Impact of Interventions on Clonally Expanded Proviruses and Their RNA Expression

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

BACKGROUND: Proposed curative interventions for HIV have included treating with agents, such as HDAC inhibitors, that activate latent proviruses, inducing expression of intracellular RNA, in the hopes that such expression will result in viral production and killing of infected cells by viral cytotoxicity or targeted cytotoxic T-lymphocyte (CTL) response. However, previous studies, in which we collaborated with Dr. David Margolis (University of North Carolina), showed only a limited effect on reservoir reduction in participants treated with single or multiple doses of the HDAC inhibitor vorinostat (Archin et al., J. Infect. Dis. 210:728-735, 2014; Archin et al., Nature 487:482-485, 2012), including a lack of increased viral production in vivo measured by the HIV single-copy assay (SCA). More promising data have been obtained from more potent inhibitors and from combinations of HDAC inhibitors in in vitro studies, some of which were conducted by the University of Pittsburgh directed by Dr. John Mellors (Cillo et al., PNAS 111:7078-7083, 2014; Wei et al., PLoS Pathog. 10:e1004071, 2014). Although these potent inhibitors are believed to be more effective at inducing proviral expression, it is not currently known what levels of proviral expression are necessary to induce cell killing. Furthermore, by comparing uninduced and induced PBMCs from the same individuals, we will determine which inhibitors are capable of reactivating latent proviruses (those that are not expressing HIV RNA prior to induction) in expanded cell clones and which only increase expression of proviruses that were already expressing at low levels prior to the induction, and the heterogeneity of these effects among proviruses. While conducting the in vitro studies on the HDAC inhibitors, we also plan to assess the efficacy of curative interventions on expanded clones in vivo. We will use samples accessible through the Pitt contract from the single-dose infusion of the HDAC inhibitor romidepsin study (protocol A5315), the broadly neutralizing antibody VRC-01 study (protocol A5342), the low-dose methotrexate study (protocol A5314), and others as they are completed, by performing the integration sites assay (ISA) and quantitative digital droplet PCR (ddPCR) of specific clones on samples collected before, during, and after treatment in collaboration with Drs. Frank Maldarelli and Stephen Hughes (HIV Dynamics and Replication Program). ____ACCOMPLISHMENTS: In addition to our contribution to studies on the effect of vorinostat on HIV viremia levels in individuals treated with antiretroviral therapy (ART) (Gay et al., AIDS Res. Hum. Retroviruses 34:111-122, 2018), we also participated in an early ART intervention study (Henrich et al., PLoS Med. 14(11):e1002417, 2017) that showed that initiating ART in very early infection significantly delayed the time to viral rebound. Consistent with this finding, we conducted another study using samples from the AIDS clinical trial group (protocol A5142) showing that higher HIV genetic diversity at the time of initiating ART may be associated with the emergence of drug resistance and ART failure (Kearney et al., PLoS ONE 13(1):e0190438, 2018). Our studies lead to the conclusion that early ART initiation will reduce the size of the HIV reservoir and limit virologic failure. ____Our current research is focused on the effect of anti-PD-1 on the HIV reservoir in vivo. In collaboration with Dr. Eli Boritz at NIAID, we obtained samples from HIV-1-infected patients who received anti-PD-1 infusions to determine the effect of this checkpoint inhibitor on levels of HIV-infected cells during ART. Using our FLIP-SGS assay (described in Project ZIA BC 011681), we are characterizing the sites of integration into the host genome and the proviral structure in infected cells obtained before and after treatment with anti-PD-1.