Research on the mechanism of action of a new class antivirals, the LEDGINs, with a potential application for the functional cure of HIV infection
HIV-1 persists lifelong in memory cells of the immune system as latent provirus that rebounds upon treatment interruption. Therefore, the latent reservoir is the main target for an HIV cure. In order to find such cure further research on the determinants of HIV latency is essential. During my PhD, I investigated the role of integration sites in HIV-1 pathogenesis.
HIV integration is catalyzed by the viral integrase (IN) enzyme that employs the cellular chromatin reader LEDGF/p75 to target the virus to active transcription units. Our lab developed small molecule inhibitors of the interaction between LEDGF/p75 and IN, named LEDGINs. LEDGINs have a multimodal mechanism of action: they inhibit HIV integration (early effect) and enhance IN oligomerization resulting in defective progeny virions (late effect). In 2016, we have shown that LEDGIN treatment during infection inhibits integration and retargets residual integrants out of active genes. Moreover, these proviruses were more often in a latent state and refractory to reactivation, suggesting a link between HIV-1 integration and transcription.
During my PhD, I continued this research and studied the link between integration and HIV-1 expression with an advanced barcoded HIV technology (B-HIVE) developed by the Filion lab. B-HIVE tags individual HIV genomes with a unique barcode allowing for detection of insert-specific expression. In collaboration with the Filion lab, I confirmed that LEDGIN treatment during infection retargets integration out of active genes and reduces HIV RNA expression. Silent proviruses obtained after treatment with LEDGINs were located at increased distance from H3K36me3, the marker recognized by LEDGF/p75, and enhancers. Interestingly, enhancers stimulated HIV transcription irrespective of the presence of LEDGINs.
In a second project, I investigated whether LEDGIN treatment during virus production (the late effect) affects HIV-1 latency. Residual integrants obtained after infection of cells with virus produced in the presence of LEDGINs were more latent and refractory to reactivation. The chromatin environment surrounding these proviruses was associated with latency. However, LEDGIN treatment during virus production did not alter LEDGF/p75-mediated targeting to active genes, indicating that LEDGF/p75 is not the only determinant of integration site selection.
Altogether, these results show that LEDGINs retarget integration out of active genes to sites that are less susceptible to reactivation. As such, they might be useful in an alternative ‘block and lock’ HIV cure strategy that aims to permanently silence HIV provirus even after treatment interruption.