Transcriptomic profiling of micro RNAs in mock-infected cells and an in vitro model of HIV latency before and after activation
Purpose: The goal of this study is to identify host micro RNAs (miRNAs) whose expression is dysregulated during HIV latency, cell activation and productive infection. This information provides a mechanistic insight into an additional layer of miRNA-mediated regulation of gene expression and cellular pathways that are involved in HIV latency establishment and maintenance. Methods: An in vitro model of HIV latency and mock-infected cells before and after activation with antiCD3/antiCD28 coated magnetic beads was used for miRNA expression profiling using small RNA sequencing (smRNA-Seq). Results: Read counts of the 418 miRNAs survived filtering. Differential expression analysis identified 26 miRNAs dysregulated in latency. Messenger RNA (mRNA) targets and cellular pathways enriched for mRNA targets were identified using several analytical methods. Our analyses showed that many protein-coding genes and pathways targeted by dysregulated miRNAs have relevance to regulation of HIV expression or establishment of HIV latency. The p53 signalling pathway was found among pathways that were targeted by dysregulated miRNAs at a greater level than expected by chance. Conclusions: The present study identifies miRNAs dysregulated during HIV latency and provides a mechanistic insight into regulation of the p53 pathway via miRNAs that may contribute to latency establishment. Overall design: Transcriptomic profiling of the in vitro model of HIV latency and mock-infected cells before and after activation. The experiment had 4 biological replicates, 4 conditions for each, for a total of 16 samples.