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Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [RNA-Seq]

ABSTRACT: Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [RNA-Seq]

PROVIDER: PRJNA480894 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7516600_1.fastq.gz	Fastqsanger.gz
	SRR7516600_2.fastq.gz	Fastqsanger.gz
	SRR7516601_1.fastq.gz	Fastqsanger.gz
	SRR7516601_2.fastq.gz	Fastqsanger.gz
	SRR7516602_1.fastq.gz	Fastqsanger.gz

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Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization

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Transcriptional profiling identifies novel regulators of macrophage polarization.

Project description:Macrophages are key inflammatory immune cells that display dynamic phenotypes and functions in response to their local microenvironment. Major advances have occurred in understanding the transcriptional, epigenetic, and functional differences in various macrophage subsets by in vitro modeling and gene expression and epigenetic profiling for biomarker discovery. However, there is still no standardized protocol for macrophage polarization largely due to the lack of thorough validation of macrophage phenotypes following polarization. In addition, transcriptional regulation is recognized as a major mechanism governing differential macrophage polarization programs and as such, many genes have been identified to be associated with each macrophage subset. However, the functional role of many of these genes in macrophage polarization is still unknown. Moreover, the role of other regulatory mechanisms, such as DNA methylation, in macrophage polarization remains poorly understood. Here, we employed an optimized model of human M1 and M2 macrophage polarization which we used for large-scale transcriptional and DNA methylation profiling. We were unable to demonstrate a role for DNA methylation in macrophage polarization, as no significant changes were identified. However, we observed significant changes in the transcriptomes of M1 and M2 macrophages. Additionally, we identified numerous novel differentially regulated genes involved in macrophage polarization, including CYBB and DHCR7 which we show as important regulators of M1 and M2 macrophage polarization, respectively. Taken together, our improved in vitro human M1 and M2 macrophage model provides new understandings of the regulation of macrophage polarization and candidate macrophage biomarkers.

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High-throughput integration of metabolic and transcriptional profiles reveals major metabolic regulators of macrophage polarization

Project description:Macrophages polarize to divergent functional phenotypes depending on their microenvironment in a highly coordinated process of metabolic and transcriptional rewiring that is still poorly understood. We developed an Integrated Metabolomics and Gene Expression (IMAGE) profiling and analysis pipeline and applied it to extensively characterize global metabolic programs of macrophage polarization. IMAGE analysis identified 7 major (novel and known) regulatory modules responsible for metabolic rewiring during polarization, which we validated through extensive carbon and nitrogen labeling experiments. M1-specific modules included: inflammatory variant of the aspartate-arginosuccinate shunt; TCA cycle break at Idh expression accompanied by citrate accumulation and production of itaconate and fatty acid synthesis. In M2 macrophages we discovered significant role of glutamine in polarization, providing nitrogen for UDP-GlcNAc synthesis. Consistently, glutamine deprivation results in significant M2-specific defect in polarization. Our data provide, for the first time, a global view of the integrated transcriptional and metabolic changes that result in M1 and M2 polarization. Bone-marrow derived macrophages were generated from C57BL/6 mice were plated at ~100k cells per well in 96-well plate and stimulated with either Il4 or combination of LPS&IFNg or left unstimulated for 24 h mRNA was derived from lysates using Invitrogen oligo-dT beads

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Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [RNA-Seq]

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Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [MBD-Seq]

Project description:Identification of novel differential DNA methylation sites in human M1 and M2 macrophages using MBD-Seq