HIV-1 expression is heterogeneous among clones of CD4+ T cells carrying authentic intact latent proviruses
Antiretroviral therapy suppresses HIV-1 infection but is not curative because it fails to eliminate a reservoir of intact latent proviruses that reside primarily in CD4+ T cells. This compartment is composed of rare T cells that predominantly express memory and effector memory markers. The lack of precise understanding of the latent compartment has made it challenging to develop curative strategies for HIV-1 infection. Here we report on the properties of CD4+ T cells clones carrying intact latent proviruses, expanded in vitro from single cells obtained from the reservoir of people living with HIV-1. The latent proviruses in the clones were integrated into ZNF genes, non-genic satellite and centromeric regions, frequently associated with latency. Notably, the transcriptome of the cultured clones resembled their cells of origin. Despite their descent from single cells, only a fraction of the cells ranging from 0.4-14% expressed relatively low levels of HIV-1 that did not measurably alter host gene transcriptome. Latency reversing agents (LRAs) variably increased the number and amount of expression per cell, but the effects were modest and clone and LRA specific. The results suggest that pharmacologic and immunologic approaches to clear the reservoir should be optimized to accommodate intra- and inter-clonal diversity. Overall design: CD4+ T cells harboring intact latent proviruses were obtained from single cells from 7 ART-suppressed individuals and expanded in vitro. These expanded clones were analyzed at baseline (resting) and after 24 hours of stimulation (activated) with anti-CD3/CD28 + IL-2. We performed 5' single-cell RNA sequencing (scRNA-seq) and T-cell receptor (scV(D)J-seq) using the 10X Genomics platform to characterize proviral expression and the host cell transcriptome.