scRNA-seq analyses of HTO-tagged human peripheral blood mononuclear cells collected at the ART timepoint during HIV-1 disease

We investigated if differences in host gene expression modulate the size of the total HIV-1 PBMC reservoir during suppressive ART. Individuals treated with ART during acute infection who demonstrated effective viral suppression but varying frequencies of HIV-1 DNA+ cells were characterized by single-cell RNA sequencing (scRNA-seq). Differentially expressed genes and enriched pathways demonstrated increased monocyte activity in participants with undetectable HIV-1 reservoirs. This was validated in an independent study cohort comprised of 38 participants with different genetic backgrounds and HIV-1 subtype infections. Thawed unstimulated PBMC from 38 human participants at the ART timepoint were stained with HTO antibodies and subsequently pooled into 4 unique batches before single-cell RNA sequencing. Individual participant total HIV DNA and integrated HIV DNA measurements in PBMC were used to categorize participants into HIV reservoir groups.