Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment.

Cory H White,Gkikas Magiorkinis,Christopher H Woelk,Steven M Lada,Celsa A Spina,John Frater,Tara P Hurst,Douglas D Richman,Nadejda Beliakova-Bethell,Michael S Breen

doi:10.3389/fimmu.2018.00603

Abstract

The greatest obstacle to a cure for HIV is the provirus that integrates into the genome of the infected cell and persists despite antiretroviral therapy. A “shock and kill” approach has been proposed as a strategy for an HIV cure whereby drugs and compounds referred to as latency-reversing agents (LRAs) are used to “shock” the silent provirus into active replication to permit “killing” by virus-induced pathology or immune recognition. The LRA most utilized to date in clinical trials has been the histone deacetylase (HDAC) inhibitor—vorinostat. Potentially, pathological off-target effects of vorinostat may result from the activation of human endogenous retroviruses (HERVs), which share common ancestry with exogenous retroviruses including HIV. To explore the effects of HDAC inhibition on HERV transcription, an unbiased pharmacogenomics approach (total RNA-Seq) was used to evaluate HERV expression following the exposure of primary CD4+ T cells to a high dose of vorinostat. Over 2,000 individual HERV elements were found to be significantly modulated by vorinostat, whereby elements belonging to the ERVL family (e.g., LTR16C and LTR33) were predominantly downregulated, in contrast to LTR12 elements of the HERV-9 family, which exhibited the greatest signal, with the upregulation of 140 distinct elements. The modulation of three different LTR12 elements by vorinostat was confirmed by droplet digital PCR along a dose–response curve. The monitoring of LTR12 expression during clinical trials with vorinostat may be indicated to assess the impact of this HERV on the human genome and host immunity.

Highlights

Vorinostat is a histone deacetylase (HDAC) inhibitor known as suberoylanilide hydroxamic acid
These eight samples were subjected to total RNA-Seq analysis, and the resulting data mapped against human endogenous retroviruses (HERVs) sequences curated in Human Endogenous Retrovirus Database (HERVd) [23]
LTR16C and LTR33 elements, which originated from the ERVL family, were predominantly downregulated, whereas LTR12 elements from the HERV-9 family were predominantly upregulated

Summary

Introduction

Vorinostat is a histone deacetylase (HDAC) inhibitor known as suberoylanilide hydroxamic acid. HDAC inhibitors act on HDAC enzymes and block the removal of acetyl groups from histones resulting in a relaxed chromatin state [1] and the modulation of the expression of large numbers of genes [2, 3]. HDAC inhibitors appear to affect the acetylation states of transcription. HDAC inhibitors have wide ranging therapeutic value and have been considered for the treatment of cancer [5] and neurodegenerative disorders [6], as well as in “shock and kill” strategies to facilitate an HIV cure [7]. Due to the pre-existing FDA approvals for human use, vorinostat has already been used in a number of completed [9, 10] and ongoing [11] clinical trials assessing shock and kill strategies for an HIV cure

Methods

Results

Conclusion