Gene expression profile at single cell level of primary CD4+ T cells, infected with HIV in vitro and activated on plates coated with antiCD3/antiCD28 antibodies.

CD4+ T cells respond differentially to the T cell receptor (TCR) stimulus: some get fully activated and proceed to cell proliferation; others are only minimally activated and remain non-dividing for as long as 7 days following exposure to the TCR stimulus. In this study, we identified genes expressed differentially in cells infected with HIV, compared to uninfected cells, in cell subsets with different proliferative responses to the TCR stimulus. We show common and unique gene expression signatures in HIV-positive cells depending on cellular proliferative response. Primary CD4+ T cells were isolated from peripheral blood of 3 different HIV-seronegative blood donors and viably frozen. On the day of the experiment, cells were thawed, cultured overnight, and then stained with a viable dye carboxyfluorescein diacetate succinimidyl ester to allow tracking of cell proliferation. The next day, cells were infected with HIV NL4-3 for 4-6 hours, and activated on plates coated with antiCD3/antiCD28 antibodies for 4 days. The cells were then removed from plates and incubated for additional 3 days in RPMI medium supplemented with 5% human serum and IL2+IL-15 cytokines. On day 7, cells were collected and processed for single cell RNA-Seq.