The biology of nematode- and IL4R¿-dependent murine macrophage polarization in vivo as defined by RNA-Seq and targeted lipidomics

Alternatively activated macrophages (AAM¿) are a major component of the response to helminth infection; however, their functions remain poorly defined. To better understand the helminth-induced AAM¿ phenotype, we performed a systems-level analysis of in vivo derived AAM¿ using an established mouse model. With next-generation RNA sequencing, we characterized the transcriptomes of peritoneal macrophages from BALB/c and IL4R¿(-/-) mice elicited by the nematode Brugia malayi, or via intraperitoneal thioglycollate injection. We defined expression profiles of AAM¿-associated cytokines, chemokines, and their receptors, providing evidence that AAM¿ contribute toward recruitment and maintenance of eosinophilia. Pathway analysis highlighted complement as a potential AAM¿-effector function. Up-regulated mitochondrial genes support in vitro evidence associating mitochondrial metabolism with alternative activation. We mapped macrophage transcription start sites, defining over-represented cis-regulatory motifs within AAM¿-associated promoters. These included the binding site for PPAR transcription factors, which maintain mitochondrial metabolism. Surprisingly PPAR¿, implicated in the maintenance of AAM¿, was down-regulated on infection. PPAR¿ expression, however, was maintained. To explain how PPAR-mediated transcriptional activation could be maintained, we used lipidomics to quantify AAM¿-derived eicosanoids, potential PPAR ligands. We identified the PPAR¿ ligand PGI(2) as the most abundant AAM¿-derived eicosanoid and propose a PGI(2)-PPAR¿ axis maintains AAM¿ during B malayi implantation.