[PDF][PDF] Combined single-cell transcriptional, translational, and genomic profiling reveals HIV-1 reservoir diversity

G Sannier, M Dube, C Dufour, C Richard, N Brassard… - Cell reports, 2021 - cell.com
G Sannier, M Dube, C Dufour, C Richard, N Brassard, GG Delgado, A Pagliuzza, AE Baxter
Cell reports, 2021cell.com
Although understanding the diversity of HIV-1 reservoirs is key to achieving a cure, their
study at the single-cell level in primary samples remains challenging. We combine flow
cytometric multiplexed fluorescent in situ RNA hybridization for different viral genes with HIV-
1 p24 protein detection, cell phenotyping, and downstream near-full-length single-cell vDNA
sequencing. Stimulation-induced viral RNA-positive (vRNA+) cells from viremic and
antiretroviral-therapy (ART)-suppressed individuals differ in their ability to produce p24. In …
Summary
Although understanding the diversity of HIV-1 reservoirs is key to achieving a cure, their study at the single-cell level in primary samples remains challenging. We combine flow cytometric multiplexed fluorescent in situ RNA hybridization for different viral genes with HIV-1 p24 protein detection, cell phenotyping, and downstream near-full-length single-cell vDNA sequencing. Stimulation-induced viral RNA-positive (vRNA+) cells from viremic and antiretroviral-therapy (ART)-suppressed individuals differ in their ability to produce p24. In participants on ART, latency-reversing agents (LRAs) induce a wide variety of viral gene transcription and translation patterns with LRA class-specific differences in reactivation potency. Reactivated proviruses, including in p24+ cells, are mostly defective. Although LRAs efficiently induce transcription in all memory cell subsets, we observe induction of translation mostly in effector memory cells, rather than in the long-lived central memory pool. We identify HIV-1 clones with diverse transcriptional and translational patterns between individual cells, and this finding suggests that cell-intrinsic factors influence reservoir persistence and heterogeneity.
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