miRNA biology in chronic infections and the shaping of the adaptive immune response

In our studies focused on the interplay of miRNA biology and vertebrate viruses, we discovered that poxviruses tailed and degraded all small RNAs loaded into the RNA induced silencing complex (RISC). This finding was the result of efforts to engineer Vaccinia virus (VACV) to express miR-124 (VACV124). VACV124 infection resulted in dramatic tailing of the virus-encoded miR-124 as well as corresponding loss of endogenous miRNAs such as miR-93 (Paper here). While we speculate that this activity is required to expand the ribonucleotide pool of the infected cell (rather than being due to a selection pressure imposed by post transcriptional silencing), the discovery itself provided us with a novel tool to study RNAi biology in vivo. As such, we cloned the gene responsible for tailing and degradation of miRNAs (called VP55) both within a replication competent virus and as a simple Adenovirus (AdV)-based expression vector (Papers here and here). These tools further supported our earlier in vitro work suggesting RNAi did not significantly contribute to acute RNA virus infection in mammals but it also illustrated a unique role for miRNA biology in the induction of cytokines. Briefly, we found that complete loss of miRNAs resulted in little change to the transcriptome for the first 24hrs but, thereafter, resulted in a burst of cytokine expression. At later time points (i.e. 9 days post treatment), loss of miRNAs resulted in thousands of differentially expressed genes highlighting the importance of this post transcriptional regulatory network .  At present, we are using VP55 to study the role of miRNAs as it relates to chronic virus infections and establishment of the adaptive response.