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Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation.

Savic D, Ramaker RC, Roberts BS, Dean EC, Burwell TC, Meadows SK, Cooper SJ, Garabedian MJ, Gertz J, Myers RM - Genome Med (2016)

Bottom Line: PPARG generated a rapid and short-term response while maintaining a gene activator role.By contrast, LXR signaling was prolonged, with initial, predominantly activating functions that transitioned to repressive gene regulatory activities at late time points.Through the use of a multi-tiered strategy that integrated various genomic datasets, our data illustrate that distinct gene regulatory programs elicit common phenotypic effects, highlighting the complexity of the genome.

View Article: PubMed Central - PubMed

Affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.

ABSTRACT

Background: The liver X receptors (LXRs, NR1H2 and NR1H3) and peroxisome proliferator-activated receptor gamma (PPARG, NR1C3) nuclear receptor transcription factors (TFs) are master regulators of energy homeostasis. Intriguingly, recent studies suggest that these metabolic regulators also impact tumor cell proliferation. However, a comprehensive temporal molecular characterization of the LXR and PPARG gene regulatory responses in tumor cells is still lacking.

Methods: To better define the underlying molecular processes governing the genetic control of cellular growth in response to extracellular metabolic signals, we performed a comprehensive, genome-wide characterization of the temporal regulatory cascades mediated by LXR and PPARG signaling in HT29 colorectal cancer cells. For this analysis, we applied a multi-tiered approach that incorporated cellular phenotypic assays, gene expression profiles, chromatin state dynamics, and nuclear receptor binding patterns.

Results: Our results illustrate that the activation of both nuclear receptors inhibited cell proliferation and further decreased glutathione levels, consistent with increased cellular oxidative stress. Despite a common metabolic reprogramming, the gene regulatory network programs initiated by these nuclear receptors were widely distinct. PPARG generated a rapid and short-term response while maintaining a gene activator role. By contrast, LXR signaling was prolonged, with initial, predominantly activating functions that transitioned to repressive gene regulatory activities at late time points.

Conclusions: Through the use of a multi-tiered strategy that integrated various genomic datasets, our data illustrate that distinct gene regulatory programs elicit common phenotypic effects, highlighting the complexity of the genome. These results further provide a detailed molecular map of metabolic reprogramming in cancer cells through LXR and PPARG activation. As ligand-inducible TFs, these nuclear receptors can potentially serve as attractive therapeutic targets for the treatment of various cancers.

No MeSH data available.


Related in: MedlinePlus

Cofactor enrichment and genome-wide binding patterns. a The fold enrichment of various canonical motifs for the top 50 % of significance-ranked LXRB and PPARG binding sites that exhibited stronger occupancy at 2 (light green) or 48 (dark green) h. b Normalized sequencing read depth rank correlation (top left) at all binding sites identified across replicate JunD ChIP-seq experiments. c Enriched AP1 motif identified at JunD ChIP-seq binding sites. d Percentage of LXRB and PPARG sites after 2 and 48 h of stimulation coincident with JunD. e Percentage of JunD sites overlapping with LXRB and PPARG nuclear receptor (NR) binding events after 2 and 48 h of drug treatment
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Fig4: Cofactor enrichment and genome-wide binding patterns. a The fold enrichment of various canonical motifs for the top 50 % of significance-ranked LXRB and PPARG binding sites that exhibited stronger occupancy at 2 (light green) or 48 (dark green) h. b Normalized sequencing read depth rank correlation (top left) at all binding sites identified across replicate JunD ChIP-seq experiments. c Enriched AP1 motif identified at JunD ChIP-seq binding sites. d Percentage of LXRB and PPARG sites after 2 and 48 h of stimulation coincident with JunD. e Percentage of JunD sites overlapping with LXRB and PPARG nuclear receptor (NR) binding events after 2 and 48 h of drug treatment

Mentions: We analyzed the sequence content of LXRB and PPARG binding sites to identify cooperating TFs that may be necessary for LXR and PPARG function. To elucidate potential temporal changes in cofactor preference, we used the top 50 % of sites ranked by significance that displayed stronger occupancy at 2 or 48 h for this assessment. The analysis of several canonical TF sequence motifs at these sites identified a strong enrichment for the AP1 motif (Fig. 4a). Indeed, temporal changes in AP1 motif enrichment differed substantially and in an opposing manner for both nuclear receptors, with more pronounced enrichment at LXRB and PPARG sites harboring strong 48- and 2-h occupancy, respectively.Fig. 4


Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation.

Savic D, Ramaker RC, Roberts BS, Dean EC, Burwell TC, Meadows SK, Cooper SJ, Garabedian MJ, Gertz J, Myers RM - Genome Med (2016)

Cofactor enrichment and genome-wide binding patterns. a The fold enrichment of various canonical motifs for the top 50 % of significance-ranked LXRB and PPARG binding sites that exhibited stronger occupancy at 2 (light green) or 48 (dark green) h. b Normalized sequencing read depth rank correlation (top left) at all binding sites identified across replicate JunD ChIP-seq experiments. c Enriched AP1 motif identified at JunD ChIP-seq binding sites. d Percentage of LXRB and PPARG sites after 2 and 48 h of stimulation coincident with JunD. e Percentage of JunD sites overlapping with LXRB and PPARG nuclear receptor (NR) binding events after 2 and 48 h of drug treatment
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940857&req=5

Fig4: Cofactor enrichment and genome-wide binding patterns. a The fold enrichment of various canonical motifs for the top 50 % of significance-ranked LXRB and PPARG binding sites that exhibited stronger occupancy at 2 (light green) or 48 (dark green) h. b Normalized sequencing read depth rank correlation (top left) at all binding sites identified across replicate JunD ChIP-seq experiments. c Enriched AP1 motif identified at JunD ChIP-seq binding sites. d Percentage of LXRB and PPARG sites after 2 and 48 h of stimulation coincident with JunD. e Percentage of JunD sites overlapping with LXRB and PPARG nuclear receptor (NR) binding events after 2 and 48 h of drug treatment
Mentions: We analyzed the sequence content of LXRB and PPARG binding sites to identify cooperating TFs that may be necessary for LXR and PPARG function. To elucidate potential temporal changes in cofactor preference, we used the top 50 % of sites ranked by significance that displayed stronger occupancy at 2 or 48 h for this assessment. The analysis of several canonical TF sequence motifs at these sites identified a strong enrichment for the AP1 motif (Fig. 4a). Indeed, temporal changes in AP1 motif enrichment differed substantially and in an opposing manner for both nuclear receptors, with more pronounced enrichment at LXRB and PPARG sites harboring strong 48- and 2-h occupancy, respectively.Fig. 4

Bottom Line: PPARG generated a rapid and short-term response while maintaining a gene activator role.By contrast, LXR signaling was prolonged, with initial, predominantly activating functions that transitioned to repressive gene regulatory activities at late time points.Through the use of a multi-tiered strategy that integrated various genomic datasets, our data illustrate that distinct gene regulatory programs elicit common phenotypic effects, highlighting the complexity of the genome.

View Article: PubMed Central - PubMed

Affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.

ABSTRACT

Background: The liver X receptors (LXRs, NR1H2 and NR1H3) and peroxisome proliferator-activated receptor gamma (PPARG, NR1C3) nuclear receptor transcription factors (TFs) are master regulators of energy homeostasis. Intriguingly, recent studies suggest that these metabolic regulators also impact tumor cell proliferation. However, a comprehensive temporal molecular characterization of the LXR and PPARG gene regulatory responses in tumor cells is still lacking.

Methods: To better define the underlying molecular processes governing the genetic control of cellular growth in response to extracellular metabolic signals, we performed a comprehensive, genome-wide characterization of the temporal regulatory cascades mediated by LXR and PPARG signaling in HT29 colorectal cancer cells. For this analysis, we applied a multi-tiered approach that incorporated cellular phenotypic assays, gene expression profiles, chromatin state dynamics, and nuclear receptor binding patterns.

Results: Our results illustrate that the activation of both nuclear receptors inhibited cell proliferation and further decreased glutathione levels, consistent with increased cellular oxidative stress. Despite a common metabolic reprogramming, the gene regulatory network programs initiated by these nuclear receptors were widely distinct. PPARG generated a rapid and short-term response while maintaining a gene activator role. By contrast, LXR signaling was prolonged, with initial, predominantly activating functions that transitioned to repressive gene regulatory activities at late time points.

Conclusions: Through the use of a multi-tiered strategy that integrated various genomic datasets, our data illustrate that distinct gene regulatory programs elicit common phenotypic effects, highlighting the complexity of the genome. These results further provide a detailed molecular map of metabolic reprogramming in cancer cells through LXR and PPARG activation. As ligand-inducible TFs, these nuclear receptors can potentially serve as attractive therapeutic targets for the treatment of various cancers.

No MeSH data available.


Related in: MedlinePlus