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

Although the ability of HIV-1 to reside in a latent state in CD4+ T cells constitutes a critical hurdle to a curative therapy, the biomolecular mechanisms by which latent HIV-1 infection is established and maintained are only partially understood. E x vivo studies have shown that T cell receptor/CD3 stimulation only triggered HIV-1 reactivation in a fraction of the latently infected CD4+ T cell reservoir, suggesting that parts of the T cell population hosting latent HIV-1 infection events are altered to be TCR/CD3-activation-inert. We provide experimental evidence that HIV-1 infection of primary T cells and T cell lines indeed generates a substantial amount of TCR/CD3 activation-inert latently infected T cells. HIV-1 induced host cell TCR/CD3 inertness is thus a conserved mechanism that contributes to the stability of latent HIV-1 infection. Proteomic and genome-wide RNA-level analysis comparing CD3-responsive and CD3-inert latently HIV-1 infected T cells, followed by software-based integration of the data into protein-protein interaction networks (PINs) 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. In extension, the data imply that therapeutic restoration of host cell TCR/CD3 responsiveness could enable gradual reservoir depletion without the need for therapeutic activators, driven by cognate antigen recognition. AUTHOR SUMMARY A curative therapy for HIV-1 infection will at least require the eradication of a small pool of CD4+ helper T cells in which the virus can persist in a latent state, even after years of successful antiretroviral therapy. It has been assumed that activation of these viral reservoir T cells will also reactivate the latent virus, which is a prerequisite for the destruction of these cells. Remarkably, this is not the case and following application of even the most potent stimuli that activate normal T cells through their T cell receptor, a large portion of the latent virus pool remains in a dormant state. Herein we demonstrate that a large part of latent HIV-1 infection events reside in T cells that have been rendered activation inert by the actual infection event. We provide a systemwide, biomolecular description of the changes that render latently HIV-1 infected T cells activation inert and using this description, devise pharmacologic interference strategies that render initially activation inert T cells responsive to stimulation. This in turn allows for efficient triggering of HIV-1 reactivation in a large part of the latently HIV-1 infected T cell reservoir.