The biology of nematode- and IL4Rα-dependent murine macrophage polarization in vivo as defined by RNA-Seq and targeted lipidomics.

Alternatively activated macrophages (AAMϕ) are a major component of the response to helminth infection; however, their functions remain poorly defined. To better understand the helminth-induced AAMϕ phenotype, we performed a systems-level analysis of in vivo derived AAMϕ using an established mouse model. With next-generation RNA sequencing, we characterized the transcriptomes of peritoneal macrophages from BALB/c and IL4Rα(-/-) mice elicited by the nematode Brugia malayi, or via intraperitoneal thioglycollate injection. We defined expression profiles of AAMϕ-associated cytokines, chemokines, and their receptors, providing evidence that AAMϕ contribute toward recruitment and maintenance of eosinophilia. Pathway analysis highlighted complement as a potential AAMϕ-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 AAMϕ-associated promoters. These included the binding site for PPAR transcription factors, which maintain mitochondrial metabolism. Surprisingly PPARγ, implicated in the maintenance of AAMϕ, was down-regulated on infection. PPARδ expression, however, was maintained. To explain how PPAR-mediated transcriptional activation could be maintained, we used lipidomics to quantify AAMϕ-derived eicosanoids, potential PPAR ligands. We identified the PPARδ ligand PGI(2) as the most abundant AAMϕ-derived eicosanoid and propose a PGI(2)-PPARδ axis maintains AAMϕ during B malayi implantation.