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.

HIV-1 infection impacts core T cell functionality by 12 hpi. We determined the possible impact of these DE genes by analyzing the corresponding annotations (biological processes, molecular functions, and pathways) using the NIH DAVID resource. We found that T cell activation and differentiation were the most overrepresented annotations among DE host genes at 12 hpi overall ( Fig. 2A) . Other annotations associated with DE genes included protein kinase regulation, DNA recombination, and caspase activity regulation ( Fig. 2A ). In addition, several of the DE genes at 12 hpi encoded transcriptional regulators; these genes include EGR1, KLF13, and MYC. Interestingly, four of the nine genes DE at 12 hpi but not at 24 hpi also encoded transcriptional regulators (CREB3L3, HEXIM1, ZNF660, and ZKSCAN4), indicating regulation specific to early viral replication. Seven genes contributed to the overrepresentation of T cell activation among DE genes at 12 hpi (BCL11B, CD1D, EGR1, IKZF1, IRF1, RAG1, and SOX4), six of which were downregulated, indicating a net suppression of T cell activation (as T cell differentiation in Fig. 2 ). Five T cell activation-related DE genes (BCL11B, EGR1, IRF1, IKZF1, and SOX4) encoded transcription factors, some of which had known relevance to HIV infection. For example, the BCL11B gene product binds directly to the HIV-1 sample relative to averaged time-matched mock-infected cell samples. Genes were segregated by the direction of change relative to mock infection at 12 hpi, and hierarchical clustering was done within each directional group. Genes that were not also DE at 24 hpi (purple type) and genes that were also DE at 24 hpi but with changed directionality (gold type) are indicated. Annotations indicate overrepresented categories in DAVID (Fig. 2 ). Matches to top-scoring categories in each DAVID annotation cluster (matching numbers in Fig. 2 ) (solid black squares) and matches to related categories in the same DAVID cluster as the top-scoring category (solid gray squares) are indicated. reg, regulation. long terminal repeat (LTR) and inhibits LTR expression (9) . BCL11B downregulation may therefore allow more efficient HIV-1 replication. Other DE genes related to T cell activation not encoding transcription factors also had known relevance to HIV infection. For example, the CD1D product presents lipid antigens on the surface and is directed by HIV-1 Nef for internalization and degradation (10) . Downregulation of CD1D at the mRNA level would further reduce surface expression and facilitate immune evasion.