Gene expression changes in response to microparticle treatment in mouse macrophages

To investigate the potential molecular mechanisms of the microparticles' ability to rescue TLR4-deficient mice under Gram-negative infection, we performed RNA-seq experiments in J774A.1 mouse macrophage cell lines, under MP, LPS, and LPS+MP treatments. As expected, ~2000 genes were induced in response to LPS, and the degree of upregulation is significantly higher than down-regulation. In the presence of MP, LPS still upregulated ~1800 genes, similar to LPS treatment alone, but there were significantly more downregulated genes, indicating that MP has profound effects under LPS challenge, primarily through down-regulation of gene expression. A total of 1267 DEGs were found in the MP-treatment group, including 631 upregulated genes and 636 downregulated genes. The average fold change is much smaller than LPS and LPS+MP groups. Functional category analyses of these MP-upregulated genes revealed significant enrichment of immune-related GO terms, including response to stress, toxic substances, and homeostatic process. The results suggest that the MP upregulated the expression of ~600 genes, fine-tuning the immune profile. J774A.1 mouse macrophages were mock-treated (control), or treated by microparticles (MP), lipopolysaccharide (LPS), and both compounds (LPS+MP). As the major component of the outer membrane of Gram-negative bacteria, LPS triggers Toll-like receptor 4 and the innate immune response. We conducted RNA-seq with three biological replicates in each group, and identified significantly differentially expressed genes (DEGs, FDR<0.05, fold-change>2).