Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection

Chang, Stewart T.; Thomas, Matthew J.; Sova, Pavel; Green, Richard R.; Palermo, Robert E.; Katze, Michael G.

MicroRNA regulators of T cell activation in HIV-infected cells. We found that several other pathways were enriched with target mRNAs, albeit at a relaxed threshold for significance (P Ͻ 0.10 by one-sided Fisher's exact test; see Table S3 in the supplemental material). By this threshold, some pathways, including "regulation of small GTPase-mediated signal transduction," "phosphoinositide binding," and "regulation of Ras protein signal transduction," were enriched in upregulated targeted mRNAs, suggesting microRNA downregulation may have contributed to increased receptor signaling (see Table S3 ). By the same criterion, other pathways, including "intracellular transport" and "secretion by cell," were enriched in downregulated targeted mRNAs, suggesting microRNA upregulation may have contributed to the suppression of intracellular trafficking (see Table S3 ). T cell activation-related pathways were also enriched with downregulated target mRNAs (as "costimulatory signal during T-cell activation" and "positive regulation of T cell activation" with P values of 0.05 and 0.08, respectively) (see Table S3 and Fig. S3C ). We previously found that T cell activation-associated mRNA expression was strongly suppressed at 12 and 24 hpi (1). In this study, we found that microRNAs were predicted to target key molecules involved in T cell activation, such as CD4, CD28, and TP53 (see Fig. S3C ). In particular, CD4 mRNA was targeted by five micro-RNAs (miR-181d, -663, -663b, -1248, and -1303), the most highly targeted hub mRNA in this subnetwork (see Fig. S3C ). Possible hub microRNAs and mRNAs for other pathways are shown in Fig. S3 .