Incomplete HIV-1 activation in latently infected U1 cells demonstrated by double in situ hybridization

Triple combination antiretroviral therapy can reduce HIV-1 infection to a relatively small pool of latently infected cells. To eliminate this residual source of virus, new therapies designed to activate latently infected cells are currently being tested. We therefore investigated the kinetics of in vitro HIV-1 RNA induction using chronically infected U1 cells. A new two-probe fluorescence in situ hybridization (double ISH) method was devised to simultaneously assess total HIV-1 RNA (T-RNA) and unspliced HIV-1 RNA (U-RNA) expression in individual cells. Activation of the U1 cells resulted in increasing expression of T-RNA between 0 and 24 h with lagging expression of U-RNA between 6 and 30 h. Both the positive area per cell and the number of positive cells increased with time. Although activation induced 98.5% of the cells to express HIV-1 T-RNA by 24 h, 52% remained negative for U-RNA. In contrast, 100% of 8E5 cells, which constitutively express HIV-1, scored positive for U-RNA as well as T-RNA with the double ISH. This study provides, for the first time, a semiquantitative cell-by-cell analysis of HIV-1 mRNA subsets in latently infected cells. Our results establish the advantages of using double fluorescence ISH to study gene expression and demonstrate that chronically infected U1 cells remain in a partially induced state despite potent activation.