Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model
Panel A. Illustrated are 9729 genes with statistically significant association to at least one of the two experimental conditions, HIV infection and TCR stimulation, as evaluated by 2-way analysis of variance of 14513 expressed genes (FDR<0.05). Data are presented in three non-exclusive groups: those regulated in concordance with viral presence (345 genes, top panel), those regulated in concordance with TCR-stimulation 9647 genes, (middle panel), and those showing non-additive synergetic effects by viral presence and TCR stimulation (59 genes, bottom panel). The bold lines represent the group average, and color intensities are proportional to statistical significance of the effects within each group. Panel B. Principal component analysis of host whole-transcriptome data supports a three-step model of entry-latency-reactivation. There is a transcriptionally coherent latency phase between week 4 and week 10, and a distinct reactivation phase at 8, 24, and 72 hours after TCR stimulation. All data, including differentially expressed genes and enrichment analysis, are available at http://litchi.labtelenti.org.