HIV-infected cells from PLWH. (A) Schematic representation of the methods used to grow out HIV-1–infected cells from ART-suppressed individuals (Weymar et al., 2022). Created with https://BioRender.com. (B and C) UMAP of 10X single-cell gene expression data showing the position of the cells expressing the latent clones’ specific TCR (red dots) (B) and the fraction of latent cells in each cluster (C), for participants 603 (upper panels) and 5104 (lower panels) from ex vivo cells (left panels, data from Weymar et al. [2022]), and cultured cells under resting (middle panels) and activated (right panels) conditions. (D) Histograms show HIV-1 Gag p24 expression in HIV⁺ cells (red) and non-infected cells (blue) of cultures derived from 603 to 5104, under resting (upper panel) and activated (lower panel) conditions. (E) Relative expression of LTR (purple bars), gag (red bars), and env (blue bars) by qPCR for 603 and 5104 HIV⁺ cells under resting and activated conditions. Bars represent the mean relative expression of two independent assays (biological replicates) ± SD. (F) LTR transcripts per cell determined by qPCR, in cells from 603 to 5104 and in Jurkat and primary T cells reporter lines with proviruses integrated into ATP2B4, under resting (blue) and activated (red) conditions and HIV-1_YU2 controls. Bars represent the mean of two independent experiments (biological replicates) ± SD. (G) Relative expression determined by 10X Genomics single-cell mRNA sequencing of host gene neighboring HIV-1 proviral integration (ZNF486) in HIV-infected (HIV⁺) and non-infected (HIV⁻) cells from the same cell population under resting (blue bars) and activated (red bars) conditions. Bars represent the mean of the respective population from one assay ± standard deviation representing population variance.