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

Abstract

The biomolecular mechanisms controlling latent HIV-1 infection, despite their importance for the development of a cure for HIV-1 infection, are only partially understood. For example, ex vivo studies have recently shown that T cell activation only triggered HIV-1 reactivation in a fraction of the latently infected CD4+ T cell reservoir, but the molecular biology of this phenomenon is unclear. We demonstrate that HIV-1 infection of primary T cells and T cell lines indeed generates a substantial amount of T cell receptor (TCR)/CD3 activation-inert latently infected T cells. RNA-level analysis identified extensive transcriptomic differences between uninfected, TCR/CD3 activation-responsive and -inert T cells, but did not reveal a gene expression signature that could functionally explain TCR/CD3 signaling inertness. Network analysis suggested a largely stochastic nature of these gene expression changes (transcriptomic noise), raising the possibility that widespread gene dysregulation could provide a reactivation threshold by impairing overall signal transduction efficacy. Indeed, compounds that are known to induce genetic noise, such as HDAC inhibitors impeded the ability of TCR/CD3 activation to trigger HIV-1 reactivation. Unlike for transcriptomic data, pathway enrichment analysis based on phospho-proteomic data directly identified an altered TCR signaling motif. Network analysis of this data set identified drug targets that would promote TCR/CD3-mediated HIV-1 reactivation in the fraction of otherwise TCR/CD3-reactivation inert latently HIV-1 infected T cells, regardless of whether the latency models were based on T cell lines or 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 responsiveness prior to the use of any activating stimulus will likely have to be an element of future HIV-1 cure therapies.

Effects of Caspase-3 on HIV-1 Latency in a 3.01 Cells

“…Host transcription factors, such NF-ĸB p65, Ap-1, Sp-1 and NFAT, with binding sites located within the viral Long Terminal Repeat (LTR), are required for HIV-1 gene expression and replication which can be regulated by activation/inhibition of TCR-related signaling pathways [9,10,17,19,21]. Knock-down of the expression of FADD [9] and inhibition of caspase-3 activities (Figure 1B) inactivates NF-ĸB p65, Ap-1, Sp-1 and NFAT through decreased/ inactivated signaling transduction of TCR-related pathways with down regulation of expression of TCRα/β, PKC, or PI3K/Akt [9] (Figure 2).…”

“…Latent HIV proviruses are thought to be primarily reactivated in vivo through stimulation of the T-cell receptor (TCR). It has been reported that T cell activation is required forHIV-1 replication and gene expression, and T cells are generally activated through TCR, and CD3 [19,21], or/and PI3K/Akt [19]-related cell signaling pathways. These pathways can trigger and activate downstream molecules, such as Zap-70 and PLCγ1, and serially activate transcription factors, NF-ĸB p65, Ap-1, Sp-1 and NFAT.…”

Controversies in the Design of Strategies for the Cure of HIV Infection

“…Moreover, given the increasingly well-established relationship between HIV infection and the persistent proinflammatory state, the search for drugs that cover the largest possible proportion of the viral reservoir have become a priority [ 75 ]. There is research into new molecular signaling pathways to improve the latency reversal process [ 76 , 77 , 78 ], although the complex signaling process regulating CD4+ T cell expression is not yet fully understood [ 79 ].…”

CXCR4 Targeting Nanoplatform for Transcriptional Activation of Latent HIV-1 Infected T Cells

“…8 The impact of latent reservoir cells on ART highlights the need for continuous research and the development of new therapies that can target and eliminate these reservoir cells. 9 In this work, we developed a nanoparticle formulation to improve ART for retroviral infections, with a focus on inactive HIV reservoir cells.…”

“…These reservoir cells comprise dormant viruses integrated to host genomes that cannot be eliminated by ART and can become active later, resulting in treatment failure and drug resistance . The impact of latent reservoir cells on ART highlights the need for continuous research and the development of new therapies that can target and eliminate these reservoir cells . In this work, we developed a nanoparticle formulation to improve ART for retroviral infections, with a focus on inactive HIV reservoir cells.…”