GSE128006
Integrative Proteome, Transcriptome and DNA Methylome Analysis of Regulatory Networks During U937-derived Macrophage Polarization from an M2 to M1 Phenotype [MeDIP-Seq]
We report the application of MeDIP sequencing technology for high-throughput profiling of M2 and M1 phenotype U937 cells. A total of 260 differentially methylated regions (DMRs) within promotor regions were identified, with 191 hyper-methylated and 69 hypo-methylated every chromosome. These DMRs were then further examined using GO analysis, with the top10 most enriched GO terms for both the hyper- and hypo-methylation groups isolated. The processes associated with hyper-methylation included the regulation of protein processes (targeting, processing, maturation and localization) and tyrosine phosphorylation of STAT5 protein, while the hypo-methylated processes included the regulation of epithelial to mesenchymal transition, mesenchymal cell differentiation and epithelial to mesenchymal transition. When further analyzing the regulation of tyrosine STAT5 phosphorylation, three associated genes (IL-31RA, IL-3, and NF2) previous shown to be associated with tumor or cancer development  were also identified, thus suggesting that hyper-methylation may be important during M2 polarization into M1 cells. The epithelial to mesenchymal transition (EMT) process has been long accepted to be associated with cancer metastasis and malignance. Herein, four genes (TGFB1I1, TWIST1, HPN, and PHLDB2) that have been previously reported to participate in cancer invasion and metastasis were hypo-methylated during the EMT process, thus suggesting that these hypo-methylation sites might be a potential therapeutic target to control cancer metastasis. Moreover, the hyper-methylation was found to be predominantly localized to membranes, including the leading edge membrane, whole membrane, endoplasmic reticulum-Golgi intermediate compartment membrane, recycling endosome membrane and ruffle membrane, whereas the hypo-methylation was predominantly localized to the cytoskeleton, cell junction and cell cortex. These findings also suggest a potential ability for epigenetic therapy due to both the membrane and cytoskeleton being feasible targets for therapeutic chemical or antibody targeting. When performing pathway enrichment analysis for the hyper-methylated genes, fatty acid biosynthesis, ubiquitin mediated proteolysis, mRNA surveillance and AMPK signaling pathways were enriched; while for the hypo-methylated genes, pathways associated with cancers, such as tight junction, VEGF signaling, cAMP signaling, proteoglycans and Ras signaling pathways were enriched during polarization from M2 to M1 cells Overall design: Examination of 2 different phenotypes of U937 cells.