Macrophage Polarization: Different Gene Signatures in M1(LPS+) vs. Classically and M2(LPS–) vs. Alternatively Activated Macrophages

Macrophages are found in tissues, body cavities, and mucosal surfaces. Most tissue macrophages are seeded in the early embryo before definitive hematopoiesis is established. Others are derived from blood monocytes. The macrophage lineage diversification and plasticity are key aspects of their functionality. Macrophages can also be generated from monocytes <i>in vitro</i> and undergo classical (LPS+IFN-γ) or alternative (IL-4) activation. <i>In vivo</i>, macrophages with different polarization and different activation markers coexist in tissues. Certain mouse strains preferentially promote T-helper-1 (Th1) responses and others Th2 responses. Their macrophages preferentially induce iNOS or arginase and have been called M1 and M2, respectively. In many publications, M1 and classically activated and M2 and alternatively activated are used interchangeably. We tested whether this is justified by comparing the gene lists positively [M1(=LPS+)] or negatively [M2(=LPS-)] correlated with the ratio of <i>IL-12</i> and <i>arginase 1</i> in transcriptomes of LPS-treated peritoneal macrophages with <i>in vitro</i> classically (LPS, IFN-γ) vs. alternatively activated (IL-4) bone marrow derived macrophages, both from published datasets. Although there is some overlap between <i>in vivo</i> M1(=LPS+) and <i>in vitro</i> classically activated (LPS+IFN-γ) and <i>in vivo</i> M2(=LPS-) and <i>in vitro</i> alternatively activated macrophages, many more genes are regulated in opposite or unrelated ways. Thus, M1(=LPS+) macrophages are not equivalent to classically activated, and M2(=LPS-) macrophages are not equivalent to alternatively activated macrophages. This fundamental discrepancy explains why most surface markers identified on <i>in vitro</i> generated macrophages do not translate to the <i>in vivo</i> situation. Valid <i>in vivo</i> M1/M2 surface markers remain to be discovered.