Extensive proteomic and transcriptomic changes quench the TCR/CD3 activation signal of latently HIV-1 infected T cells

HIV-1 latency is a critical hurdle to a cure for HIV-1 infection, but our understanding of the molecular biology of latency control is still incomplete. We provide experimental evidence that HIV-1 infection of primary T cells and T cell lines generates a substantial amount of TCR/CD3 activation-inert latently infected T cells. Proteomic and genome-wide RNA-level analysis comparing CD3-responsive and CD3-inert latently HIV-1 infected T cells, followed by software-based data integration suggested two phenomena to govern CD3-inertness: (i) the presence of extensive transcriptomic noise that affected the efficacy of CD3 signaling and (ii) defined changes to specific signaling pathways. Validation experiments demonstrated that compounds known to increase transcriptomic noise further diminished the ability of TCR/CD3 stimulation to trigger HIV-1 reactivation. Conversely, targeting specific central nodes in the generated PINs such as STAT3 improved the ability of TCR/CD3 activation to trigger HIV-1 reactivation in T cell lines and primary T cells. The data emphasize that latent HIV-1 infection is largely the result of extensive, stable biomolecular changes to the signaling network of the host T cells harboring latent HIV-1 infection events. We discuss the implications of these findings for the idea of using single drug therapies to trigger HIV-1 reactivation in the latent T cell reservoir in patients. Gene expression profiling of two replicates each: uninfected Jurkat cells, latently HIV-1 infected CD3 responsive JWEAU-A10 cells, and latently HIV-1 infected CD3 unresponsive JWEAU-C6 cells.