Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4

Abstract

The innate immune system is absolutely required for host defence, but, uncontrolled, it leads to inflammatory disease. This control is mediated, in part, by cytokines that are secreted by macrophages. Immune regulation is extraordinarily complex, and can be best investigated with systems approaches (that is, using computational tools to predict regulatory networks arising from global, high-throughput data sets). Here we use cluster analysis of a comprehensive set of transcriptomic data derived from Toll-like receptor (TLR)-activated macrophages to identify a prominent group of genes that appear to be regulated by activating transcription factor 3 (ATF3), a member of the CREB/ATF family of transcription factors. Network analysis predicted that ATF3 is part of a transcriptional complex that also contains members of the nuclear factor (NF)-kappaB family of transcription factors. Promoter analysis of the putative ATF3-regulated gene cluster demonstrated an over-representation of closely apposed ATF3 and NF-kappaB binding sites, which was verified by chromatin immunoprecipitation and hybridization to a DNA microarray. This cluster included important cytokines such as interleukin (IL)-6 and IL-12b. ATF3 and Rel (a component of NF-kappaB) were shown to bind to the regulatory regions of these genes upon macrophage activation. A kinetic model of Il6 and Il12b messenger RNA expression as a function of ATF3 and NF-kappaB promoter binding predicted that ATF3 is a negative regulator of Il6 and Il12b transcription, and this hypothesis was validated using Atf3-null mice. ATF3 seems to inhibit Il6 and Il12b transcription by altering chromatin structure, thereby restricting access to transcription factors. Because ATF3 is itself induced by lipopolysaccharide, it seems to regulate TLR-stimulated inflammatory responses as part of a negative-feedback loop.

ATF4 is directly recruited by TLR4 signaling and positively regulates TLR4-trigged cytokine production in human monocytes

“…27 TLR signaling represents one of the key mechanisms involved in these processes. 28 Although ATF3, an ATF4 homologue, has been reported to participate in the TLR4 signaling pathway 8,29 and recent reports have indicated that ATF4 is capable of regulating cytokine secretion, 9 it remains unclear whether ATF4 plays a role in TLR signaling. In this study, we defined a novel mechanism in which ATF4 is recruited by TLR4 signaling via the MyD88-dependent pathway, translocates to the nucleus and stimulates TLR-triggered cytokine production to further promote an inflammatory reaction.…”

“…First, an ATF4 homologous molecule, ATF3, is an important negative regulator of the TLR4 signaling pathway. 8 Second, TLR ligand stimulation causes macrophages to secrete high levels of IL-8, while ATF4 positively regulates IL-8 secretion in the same type of cells. 9,10 In this study, we demonstrated that ATF4 participates in the TLR4 signaling pathway and positively regulates TLR4-triggered cytokine production.…”

Lipidomics of host–pathogen interactions

“…Many of the TLR bind lipid structures. Thus it can be expected that the advances made in the systems biology of TLRs [23], and chemical analysis of naturally occurring forms of LPS [24] will bring together knowledge from different fields in order to understand better the molecular mechanisms of pathogen recognition.…”

Imbalance of Clara cell-mediated homeostatic inflammation is involved in lung metastasis

“…TLR4 activates nuclear factor-kB on which concomitant activation of activating transcription factor 3 (ATF3) has been proposed to give a negative feedback (Gilchrist et al, 2006). TLR4 knockout mice display pulmonary emphysema at high age (Zhang et al, 2006).…”