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

Alternatively activated macrophages (AAM phi) are a major component of the response to helminth infection; however, their functions remain poorly defined. To better understand the helminth-induced AAM phi phenotype, we performed a systems-level analysis of in vivo derived AAM phi using an established mouse model. With next-generation RNA sequencing, we characterized the transcriptomes of peritoneal macrophages from BALB/c and IL4R alpha(-/-) mice elicited by the nematode Brugia malayi, or via intraperitoneal thioglycollate injection. We defined expression profiles of AAM phi-associated cytokines, chemokines, and their receptors, providing evidence that AAM phi contribute toward recruitment and maintenance of eosinophilia. Pathway analysis highlighted complement as a potential AAM phi 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 phi-associated promoters. These included the binding site for PPAR transcription factors, which maintain mitochondrial metabolism. Surprisingly PPAR gamma, implicated in the maintenance of AAM phi, was down-regulated on infection. PPAR gamma expression, however, was maintained. To explain how PPAR-mediated transcriptional activation could be maintained, we used lipidomics to quantify AAM phi-derived eicosanoids, potential PPAR ligands. We identified the PPAR gamma ligand PGI(2) as the most abundant AAM phi-derived eicosanoid and propose a PGI(2)-PPAR gamma axis maintains AAM phi during B malayi implantation. (Blood. 2012; 120(25): e93-e104)