Identification of a forkhead box protein transcriptional network induced in human neutrophils in response to inflammatory stimuli

Abstract

Neutrophils represent the largest proportion of circulating leukocytes and, in response to inflammatory stimuli, are rapidly recruited to sites of infection where they neutralize pathogens. We have identified a novel neutrophil transcription network induced in response to inflammatory stimuli. We performed the first RNAseq analysis of human neutrophils exposed to lipopolysaccharide (LPS), followed by a meta-analysis of our dataset and previously published studies of LPS-challenged neutrophils. This revealed a robustly enhanced transcriptional network driven by forkhead box (FOX) transcription factors. The network is enriched in genes encoding proinflammatory cytokines and transcription factors, including MAFF and ATF3, which are implicated in responses to stress, survival and inflammation. Expression of transcription factors FOXP1 and FOXP4 is induced in neutrophils exposed to inflammatory stimuli, and potential FOXP1/FOXP4 binding sites were identified in several genes in the network, all located in chromatin regions consistent with neutrophil enhancer function. Chromatin immunoprecipitation (ChIP) assays in neutrophils confirmed enhanced binding of FOXP4, but not FOXP1, to multiple sites in response to LPS. Binding to numerous motifs and transactivation of network genes were also observed when FOXP proteins were transiently expressed in HEK293 cells. In addition to LPS, the transcriptional network is induced by other inflammatory stimuli, indicating it represents a general neutrophil response to inflammation. Collectively, these findings reveal a role for the FOXP4 transcription network as a regulator of responses to inflammatory stimuli in neutrophils. Author SummaryIn response to pathogens, neutrophils, the most abundant white blood cells in the body, are the first to be recruited to sites of infection. However, defects in neutrophil responses lead to common chronic inflammatory conditions such as atherosclerosis, chronic obstructive lung disease and autoimmune disorders. As such, it is critical to uncover the molecular players implicated in neutrophil responses to signals that induce inflammation. Here we profile how bacterial lipopolysaccharide (LPS), which is derived from the cell walls of bacteria and is a commonly used agent to mimic inflammation, alters gene transcription in isolated human neutrophils. We also combined our data with those of other published studies to identify conserved molecular pathways stimulated in LPS-exposed neutrophils. This analysis revealed a network of genes whose transcription is regulated by members of the so-called forkhead box (FOX) transcription factors. We provide evidence that FOXP4 regulates transcription of genes within the network in neutrophils. We also find that the same network of genes is induced by other inflammatory stimuli, suggesting it plays a role in neutrophil responses to inflammation.