Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

The latent reservoir is a main barrier for curing HIV. But because
latently-infected cells cannot be phenotyped directly, the features of the
in vivo reservoir have remained elusive. Here, we describe a method that
leverages high-dimensional phenotyping using CyTOF to trace
latently-infected cells reactivated ex vivo to their original
pre-activation states. Our results suggest that contrary to common
assumptions, the reservoir is not randomly distributed among cell subsets,
and is remarkably conserved between individuals. However, reservoir
composition differs between tissues and blood, as do cells successfully
reactivated by different latency reversing agents. By selecting 8-10 of
our 39 original CyTOF markers, we were able to isolate highly purified
populations of unstimulated in vivo latent cells. These purified
populations were highly enriched for replication-competent and intact
provirus, transcribed HIV, and displayed clonal expansion. The ability to
isolate unstimulated latent cells from infected individuals enables
previously impossible studies of HIV persistence.