The innate immune response of an organism is the primary response to challenges including inflammatory stimuli, infectious agents or the presence of cancer cells. The protective IFN activation and signalling is a key component of this response. IFN signalling is essential for host survival, fundamental to vaccine responses, can be activated therapeutically and is often the target for pathogen evasion strategies. While there is considerable knowledge of transcriptional regulation and role of protein coding transcripts in the IFN response equivalent knowledge of non-coding responses and their regulatory mechanism remain to be elucidated. Furthermore the role of miRNA in regulating the biological response to IFN remains to be elucidated despite therapeutic approaches targeting miRNA actions already present in Phase 2 clinical trials for the treatment of Hepatitis C Virus.
Next generation sequencing technologies have unlocked the ability to measure the complete transcriptional landscape of a cell required for this type of analysis ultimately revolutionizing our ability to understand these complex systems. We present the results of parallel small and ribosomal depleted total RNA with complementary miRNA expression and target network identification in murine bone marrow derived macrophages across a time course of IFNβ stimulation. Analysis of this data has resulted in comprehensive network level understanding of the complete transcriptional response to IFNβ including the identification of putative novel miRNA and potential targets. Novel computational algorithms and analysis approaches within our custom designed RNA-eXpress framework have been developed and applied resulting in the generation of predictive target networks. Results of experimental validation of these related miRNA pathways will also be presented.
This systems level interpretation of IFN mediated signaling has the potential to provide a basis for novel insights into both host-pathogen interactions and host response critical in the efficient development of effectively targeted therapeutics