Monitor behavior of latent proviruses in the frame of
antiretroviral therapy
In many cases of viruses, the status of viral transcription shows a
strong correlation to their pathogenesis. Viruses, such as hepatitis B
virus, herpes virus and
HIV[83–85]require a transcriptionally silent state, so-called latency throughout
their life cycles, allowing viruses to persist in host cells for a long
time and establish chronic infections. In the case of HIV, viral rebound
frequently occurs when the antiretroviral therapy is interrupted,
subsequently leading to the AIDS symptoms resurface. It thus becomes an
obvious obstacle for curing HIV-1 infection. In the previous section we
talked about molecular barcodes used to quantitatively measure single
virus transcription. Here we are going to give several examples that
illustrate how molecular barcodes help us to interfere with translation
research involving antiretroviral therapy in addition to the measurement
of viral transcription.
The “shock and kill” antiretroviral therapy has been the most
attractive strategy for purging HIV latent infection as it was first
proposed in
2012[86].
The concept of this strategy is to give HIV-1-infected individuals
latency reversing agents (LRAs) such as histone deacetylase inhibitors
to deliberately reactivate proviral transcription in latently infected
cells, rendering reactivated cells destroyed by the host immune system.
The success of this strategy relies on the drugs used to reactivate
latent proviruses, yet several exploratory clinical trials have already
shown limited evidence of
efficacy[87].
Since molecular barcodes allow us to quantitative measure HIV
transcription at a single-virus level, Chen and colleagues thus
attempted to use them for estimating the spectrum of vorinostat, an
histone deacetylase inhibitor used in clinical
trials[88]as a proof of concept. Comparing with phytohemagglutinin, a strong
activator for T cells, it turned out that the same provirus can either
respond more strongly to phytohemagglutinin than vorinostat, orvice versa , indicating that vorinostat fully reactivate only a
subset of the proviruses in a cell population. Proviruses that were
prone to be reactivated by vorinostat were more frequently in the
vicinity of active regulatory elements (H3K27ac and histone H3
trimethylated at K4 and monomethylated at
K4)[25].
This observation was later confirmed by Battivelli and
colleagues[89]using a second generation of full-length dual-fluorescence reporter HIV,
HIVGKO, to investigate the reactivation potential of
various LRAs, including
panobinostat[90],
JQ1[91–95]and
bryostatin[96,97]in pure latent populations. They showed that less than 5% of the
latently infected primary CD4+ T cells were able to be reactivated by
LRAs and confirmed that the proviruses refractory to be reactivated
appeared to be present closer to heterochromatin (histone H3
trimethylated at K27 and at K9) and non-accessible regions (DNase
hyposensitivity)[89].
In vivo barcoded HIV has also been used to track viral rebounds
in animal models. Marsden and
colleagues[61]infected bone marrow-liver-thymus mice, an animal model that can
represent the human immune
system[98],
with barcoded nearly full-length and replication-competent HIV and
measured viral rebound after giving a synthetic bryostatin analog,
SUW133[99],
which is a PKC
inhibitor[100].
It was observed that mice treated with SUW133 showed a delay of viral
rebound after antiretroviral treatment was stopped compared with vehicle
control. In addition, barcode diversity present in reactivated viruses
showed a decrease compared with the mice treated with vehicle control,
meaning that the administration of SUW133 can eliminate a subset of
latently infected cells in this in vivo model.
Nonhuman primates are another useful animal model to study retroviruses.
SIV-infected nonhuman primates are similar in their pathophysiology and
viral dynamics to humans infected with
HIV-1[101–105]and therefore make ideal models for HIV studies in many aspects.
Fennessey and
colleagues[63]successfully employed the model of rhesus macaques infected with
barcoded SIV to identify and quantify the dynamics of the establishment
of viral reservoir and viral rebound after combination antiretroviral
therapy administration and interruption, demonstrating that the time of
initiation and duration of therapy administration in nonhuman primates
can alter the size of the reservoir. Soon afterwards Khanal and
colleagues[106]generated a derivative based on this barcoded SIV. At present barcoded
SIV continues to be applied on animal models of rhesus macaques to
tackle several important questions in the field of HIV/AIDS in many
aspects[107–111].