Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages

Abstract

Inflammation is a powerful response of the immune system against invading pathogens, and must be cancelled when unneeded or otherwise death inevitably follows. In macrophages, the anti-inflammatory response (AIR) is driven by STAT3 upon IL-10 signaling. The role of STAT3 is to stimulate the expression of specific genes that in-turn suppress the transcription of proinflammatory genes. Here we describe a systematic approach to identify the elusive STAT3-controlled effectors of the AIR. In vivo STAT3-binding sites were identified by ChIP-seq, coupled to expression analysis by RNA-seq, both in resting and IL-10-treated peritoneal macrophages. We report the genomic targets of STAT3 and show that STAT3's transcriptional program during the AIR is highly specific to IL-10-stimulated macrophages, that STAT3 is a positive transcriptional regulator, and we predict severalputative AIR factors that merit further investigation. This is the first in-depth study of the AIR by next-generation sequencing and provides an unprecedented degree of detail into this fundamental physiologic response.

Interleukin-10 Inhibits Lipopolysaccharide-induced Tumor Necrosis Factor-α Translation through a SHIP1-dependent Pathway

“…The IL-10 receptor signaling pathway is well known for activation of the STAT3 transcription factor (15)(16)(17)(18)(19). However, in other studies, we found that IL-10 also activates the SHIP1 inositol 5Ј-phosphatase.…”

“…The anti-inflammatory cytokine IL-10 is a key moderator of inflammation, and loss of normal levels of IL-10 or its receptor results in inflammatory disorders in both mouse and man (11)(12)(13)(14). Studies on the mechanism by which IL-10 receptor signaling inhibits TNF␣ expression have concentrated on activation of the STAT3 transcription factor and induction of STAT3-regulated genes (15)(16)(17)(18)(19). The gene products implicated in inhibiting TNF␣ expression include Bcl-3, an inhibitor of TNF␣ transcription (20); tristetraprolin, which destabilizes TNF␣ mRNA (21); and ETV3 and SBNO2, which modify the chromatin structure of the TNF␣ gene (22).…”

Exploring the IL-21–STAT3 Axis as Therapeutic Target for Sézary Syndrome

“…This nicely correlates with the previously reported overexpression of miR-21 (van der Fits et al, 2011), TWIST1 (van Doorn et al, 2004), and MYC (Vermeer et al, 2008) in SS, and indicates that these genes are downstream STAT3 target genes mediating the oncogenic effects of STAT3. STAT3 binding to its target genes is cell type-and context-dependent, as illustrated by the limited overlap between data sets of genome-wide studies on different cell types (Chen et al, 2008;Kwon et al, 2009;Hutchins et al, 2012). Studies on selected candidate genes identified several bona fide STAT3 target genes mediating the oncogenic function of STAT3 in various tumor types.…”

Discovery and characterization of new transcripts from RNA-seq data in mouse CD4+ T cells

“…cDNA molecules were sequenced on an Illumina HiSeq 2000 platform. Reads were aligned to the most recent mouse genome (mm9) and assembled into transcripts using the TopHat/Cufflinks combination [11], as previously described [41]. TopHat (v.1.3.2) assembled the genes assuming a mate inner pair size of 20 base pairs, 'Solexa1.3-quals'.…”