IL-4 induced regulation in the transcriptome and translatome during M2 macrophage polarization

Abstract

Classified as M1 and M2, the macrophage facilitates diverse functional properties and dynamic gene expression due to the surrounding microenvironment and is a key component in the innate immune response. The prevalence and association with pathogen induced diseases are one of many reasons why M1 macrophage is widely studied on a genome-wide scale. On the other hand, M2 macrophage exhibits an anti-inflammatory characteristics and is affiliated with other various systems such as lipid metabolism, wound healing and augmentation of tumor progression. Despite the multiple studies involving regulations of M2 macrophage, the translatome landscape has yet to be fully elucidated. Extraction of ribosome protected fragments by Ribosome Profiling (RPF) followed with high throughput sequencing helps us to analyze mRNAs which are actively translated during given time points. Combined with RNA-seq and computational analysis, I identified the regulational activities within the transcriptome and translatome during IL-4 induced M2 macrophage polarization. Computational analysis revealed an increase in regulated genes over time with upregulated genes being more than the down regulated genes in both landscapes. Differentially expressed genes (DEGs) during different time points showed a shifting movement towards the 48-hours of RNA but no significant changes in RPF. However, uniquely regulated DEGs of RPF during 48-hours were decreased when compared to the RNA. Further in depth analysis showed cytosolic ribosome associated genes were more enriched during 24-hours but decreased at 48-hours, exclusively from the RNA level. Translation efficiency based Ingenuity Pathway Analysis (IPA) revealed enriched-upregulation of translation initiation and cell transformation but enriched-downregulation of anti-inflammatory pathways during both time points. These results demonstrate that M2 macrophage regulates cell transformational signals in early time points and is more translationally active in late time points. Also, after activation, M2 macrophage still harbors pro-inflammatory characteristics to a certain extent.