Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line

Chang, Stewart T.; Sova, Pavel; Peng, Xinxia; Weiss, Jeffrey; Law, G. Lynn; Palermo, Robert E.; Katze, Michael G.

In this study, we investigated changes in host and viral transcription occurring in a T lymphoblast-based model of HIV infection. SUP-T1 cells (5 Ï« 10 6 ) were infected in triplicate with HIV-1 strain LAI at a multiplicity of infection (MOI) of 5 which resulted in near-complete infection at 24 hours postinfection (hpi). The phenotype of infected cells (including appearance, viability, and the amount of viral mRNA and protein) was used to guide the selection of samples for NGS. At 12 hpi, viral mRNA could be detected in infected cells at appreciable levels (see Fig. S1 in the supplemental material). Few cells expressed the viral antigen p24 Gag, and visually, the cells appeared to be intact. By 24 hpi, high copy numbers of viral mRNA were present (Fig. S1 ). Nearly all cells showed the presence of p24 Gag antigen, syncytia were observed, and nonsyncytial cells had increased in volume. By 28 hpi, the effects of viral infection were more pronounced. The amount of viral RNA peaked (Fig. S1 ), and cell viability decreased. The bulk of cell death occurred between 32 and 48 hpi.