Dose-responsive gene expression in suberoylanilide hydroxamic acid-treated resting CD4+ T cells

Abstract

Design Persistent latently infected CD4+ T cells represent a major obstacle to HIV eradication. Histone deacetylase inhibitors (HDACis) are a proposed activation therapy. However, off-target effects on expression in host immune cells are poorly understood. We hypothesized that HDACi-modulated genes would be best identified with dose-response analysis. Methods Resting primary CD4+ T cells were treated with 0.34, 1, 3, or 10 μM of the HDACi, SAHA, for 24 hours and subjected to microarray gene expression analysis. Genes with dose-correlated expression were filtered to identify a subset with consistent up or downregulation at each SAHA dose. Histone modifications were characterized in 6 SAHA dose-responsive genes by chromatin immunoprecipitation (ChIP-RT-qPCR). Results A large number of genes were shown to be up (N=657) or downregulated (N=725) by SAHA in a dose-responsive manner (FDR p-value < 0.05, fold change ≥ |2|). Several genes (CTNNAL1, DPEP2, H1F0, IRGM, PHF15, and SELL) are potential in vivo biomarkers of SAHA activity. SAHA dose-responsive genes included transcription factors, HIV restriction factors, histone methyltransferases, and host proteins that interact with HIV. Pathway analysis suggested net downregulation of T cell activation with increasing SAHA dose. Histone acetylation was not correlated with host gene expression, but plausible alternative mechanisms for SAHA-modulated gene expression were identified. Conclusions Numerous genes in CD4+ T cells are modulated by SAHA in a dose-responsive manner, including genes that may negatively influence HIV activation from latency. Our study suggests that SAHA influences gene expression through a confluence of several mechanisms, including histone modification, and altered expression and activity of transcription factors.

Interval dosing with the HDAC inhibitor vorinostat effectively reverses HIV latency

“…Consistent with the potential for complex interactions between the cellular effects of HDAC inhibition and the expression of latent HIV, several studies reported that exposure to HDAC inhibitors is associated with a subsequent downregulation of positive regulators of transcription, such as histone acetyl transferases (HATs) (11,12). Furthermore, HDAC inhibition can lead to an increase in trimethylation of lysine 27 on histone 3 (H3K27me3) at transcriptional start sites (12).…”

Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency

“…However, their non-targeted detection suggests that these in vivo modified proteins had higher abundance relative to other in vivo modified proteins not detected in this study that typically require prior enrichment for their analysis (Papachristou et al., 2013). To compare the effect of SAHA treatment between the proteome and transcriptome, microarray gene expression data were selected from our previous SAHA dose responsive study (Reardon et al, 2015). A paired analysis identified 2,982 genes modulated by SAHA (FDR<0.05) in CD4+ T cells from 6 donors (see Table S2 for the complete list of DEGs at the probe level).…”

“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al, 2014) via the PRIDE partner repository (PXD002150). Transcriptomic data that assessed the effects of SAHA (1 µM) in CD4+ T cells was obtained from our previously published SAHA dose responsive Illumina microarray dataset (Reardon et al, 2015) at the Gene Expression Omnibus (GSE66994).…”

Genetic divergence in the transcriptional engram of chronic alcohol abuse: A laser-capture RNA-seq study of the mouse mesocorticolimbic system

“…For example, Parn is required for telomere function, and mutations in this gene are part of a collection of Mendelian disorders that result in telomere shortening (Bertuch, 2015; Moon et al, 2015; Tseng et al, 2015). Interestingly, H1f0 has been identified as a potential biomarker of acetylation based on response to pharmacological application of histone deacetylase inhibitors (Reardon et al, 2015). Yme1l1 is an oxidative stress-sensitive mitochondrial inner membrane protein that is up-regulated in response to the mitochondrial unfolded protein response (Aldridge, Horibe, & Hoogenraad, 2007; Rainbolt, Saunders, & Wiseman, 2015; Stiburek et al, 2012), and Atp5a1 functions as a component in mitochondrial complex V and is involved in energy production (Hejzlarová et al, 2014; Lucas et al, 2014).…”