Porcine nasal and lung macrophage subsets isolated by FACS and LCM show different transcriptomic profiles depending on tissue origin and location
Macrophages have a pivotal role during viral infections in pigs. By expressing cell surface receptors, macrophages become viral targets and reservoirs. In the case of upper respiratory tract infections, many viruses target the peripheral nasal mucosa. Recent in vivo and in vitro (primary nasal cell cultures) porcine reproductive and respiratory syndrome virus (PRRSV) studies demonstrated that several macrophage subsets exist in the porcine nasal mucosa, and that virus strains with different virulence showed altered tropism for these different macrophage populations. To further investigate these macrophage subsets, total RNA sequencing was performed in parallel on two subsets from the nasal mucosa and lung macrophages. Macrophages were isolated by either fluorescent activated cell sorting (FACS; cf. bulk RNAseq) or laser capture microdissection (LCM; cf. LCM RNAseq) in combination with immunofluorescence staining against two macrophage markers, CD163 and Sialoadhesin (Sn). With both RNAseq methods, nasal macrophages showed a different transcriptomic profile compared to lung macrophages. Differentially expressed genes were identified in the two subsets of nasal macrophages. Gene set enrichment analysis on the three macrophage populations showed that GO terms and KEGG pathways on LCM RNAseq data were more specific to the spatial location of macrophage subsets than bulk RNAseq data. Cell type signature analysis revealed that nasal CD163+Sn- cells resemble squamous epithelial cells (LCM RNAseq) or antigen presenting cells (bulk RNAseq) while nasal CD163+Sn+ cells are more like fibroblasts/stromal cells (LCM RNAseq) or vascular endothelial cell (bulk RNAseq). Our results confirmed that not only macrophages in different tissues but also macrophages in different areas within the same tissue have different transcriptional programs, suggesting their differential roles in their interaction with pathogens and corresponding immune responses.