Combined Host-Pathogen Fate Mapping to Investigate Lung Macrophages in Viral Infection

Macrophage identity, as defined by epigenetic, transcriptional, proteomic, and functional programs, is greatly impacted by cues originating from the microenvironment. As a consequence, immunophenotyping based on surface marker expression is established and reliable in homeostatic conditions, whereas environmental challenges, in particular infections, severely hamper the determination of identity states. This has become more evident with recent discoveries that macrophage-inherent plasticity may go beyond limits of lineage-defining immunophenotypes. Therefore, transgenic fate mapping tools, such as the phage-derived loxP-cre-system, are essential for the analysis of macrophage adaptation in the tissue under extreme environmental conditions, for example, upon encounter with pathogens. In this chapter, we describe an advanced application of the loxP-cre-system during infection. Here, the host encodes a cell type-specific cre-recombinase, while the pathogen harbors a STOP-floxed fluorescent reporter gene. As an instructive example for the versatility of the system, we demonstrate that alveolar macrophages are predominantly targeted after respiratory tract infection with mouse cytomegalovirus (MCMV). Combined host-pathogen fate mapping not only enables to distinguish between infected and non-infected (bystander) macrophages but also spurs exploration of phenotypic adaptation and tracing of cellular localization in the context of MCMV infection. Moreover, we provide a gating strategy for resolving the diversity of pulmonary immune cell populations.