ABSTRACT: Toll-like receptors (TLRs), a family of pattern recognition receptors, bind microbial and host-derived molecules, leading to intracellular signaling and activation of host innate immune responses. TLR4 is unique in that ligand-mediated activation initiates two signaling cascades: the MyD88-dependent pathway, localized to the cell membrane, elicits rapid MAP kinase and NF-κB activation, and the TRIF-dependent pathway, localized to TLR4-containing endosomes, results in IRF-3 activation. Previous studies have associated adjuvanticity with the TRIF pathway. Gram-negative LPS is a potent TLR4 agonist, and structurally related molecules also signal through TLR4 to different extents. Herein, we compared two synthetic, non-toxic lipid A analogs used previously as vaccine adjuvants, monophosphoryl lipid A (PHAD®, sMPL) and E6020, for their capacity to activate TLR4-mediated innate immune responses. In primary mouse macrophages, high dose sMPL activates the MyD88-dependent signaling equivalently to E6020. In contrast to sMPL, E6020 exhibits robust activation of the TRIF pathway, including TLR4 internalization and IRF-3-dependent transcription, at all doses examined. Eritoran, a TLR4/MD2 antagonist, competitively inhibited sMPL more strongly than E6020. Despite these differences, sMPL and E6020 adjuvants induced antibody responses to a similar level and with balanced Ig isotypes, in two separate mouse immunization models. However, E6020 induced superior non-specific protection in a model of Streptococcus pneumoniae infection, compared to sMPL, which correlates with the activation of reactive nitrogen and oxygen species. These data provide evidence that a TRIF bias is not necessarily predictive of superior adjuvanticity, but may activate stronger innate defenses from infection. TLR4 is unique among TLRs that it stimulates both the MyD88- and TRIF-dependent pathways (reviewed in Takeda K and Akira S, 2004, Semin Immunol). To compare the relative stimulatory capacities of two synthetic TLR4 agonist adjuvants, PHAD® (sMPL; Avanti Polar Lipids LLC) and E6020 (Eisai, Inc), we performed microarray analysis of primary thioglycollate-elicited mouse peritoneal macrophages that were either cultured in media alone (control) or stimulated with 100 ng/mL (57.3 uM sMPL, 61.6 uM E6020) of the TLR4 agonists for two hours. Total RNA was extracted from three biological repicates (numbered 1-3) per treatment, and the transcriptomes analyzed individually by whole transcriptome microarray (Affymetrix Clariom D). Of the differentially expressed genes (DE genes; average of three replicates greater or equal to 2-fold difference in any comparison of treatments and false discovery rate below 0.05) almost 94% were protein-coding genes (includes those listed as either protein-coding or complex in the database), on which we focused for further analysis. sMPL induced expression of 155 protein-coding genes, including those that encode IL-1beta, TNF-alpha, Cxcl1 and Cxcl2--proteins that are associated with classic macrophage activation and are essential for inducing fever and attracting neutrophils. sMPL suppressed 15 protein-coding genes. In contrast, E6020 induced expression of 413 protein-coding genes and suppressed 88 protein-coding genes, which included all but one of the sMPL-regulated protein-coding genes. The majority of the genes induced by E6020, but not sMPL, are associated with Type I IFN expression (reference: Interferome.org database). This interferon signature points to stronger activation of the TRIF/IRF3 pathway in E6020-treated macrophages and includes genes that are secondarily induced by Type I IFNs. Similar expression of MyD88 dependent genes Il1b, Il10, and Tnf, and differential expression of TRIF-dependent genes Ifnb1, Cxcl10, and Ccl5 between the two synthetic agonists was confirmed by qRT-PCR.