Modeling the Effects of Vorinostat In Vivo Reveals both Transient and Delayed HIV Transcriptional Activation and Minimal Killing of Latently Infected Cells

Abstract

Recent efforts to cure human immunodeficiency virus type-1 (HIV-1) infection have focused on developing latency reversing agents as a first step to eradicate the latent reservoir. The histone deacetylase inhibitor, vorinostat, has been shown to activate HIV RNA transcription in CD4+ T-cells and alter host cell gene transcription in HIV-infected individuals on antiretroviral therapy. In order to understand how latently infected cells respond dynamically to vorinostat treatment and determine the impact of vorinostat on reservoir size in vivo, we have constructed viral dynamic models of latency that incorporate vorinostat treatment. We fitted these models to data collected from a recent clinical trial in which vorinostat was administered daily for 14 days to HIV-infected individuals on suppressive ART. The results show that HIV transcription is increased transiently during the first few hours or days of treatment and that there is a delay before a sustained increase of HIV transcription, whose duration varies among study participants and may depend on the long term impact of vorinostat on host gene expression. Parameter estimation suggests that in latently infected cells, HIV transcription induced by vorinostat occurs at lower levels than in productively infected cells. Furthermore, the estimated loss rate of transcriptionally induced cells remains close to baseline in most study participants, suggesting vorinostat treatment does not induce latently infected cell killing and thus reduce the latent reservoir in vivo.

Fig 1. Schematic illustrations of two latency models that describe the impact of vorinostat treatment.

The models keep track of both the within-host infection dynamics and intracellular HCV transactivation dynamics. (A) The direct activation model. CD4⁺ target cells (T) can be infected by HIV (V). Upon infection, the majority of infected target cells become productively infected cells (I), while a small fraction become latently infected cells (L). Latently infected cells (L) undergo asymmetric division and their progeny can either be activated or remain latent. Under vorinostat treatment, the latently infected cells become sustainably activated (L _A) at rate ν. In these cells, CA-US HIV RNAs (R) are produced at rate α, exported at rate ρ and degraded at rate μ. Combination antiretroviral therapy (cART) with reverse transcriptase and protease inhibitors inhibits infection and production of infectious virus. (B) The delayed activation model. This model extends the direct activation model by adding two additional states: latently infected cells that are transiently activated (L _T) upon vorinostat treatment, and cells that were transiently activated and now are in a waiting state (L _W), i.e. a period of delay, before transitioning to a sustained activation state (L _A). CA-US HIV RNAs (R) are produced from both the transiently activated cells (L _T) and the sustainably activated cells (L _A). Key rate constants are shown on the transitions (arrows) between compartments (see Table 1 for notation).

Fig 2. Fitting results of the direct activation model to the clinical data from the first 7-day’s of treatment.

Each panel shows the fitting result for a participant. Red lines are model simulations using best-fit parameter values. The black circles and vertical black lines are the mean and standard deviation of four replicate measurements made at each time point.

Fig 3. The multistage delayed activation model describes the clinical data well in a majority of the participants.

Each panel shows the simulation trajectories using best-fit parameters of the multistage delayed activation model (green lines) and the levels of CA-US RNA measured in the clinical trial. The period of vorinostat treatment is shaded in bisque.

Fig 4. Distributions of best-fit values for the production rate of CA-US HIV RNA and the loss rate of sustainably activated cells in the 20 study participants.

(A) The estimated production rates of CA-US HIV RNA, α, (in Log₁₀) in transcriptionally activated latent cells. Dashed line shows the estimated production rate of CA-US RNA in productively infected cells, α _I = 4x10⁴ molecules day^-1 [28] (see Methods). (B) The estimated loss rates of sustainably activated cells (L _A), d _LA. Dashed line shows the death rate of productively infected cells, δ = 1.0 day^-1 [27].