Catchet-MS identifies IKZF1-targeting Thalidomide analogues as novel HIV-1 latency reversal agents

A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and latency reversal, due to technical limitations, this has been challenging. Here we use a dCas9 targeted chromatin and histone enrichment strategy coupled to mass spectrometry (Catchet-MS) to probe the differential protein composition of the latent and activated HIV-1 5'LTR. Catchet-MS identified known and novel latent 5'LTR-associated host factors. Among these, IKZF1 is a novel HIV-1 transcriptional repressor, required for Polycomb Repressive Complex 2 recruitment to the LTR. We find the clinically advanced thalidomide analogue iberdomide, and the FDA approved analogues lenalidomide and pomalidomide, to be novel LRAs that, by targeting IKZF1 for degradation, reverse HIV-1 latency in CD4+T-cells isolated from virally suppressed people living with HIV-1. Overall design: ChIP-sequencing was performed using the sequentially purified chromatin from J-Lat 11.1 cells stably expressing HIV-LTR-HS2 guided HA-V5-FLAG-dCas9. Chromatin was first immunoprecipitated using V5 affinity beads to enrich for dCas9 bound sequences, eluted and re-immunoprecipitated using Histone H3-H2B affinity purification. One input and one immunoprecipitated sample were sequenced.