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Prior IL-4 exposure induces epigenetic reprograming enabling activated NF-kB p65 cistrome expansion, extreme synergistic gene activation and unique imuune response in macrophages

ABSTRACT: Prior exposure to certain signals can fundamentally change the response of innate immune cells to other stimuli underpinning phenomena such as cellular memory, tissue type-specific reactions, cytokine storm or anergy/tolerance. Our understanding about the molecular details of such interactions especially at the level of chromatin accessibility and gene expression regulation is fragmented. In particular our knowledge about the molecular links between two fundamental signaling pathways, alternative macrophage polarization signals and TLR signaling pathway is rather limited and neither the epigenomic mechanisms at play nor the biological output is well understood. Here we combined systematic signaling, epigenomic and transcriptomic approaches to map and uncover that the activation of the IL-4-STAT6 signaling pathway results in enhanced LPS responsiveness of a large, but distinct set of genes in macrophages. This interaction, we termed extreme synergy, is brought about by IL-4 priming-induced STAT6-dependent epigenomic remodeling, which includes the expansion of the LPS-activated NFκB-p65 cistrome, increased chromatin accessibility, epigenomic activation and increased enhancer activity at the genomic loci of synergistically activated genes. The IL-4-induced EGR2 transcription factor is required to enable the LPS-induced de novo and enhanced NFκB-p65 binding and synergistic gene activation. As a consequence, the previously alternatively polarized macrophages produce secreted immune-modulatory factors, including CCL17, CCL22, CCL2, and EDN1, at an extremely high level in vitro and in vivo in a murine Th2-type airway inflammation and asthma model following LPS exposure. Our findings establish that the IL-4-STAT6-EGR2 signaling pathway-induced epigenetic reprogramming is responsible for the development of a defined, robust inflammatory hyperresponsiveness to TLR4 activation in alternatively polarized macrophages and likely contribute to pathologies.

ORGANISM(S): Mus musculus

PROVIDER: GSE181223 | GEO | 2022/10/20

REPOSITORIES: GEO

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Project description:Macrophages are able to differentiate into classically polarized (M1) or alternatively polarized (M2) states upon encountering pro-inflammatory cytokines such as interferon (IFN) g or anti-inflammatory cytokines such as interleukin (IL) -4/IL-13, respectively. Moreover, macrophages are known to regulate lipid metabolism via multiple members of the nuclear hormone receptor family, including the retinoid X receptors (RXR). It has been also documented that cytokines are able to modulate macrophage responses to lipid signals but the nature of these interactions and the underlying mechanisms of these processes especially at the level of the chromatinized genome are not well understood. Previous work from our laboratory suggested that STAT6 is a facilitator of nuclear receptor mediated transcriptional activity acting at the genome level. This prompted us to investigate genome-wide DNA binding events and the development of cistromes in human CD14+ monocyte-derived macrophages upon exposure to IL-4. We determined the impact of IL-4 on the PU.1, RXR and STAT6 cistromes within the active enhancer regions marked by H3K27-acetylation using chromatin immunoprecipitation followed by deep sequencing and integrated bioinformatics analyses. We found that about 2/3rd of the IL-4 induced STAT6 peaks co-localized with RXR peaks. These STAT6/RXR co-peaks differed at least in part from the non-overlapping RXR peaks regarding the most enriched de novo transcription factor binding motifs. Interestingly, RXR-binding was not regulated at the STAT6/RXR co-bound enhancers following IL-4 stimulation, but differential enhancer interactions were observed between the IL-4/STAT6 and RXR signaling pathways acting in a gene selective manner. Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages.

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Prior IL-4 exposure induces epigenetic reprograming enabling activated NF-kB p65 cistrome expansion, extreme synergistic gene activation and unique imuune response in macrophages

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