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Gareth Hardy

Very nice summary of these important reports, Richard.

I think one of the main differences in the two approaches was that in the Bullen paper they developed a PCR assay that discriminates between host-initiated and HIV LTR-initiated transcription. I think the rationale for this assay is that if viral transcripts are initiated by upstream host gene promotors, the viral transcript will not be complete and so can not lead to functional virions (hope I have understood that correctly?). Most viral PCR assays only measure part of the gag gene or gag and LTR (which are proximal), but are not designed to detect host gene fragments upstream of initiation. Therefore viral transcripts detected by conventional HIV PCR assays, may well include partial fragments that have been initiated by the activation of host genes. These will not reflect genuine full viral transcripts. The assays used in the other papers reporting an effect of HDAC inhibitors, presumably measure HIV using conventional PCR assays for gag and LTR sequences, so they would fall foul of this.
Why does it matter? Because the mechanism of action of HDAC inhibitors is to "release" genes from a "silent" state to enable their expression. This will effect host genes as well as HIV. Therefore HDAC-inhibitors are liable to initiate HIV transcription by activating upstream host genes. As such this means that the detection of HIV gag sequences by PCR in HDAC treated cells may in fact be a "false" signal.
This all leads me to think that the Bullen paper is more robust, whereas the Wei paper may be on a false lead. What flies in the face of this is the fact that Wei claim to have pelleted HIV virions from supernatant of HDAC-inhibitor treated CD4 cells. They could identify the HIV sequences in these virion pellets as they could in the host cells. This would suggest that mature HIV virions have been formed as a result of latent viral activation by HDAC inhibitors.
However it is not impossible that this is still wrong. I'm not going to speculate about how likely this is, but extracellular forms of RNA can be found that derive from host cells, as part of normal cell biology, contained in extracellular vesicles or exosomes. These are sadly about the same size and density as HIV virions and so very hard to distinguish by centrifugation. So I would argue that, sadly, the presence of "virions" in the supernatant of HDAC inhibitor-treated CD4 cells in the Wei paper, does not 100% prove that HDAC inhibitors are inducing viral activation.
However the fact that Gregory Laird (from the Bullen group) subsequently presented data claiming an effect from combined LRAs, presumably with the same host-viral PCR assay, is perhaps cause for more optimism.

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