Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency.
Suberoylanilide hydroxamic acid (SAHA) has been assessed in clinical trials as part of a "shock and kill" strategy to cure HIV-infected patients. While it was effective at inducing expression of HIV RNA ("shock"), treatment with SAHA did not result in a reduction of reservoir size ("kill"). We therefore utilized a combined analysis of effects of SAHA on the host transcriptome and proteome to dissect its mechanisms of action that may explain its limited success in "shock and kill" strategies. CD4+ T cells from HIV seronegative donors were treated with 1μM SAHA or its solvent dimethyl sulfoxide (DMSO) for 24h. Protein expression and post-translational modifications were measured with iTRAQ proteomics using ultra high-precision two-dimensional liquid chromatography-tandem mass spectrometry. Gene expression was assessed by Illumina microarrays. Using limma package in the R computing environment, we identified 185 proteins, 18 phosphorylated forms, 4 acetylated forms and 2982 genes, whose expression was modulated by SAHA. A protein interaction network integrating these 4 data types identified the HIV transcriptional repressor HMGA1 to be upregulated by SAHA at the transcript, protein and acetylated protein levels. Further functional category assessment of proteins and genes modulated by SAHA identified gene ontology terms related to NFκB signaling, protein folding and autophagy, which are all relevant to HIV reactivation. In summary, SAHA modulated numerous host cell transcripts, proteins and post-translational modifications of proteins, which would be expected to have very mixed effects on the induction of HIV-specific transcription and protein function. Proteome profiling highlighted a number of potential counter-regulatory effects of SAHA with respect to viral induction, which transcriptome profiling alone would not have identified. These observations could lead to a more informed selection and design of other HDACi with a more refined targeting profile, and prioritization of latency reversing agents of other classes to be used in combination with SAHA to achieve more potent induction of HIV expression.
Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, USA; San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA.
Cory H
CH
White
Cancer Sciences Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK; Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK.
Harvey E
HE
Johnston
Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK.
Bastiaan
B
Moesker
Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK.
Antigoni
A
Manousopoulou
Departments of Medicine, Microbiology and Immunology, Epidemiology, University of North Carolina, Chapel Hill, NC, USA.
David M
DM
Margolis
San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
Douglas D
DD
Richman
San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
Celsa A
CA
Spina
Cancer Sciences Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK; Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK. Electronic address: s.d.garbis@soton.ac.uk.
Spiros D
SD
Garbis
Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK. Electronic address: c.h.woelk@soton.ac.uk.
Christopher H
CH
Woelk
Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA. Electronic address: nbeliako@ucsd.edu.
Nadejda
N
Beliakova-Bethell
D015496:CD4-Positive T-Lymphocytes / Q000187:drug effects / Q000821:virology; D002478:Cells, Cultured; D002853:Chromatography, Liquid; D020869:Gene Expression Profiling; D006678:HIV / Q000502:physiology*; D006801:Humans; D006877:Hydroxamic Acids / Q000378:metabolism*; D046228:Microarray Analysis; D020543:Proteome / Q000032:analysis*; D053719:Tandem Mass Spectrometry; D014775:Virus Activation / Q000187:drug effects*; D017735:Virus Latency / Q000187:drug effects*; D000077337:Vorinostat
D006877:Hydroxamic Acids; D020543:Proteome; D000077337:Vorinostat
Autophagy; HIV latency; HMGA1; Protein folding; Suberoylanilide hydroxamic acid; iTRAQ mass spectrometry