PPARgamma as an architectural regulator of gene expression in endocrine signaling

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PROJECT SUMMARY The canonical view of Nuclear Hormone Receptors (NHRs) is that these are ligand-activated transcription factors acting as DNA-bound, lipid-controlled genomic switches. A group of NHRs are acting as heterodimers with the obligate heterodimeric partner Retinoid X Receptor (RXR). One of the key partners of RXR is the Peroxisome Proliferator-Activated Receptor gamma (PPAR). PPAR is viewed as a modified fatty acid and prostanoid regulated transcription factor essential for fat cell differentiation and contributing to lipid metabolite induced transcriptional regulation in many cell types including macrophages. Using traditional ligand centric approaches, we and others were able to identify PPAR target genes and ligand regulated processes including cholesterol uptake and efflux, inhibition of inflammatory responses, regulating insulin sensitivity and promoting tissue repair in macrophages cells. These findings make this receptor a key endocrine regulator of metabolism and inflammation in this cell type. A major weakness of prior research was that it focused solely on ligand- dependent activities of the receptors and did not consider ligand-independent ones. Therefore, there is a substantial gap in our understanding of receptor biology and action. Recent genome-wide determinations of binding sites identified at least two orders of magnitude more genomic binding sites in fat cells and macrophages as regulated genes would necessitate. This prompted us to explore PPAR:RXR cistromes in alternatively polarized macrophages. We have gathered preliminary evidence to suggest that (1) The macrophage PPARγ:RXR cistrome is greatly extended upon IL-4 polarization directed by STAT6; (2) Chromatin-bound PPARγ is predominantly ligand-insensitive in alternatively polarized macrophages; (3) PPARγ:RXR heterodimers are architectural elements of the genome, and (4) the heterodimer confers transcriptional memory via retained gene-enhancer looping. This allows us to formulate new hypotheses as follows: A large fraction of PPAR:RXR heterodimers is ligand-insensitive; (a) Contributing to the epigenome of IL-4 polarized macrophages and provides links between enhancers and promoters via looping utilizing the cohesin complex and/or CTCF; (b) Establishes transcriptional cellular memory and (C) Contributes to macrophage tissue-specification and transcriptional adaptation. We are proposing to test these at three levels. At the chromatin and genome folding level we will determine the epigenomic roles for PPAR. At the cellular level we will determine the role PPAR plays in opening of chromatin and transcriptional memory. Finally at the in vivo level, contribution of PPAR to lung macrophage function and response to viral infection will be explored. The results will likely open up new avenues of research into the epigenomic programming of macrophages with translational potential in chronic inflammatory and metabolic disease and tissue regeneration.