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.

The suppression of T cell activation that we observed was consistent with previous studies on the response of T cells to infection by chemokine (C-X-C motif) receptor 4 (CXCR4)-tropic versus chemokine (C-C motif) receptor 5 (CCR5)-tropic HIV-1 strains (29) (30) (31) . For example, Sirois et al. (31) found that key T cell activation-related genes, including LCK, were downregulated at 24 hpi by a CXCR4-tropic strain, whereas these same genes were upregulated by a CCR5-tropic strain. Our study utilized the CXCR4-tropic strain LAI, and it would be interesting to generate NGS data for a CCR5-tropic virus for comparison. Interestingly, our observations of small-magnitude differences in expression were consistent with those of Sirois et al. (31) , who found the expression of T cell activation-related genes to be changed by 0.5fold or less using reverse transcription-PCR (RT-PCR).