Abstract
The innate immune response is primarily mediated by the Toll-like receptors functioning through the MyD88-dependent and TRIF-dependent pathways. Despite being widely studied, it is not yet completely understood and systems-level analyses have been lacking. In this study, we identified a high-probability network of genes activated during the innate immune response using a novel approach to analyze time-course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network. We classified the immune response into three consecutive time-dependent stages and identified the most probable paths between genes showing a significant change in expression at each stage. The resultant network contained several novel and known regulators of the innate immune response, many of which did not show any observable change in expression at the sampled time points. The response network shows the dominance of genes from specific functional classes during different stages of the immune response. It also suggests a role for the protein phosphatase 2a catalytic subunit α in the regulation of the immunoproteasome during the late phase of the response. In order to clarify the differences between the MyD88-dependent and TRIF-dependent pathways in the innate immune response, time-course gene expression profiles from MyD88-knockout and TRIF-knockout dendritic cells were analyzed. Their response networks suggest the dominance of the MyD88-dependent pathway in the innate immune response, and an association of the circadian regulators and immunoproteasomal degradation with the TRIF-dependent pathway. The response network presented here provides the most probable associations between genes expressed in the early and the late phases of the innate immune response, while taking into account the intermediate regulators. We propose that the method described here can also be used in the identification of time-dependent gene sub-networks in other biological systems.
Highlights
The innate immune system is the primary host response to invading pathogens
Toll-like receptors (TLRs) are a family of pattern-recognition receptors (PRRs) that are conserved from worm to mammals and expressed on different types of immune cells, such as macrophages, dendritic cells (DCs) and B cells, as well as nonimmune cells, such as fibroblasts and epithelial cells. 10 and 13 TLRs have been identified in human and mouse, respectively, each with distinct microbial ligands
The results indicate the dominance of the MyD88-dependent pathway during the innate immune response and the association of the TIR-domain–containing adaptor protein-inducing IFN-b (TRIF)-dependent pathway with the circadian genes and those involved in immunoproteasomal degradation
Summary
The innate immune system is the primary host response to invading pathogens. The innate immune response is characterized by germline-encoded pattern-recognition receptors (PRRs) that detect and bind to specific microbial components, known as pathogen-associated molecular patterns (PAMPs). Though much is known about the pathways activated during the innate immune response, recent perturbation studies have identified previously unknown regulators and transcription factors, highlighting the complexity of the innate immune system and the incompleteness of our current knowledge [3,4,5]. While these studies provide important information about the genes affected on perturbation of a causal gene, they do not explain the cause of the observed expression changes. This study provided a high confidence signaling network and identified
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