent infections of cells, and the resulting latent pools of virus represent the most significant barrier to elimination of virus from a patient since they persist for decades and can reactivate at any time. After HIV enters a cell, it semi-randomly integrates its genetic material into the host genome. The viral promoter then integrates several inputs to regulate the viral gene expression rate: epigenetic effects at the integration position, the level of activation of host signaling pathways and in particular host transcription factors that bind to the viral promoter, and the levels of virally-encoded proteins that feed back and regulate promoter activation. A high viral gene expression rate rapidly initiates viral replication, whereas low expression can lead to stochastic effects in viral gene expression that we have hypothesized contribute to viral latency.

We have conducted a rigorous experimental and computational analysis of the gene expression dynamics in a lentiviral model of HIV-1. This model system is derived from HIV-1 and is missing viral pathogenic functions but retains its ability to integrate chromosomally, its full enhancer and promoter elements, and its implementation of a positive feedback loop mediated by the virally-encoded factor Tat that strongly regulates transcriptional activation. We have previously reported that stochastic fluctuations in Tat lead to phenotypic diversity, or stochastic bimodality, in HIV-1 gene expression, a phenomenon that can be observed experimentally and predicted computationally with stochastic modeling. As a result, we have hypothesized that Tat-mediated feedback is activated sporadically such that after the virus infects a target activated T cell and integrates into the host genome, significant periods of time may elapse before viral expression reaches the point where reproduction and propagation can occur. This time could be enough to allow an activated T cell to transition to its memory state, thereby trapping the lentivirus in an inactive form until such time as that memory cell is reactivated.

While the majority of scientific effort is focused on the canonical variant of HIV that infects North America and Europe, however, given the rapid evolution of the virus in individual patients and across the world there is a staggering level of viral sequence diversity. We now build on our previous discovery with experimental and computational approaches that explore the question of how viral sequence diversity can impact viral transcriptional regulation and latency. These findings yield insights into the establishment of HIV-1 latency and may ultimately lead to the mechanistic understanding and design of therapies to purge and eradicate latent HIV-1 reservoirs.