Background
We and others have previously demonstrated that intact, transcriptionally competent HIV genomes persist within the brain of virally suppressed people with HIV (PWH). Long terminal repeats (LTRs) isolated from the brain of non-virally suppressed PWH are genetically distinct from those isolated in matched peripheral tissue and have a reduced responsiveness to select latency reversing agents (LRAs) in brain cell lines. Whether promotors isolated from the brain of virally suppressed individuals are functional, genetically distinct and responsive to LRAs is unclear.
Methods
Autopsy frontal cortex brain tissue and matched peripheral tissue (spleen, lymph node, gut) from virally suppressed PWH (n=6; undetectable plasma viral load for a median of 3.41 years) were provided by the National NeuroAIDS Tissue Consortium. HIV LTRs were isolated using triple nested single genome amplification. Phylogenetic compartmentalisation and transcription factor binding site analyses was performed. Transcriptional activity of isolated LTRs transfected into astrocyte and microglia cell lines was assessed in the presence and absence of LRAs.
Results
66 LTR sequences, including 45 unique sequences, were isolated from the brain and matched peripheral tissue of 6 virally suppressed PWH. In contrast to our previous findings in non-virally suppressed PWH, phylogenetic compartmentalisation was not observed between brain and peripheral sequences in virally suppressed PWH. Identical LTR sequences were isolated from frontal cortex brain, gut and lymph node of two participants. Most of the sequences isolated from the frontal cortex of virally suppressed PWH retained intact core promotor regions (TATA, Sp1, NF-κB). Some promotors had additional sites, including Sp1 and TCF-α. Hypermutated sequences within frontal cortex and gut tissue were also isolated. Promoters were demonstrated to be active under basal and tat-activated conditions, with activities heterogenous across the compartments analysed.
Conclusions
Promotors isolated from virally suppressed PWH appear to be regulated differently to those isolated from the CNS of non-virally suppressed PWH. Compartmentalization of LTR sequences characteristic of non-virally suppressed promotors was not observed in LTR sequence isolated from virally suppressed PWH.