Single-Cell Analysis of the HIV/SIV Reservoir

SUMMARY
The viral reservoir in latently infected CD4+ T lymphocytes represents the key challenge for achieving an HIV-1
cure. We recently reported that the combination of the broadly neutralizing antibody (bNAb) PGT121 together
with a TLR7 agonist resulted in a substantial delay or prevention of viral rebound following ART discontinuation
in SHIV-infected rhesus monkeys. However, the biology and heterogeneity of the viral reservoir, as well as the
mechanism(s) by which these immunotherapeutic strategies target the reservoir, remain to be determined.
We hypothesize that there is substantial heterogeneity in the anatomic locations, cellular phenotypes,
host transcriptomes, and viral sequences of the viral reservoir, and that certain subsets of reservoir cells
are more susceptible to immune-mediated destruction. An improved understanding of the different cellular
subsets that comprise the viral reservoir will be essential for understanding the partial efficacy of current
interventions and for developing improved next-generation HIV-1 cure strategies. In this proposal, we will
continue an ongoing collaboration between Alex K. Shalek at Massachusetts Institute of Technology (MIT), who
is an expert in single-cell genomic profiling approaches, and Dan H. Barouch at Beth Israel Deaconess Medical
School (BIDMC), who is an expert in conducting HIV-1 cure studies in rhesus monkeys and humans. This unique
and synergistic partnership will apply the most insightful, cutting-edge, single-cell `-omics' assays to the most
relevant blood and tissue specimens from both monkeys and humans, leading to a deeper understanding of the
viral reservoir.
Overall, we will utilize these cutting-edge, single-cell `-omics' technologies to define, at multiple levels,
the functional heterogeneity of the viral reservoir and to evaluate the mechanism by which current
immunotherapeutic interventions target subsets of replication-competent reservoir cells. Such
knowledge will be leveraged to define the susceptibility of reservoir subpopulations to immune-mediated
destruction by comparing reservoir identity and phenotype following distinct immunotherapy protocols, and to
refine and develop next generation HIV-1 cures. To accomplish this goal, we propose the following two Specific
Aims:
Aim 1: To evaluate the anatomic, cellular, molecular, and viral heterogeneity of the viral reservoir in ART-
suppressed rhesus monkeys using single-cell and population genomic profiling strategies
Aim 2: To determine the extent to which current immunotherapeutic interventions target various
subpopulations of the viral reservoir in rhesus monkeys

Grant Number: 5R01AI149670-05
NIH Institute/Center: NIH
Principal Investigator: Dan Barouch