Transcriptomic establish of pig macrophage polarization signatures and potential applications for pig health and disease

Macrophages are the main effector cells of inflammatory response and play an important role in the initiation and regression of inflammation. Macrophages are derived from monocytes which are differentiated into M1 macrophages (classically activated macrophages) or M2 macrophages (selectively activated macrophages) in response to different external stimuli, distinguished by the differential expression of cytokines, cell surface markers, and chemokines. In vitro macrophages are crucial models for understanding the regulatory mechanism of immune response and the establishment of infection models, ultimately, for the diagnosis or treatment of a variety of diseases. Porcine is the most important agricultural animal and one of the most valuable animal models for preclinical studies, but no unified method for porcine macrophage isolation and differentiation at present, neither a systematic study compared the porcine macrophage obtained by different methods. In this study, we used two strategies to induce porcine BMDM into M1 and two strategies to induce porcine BMDM into M2 macrophages. Subsequently, we compared the transcriptomic profile of BMDM treated with different induction methods by RNA-seq. The DEG analysis showed that porcine M1 macrophage and porcine M2 macrophage obtained have consistent gene signatures as mouse and human macrophages, respectively. We also observed differences in transcriptional levels in macrophages induced by different methods. We obtained the transcriptome sequencing data of macrophages infected by different pathogens from GEO and analyzed them quantitatively. We performed GSEA analysis on macrophages infected with different pathogens and porcine bone marrow-derived macrophages (BMDM). We found that the enrichment pathways of macrophages obtained by different induction methods and macrophages infected by different pathogens were different. Our study provided a framework to guide the interrogation of macrophage phenotypes in the context of health and disease. The approach described here could be used to propose new biomarkers for diagnosis in diverse clinical settings including porcine reproductive and respiratory syndrome virus (PRRSV), African swine fever virus (ASFV), and Toxoplasma gondii. We used different methods to induce and differentiate porcine bone marrow-derived macrophages, and obtained M1 macrophages and M2 macrophages induced by two methods. We compared the transcriptome differences of macrophages induced by different methods by RNA-seq. We performed Pearson's analysis, PCA analysis, edger difference analysis, pathway enrichment analysis and PPI pathway enrichment analysis. We also compared different diseases with our induced differentiated macrophages for GSEA analysis.