Geneviève Deblois

Genome-Wide Identification of Direct Target Genes Implicates Estrogen-Related Receptor α as a Determinant of Breast Cancer Heterogeneity

Estrogen-related receptor alpha (ERRalpha) is an orphan nuclear receptor, the expression of which correlates with negative prognosis in breast cancer. ERRalpha shares functional features with the estrogen receptor alpha (ERalpha) and its activity is modulated by the ERBB2 signaling pathway. Using genome-wide binding sites location analyses in ERalpha-positive and ERalpha-negative breast cancer cell lines, we show that ERRalpha and ERalpha display strict binding site specificity and maintain independent mechanisms of transcriptional activation. Nonetheless, ERRalpha and ERalpha coregulate a small subset of common target genes via binding either to a dual-specificity binding site or to distinct cognate binding sites located within the extended promoter region of the gene. Although ERRalpha signaling in breast cancer cells is mostly independent of ERalpha, the small fraction of common ERRalpha/ERalpha targets comprises genes with high relevance to breast tumor biology, including genes located within the ERBB2 amplicon and GATA3. Finally, unsupervised hierarchical clustering based on the expression profiling of ERRalpha direct target genes in human breast tumors revealed four main clusters that recapitulate established tumor subtypes. Taken together, the identification and functional characterization of the ERRalpha transcriptional network implicate ERRalpha signaling as a determinant of breast cancer heterogeneity.

Oestrogen-related receptors in breast cancer: control of cellular metabolism and beyond

Oestrogen-related receptors (ERRs) are orphan nuclear receptors that were initially investigated in breast cancer because of their structural relationship to oestrogen receptors. Recent data have shown that the ERRs control vast gene networks that are involved in glycolysis, glutaminolysis, oxidative phosphorylation, nutrient sensing and biosynthesis pathways. In the context of breast cancer, the ERRs affect cellular metabolism in a manner that promotes a Warburg-like phenotype. The ERRs also modulate breast cancer cell metabolism, growth and proliferation through the regulation of key oncoproteins. We discuss the value but also the implications of the complexity of targeting the ERRs for the development of cancer therapeutics.

An Acetylation Switch Modulates the Transcriptional Activity of Estrogen-Related Receptor α

Posttranslational modifications are instrumental to achieve gene- and tissue-specific regulatory outcomes by transcription factors. Nuclear receptors are dynamically modulated by several types of posttranslational modifications including phosphorylation, methylation, acetylation, ubiquitination, and sumoylation. The estrogen-related receptor alpha (ERRalpha, NR3B1) is phosphorylated on multiple sites, and sumoylated in the amino-terminal region in a phosphorylation-dependent manner. Here we demonstrate that ERRalpha interacts with and is acetylated by p300 coactivator associated factor (PCAF) in vitro and in mouse liver. Purified PCAF acetylated the DNA-binding domain of ERRalpha on four highly-conserved lysines. In addition, coexpression of PCAF reduced the transcriptional activity of ERRalpha and, reciprocally, a deacetylase screen identified histone deacetylase 8 (HDAC8) and sirtuin 1 homolog (Sirt1) as independent enhancers of ERRalpha transcriptional function. HDAC8 and Sirt1 were also demonstrated to interact directly with ERRalpha in vivo and to deacetylate and increase the DNA binding affinity of ERRalpha in vitro. The removal of PCAF increases the DNA binding of ERRalpha in vivo, whereas the removal of Sirt1 and HDAC8 decreases it as assessed by chromatin immunoprecipitation assay. Altogether, our results show that ERRalpha is an acetylated protein and imply the existence of a dynamic acetylation/deacetylation switch involved in the control of ERRalpha transcriptional activity.

Ligand-independent coactivation of ERα AF-1 by steroid receptor RNA activator (SRA) via MAPK activation

Nuclear receptor coactivators are factors that enhance the transcriptional activity of the receptor. Coactivators usually work in ligand-independent and/or dependent manners by interacting with activation function-1 (AF-1) and AF-2 of the receptor, respectively. The recently characterized steroid receptor RNA activator (SRA) was cloned as an AF-1-dependent coactivator and shown to enhance the transcriptional activity of selected steroid receptors. In this work, we describe the effect of SRA on the activity of the two estrogen receptor (ER) isoforms, ERalpha and ERbeta. We show that SRA potentiates the estrogen-induced transcriptional activity of both ERalpha and ERbeta. We demonstrate that the transcriptional activity of ERalpha can be enhanced by SRA in a ligand-independent manner through the AF-1 domain. However, this AF-1-dependent effect of SRA is not observed on ERbeta, denoting the ability of SRA to mediate differential activation of ERalpha and ERbeta. The presence of an intact serine residue at position 118 (S(118)) in ERalpha AF-1 is required for coactivation of ERalpha by SRA. We also show that activation of the mitogen activated protein kinase (MAPK) induces ligand-independent coactivation of ERalpha by SRA, a mechanism that is independent of the AF-2. Finally, SRA is unable to rescue the loss of activity of the S(118) ERalpha mutant in response to H-Ras(V12), suggesting that phosphorylation of S(118) by MAPK participates in the ligand-independent effect of SRA on ERalpha.

PGC-1α supports glutamine metabolism in breast cancer

BackgroundGlutamine metabolism is a central metabolic pathway in cancer. Recently, reductive carboxylation of glutamine for lipogenesis has been shown to constitute a key anabolic route in cancer cells. However, little is known regarding central regulators of the various glutamine metabolic pathways in cancer cells.MethodsThe impact of PGC-1α and ERRα on glutamine enzyme expression was assessed in ERBB2+ breast cancer cell lines with quantitative RT-PCR, chromatin immunoprecipitation, and immunoblotting experiments. Glutamine flux was quantified using 13C-labeled glutamine and GC/MS analyses. Functional assays for lipogenesis were performed using 14C-labeled glutamine. The expression of glutamine metabolism genes in breast cancer patients was determined by bioinformatics analyses using The Cancer Genome Atlas.ResultsWe show that the transcriptional coactivator PGC-1α, along with the transcription factor ERRα, is a positive regulator of the expression of glutamine metabolism genes in ERBB2+ breast cancer. Indeed, ERBB2+ breast cancer cells with increased expression of PGC-1α display elevated expression of glutamine metabolism genes. Furthermore, ERBB2+ breast cancer cells with reduced expression of PGC-1α or when treated with C29, a pharmacological inhibitor of ERRα, exhibit diminished expression of glutamine metabolism genes. The biological relevance of the control of glutamine metabolism genes by the PGC-1α/ERRα axis is demonstrated by consequent regulation of glutamine flux through the citric acid cycle. PGC-1α and ERRα regulate both the canonical citric acid cycle (forward) and the reductive carboxylation (reverse) fluxes; the latter can be used to support de novo lipogenesis reactions, most notably in hypoxic conditions. Importantly, murine and human ERBB2+ cells lines display a significant dependence on glutamine availability for their growth. Finally, we show that PGC-1α expression is positively correlated with that of the glutamine pathway in ERBB2+ breast cancer patients, and high expression of this pathway is associated with reduced patient survival.ConclusionsThese data reveal that the PGC-1α/ERRα axis is a central regulator of glutamine metabolism in ERBB2+ breast cancer. This novel regulatory link, as well as the marked reduction in patient survival time associated with increased glutamine pathway gene expression, suggests that targeting glutamine metabolism may have therapeutic potential in the treatment of ERBB2+ breast cancer.

Functional and physiological genomics of estrogen-related receptors (ERRs) in health and disease.

Orphan nuclear receptors, in a manner comparable to classic steroid hormone receptors, regulate key developmental and physiological processes. However, the lack of appropriate pharmacological tools has often hindered the identification and study of their biological functions. In this review, we demonstrate that functional and physiological genomics are effective alternatives to discover biological functions associated with orphan nuclear receptors. Indeed, we document that these approaches have allowed for the unambiguous identification of the estrogen-related receptors (ERRs) α, β, and γ (NR3B1, 2, and 3) as global regulators of cellular energy metabolism. We further show that although the three ERR isoforms control analogous gene networks, each isoform performs unique biological functions in a tissue-specific manner in response to a variety of physiological stressors. Finally, we discuss how the activity of the three ERR isoforms contributes to the development and progression of metabolic diseases as well as to the adaptation of cancer cells to their unique bioenergetic requirement. This article is part of a Special Issue entitled: Translating nuclear receptors from health to disease.

Transcriptional control of the ERBB2 amplicon by ERRα and PGC-1β promotes mammary gland tumorigenesis

Overexpression of ERBB2 and its neighboring genes on chromosome 17 occurs in approximately 25% of breast tumors and is associated with poor prognosis. While amplification of the 17q12-21 chromosomal region often correlates with an increase in the transcriptional rates of the locus, the molecular mechanisms and the factors involved in the coordinated expression of genes residing within the ERBB2 amplicon remain largely unknown. Here we demonstrate that estrogen-related receptor α (ERRα, NR3B1) and its coregulator PGC-1β are key effectors in this process. Using a mouse model of ERBB2-initiated mammary tumorigenesis, we first show that ablation of ERRα significantly delays ERBB2-induced tumor development and lowers the levels of amplicon transcripts. Chromosome 17q-wide binding site location analyses in human breast cancer cells show preferential recruitment of ERRα to DNA segments associated with the ERBB2 amplicon. Furthermore, ERRα directs the co-recruitment of the coactivator PGC-1β to segments in the 17q12 region and the recruitment of RNA polymerase II to the promoters of the ERBB2 and coamplified genes. ERRα and PGC-1β also participate in the de-repression of ERBB2 expression through competitive genomic cross-talk with estrogen receptor α (ERα) and, as a consequence, influence tamoxifen sensitivity in breast cancer cells. Taken together, our results suggest that ERRα and PGC-1β are key players in the etiology of malignant breast cancer by coordinating the transcriptional regulation of genes located in the 17q12 region, a process that also involves interference with the repressive function of ERα on ERBB2 expression.

β-catenin signaling is a critical event in ErbB2-mediated mammary tumor progression

Although ERBB2 amplification and overexpression is correlated with poor outcome in breast cancer, the molecular mechanisms underlying the aggressive nature of these tumors has not been fully elucidated. To investigate this further, we have used a transgenic mouse model of ErbB2-driven tumor progression (ErbB2(KI) model) that recapitulates clinically relevant events, including selective amplification of the core erbB2 amplicon. By comparing the transcriptional profiles of ErbB2(KI) mammary tumors and human ERBB2-positive breast cancers, we show that ErbB2(KI) tumors possess molecular features of the basal subtype of ERBB2-positive human breast cancer, including activation of canonical β-catenin signaling. Inhibition of β-catenin-dependent signaling in ErbB2(KI)-derived tumor cells using RNA interference impaired tumor initiation and metastasis. Furthermore, treatment of ErbB2(KI) or human ERBB2-overexpressing tumor cells with a selective β-catenin/CBP inhibitor significantly decreased proliferation and ErbB2 expression. Collectively, our data indicate that ERBB2-mediated breast cancer progression requires β-catenin signaling and can be therapeutically targeted by selective β-catenin/CBP inhibitors.

Nuclear receptor target gene discovery using high-throughput chromatin immunoprecipitation.

Publisher Summary Nuclear receptors are master transcription factors that regulate the development, physiology, and homeostasis of whole organisms through the direct control of gene expression in response to diverse ligands and hormonal stimuli. Nuclear receptors regulate the expression of their target genes through association with specific DNA regulatory elements. While a significant number of nuclear receptor target genes have been identified to date, it is believed that these genes represent only a small fraction of the regulatory units likely to be under the control of nuclear receptors. Most nuclear receptor target genes identified so far were characterized through ‘‘gene oriented’’ approaches that study the regulation of one candidate gene at a time, and these studies are usually limited to the promoter region. To understand the complex nuclear receptor-driven transcriptional networks that operate in a living organism, a whole genome approach is required. This chapter describes a powerful ‘‘nuclear receptor/whole genome-oriented’’ approach to identify and more accurately study nuclear receptor regulatory networks. Prior to performing the actual Chromatin Immunoprecipitation (ChIP), it is important to remove and freeze an aliquot of the diluted fragmented chromatin corresponding to 10% of the total amount used for one IP. The development of high-throughput ChIP technology now permits a whole-genome analysis of gene regulation by nuclear receptors. The efficient cloning of new regulatory elements harboring high-affinity-binding sites for specific nuclear receptors can now be efficiently achieved, and allows for the identification of new target genes within a particular cell context.

ERRα mediates metabolic adaptations driving lapatinib resistance in breast cancer

Despite the initial benefits of treating HER2-amplified breast cancer patients with the tyrosine kinase inhibitor lapatinib, resistance inevitably develops. Here we report that lapatinib induces the degradation of the nuclear receptor ERRα, a master regulator of cellular metabolism, and that the expression of ERRα is restored in lapatinib-resistant breast cancer cells through reactivation of mTOR signalling. Re-expression of ERRα in resistant cells triggers metabolic adaptations favouring mitochondrial energy metabolism through increased glutamine metabolism, as well as ROS detoxification required for cell survival under therapeutic stress conditions. An ERRα inverse agonist counteracts these metabolic adaptations and overcomes lapatinib resistance in a HER2-induced mammary tumour mouse model. This work reveals a molecular mechanism by which ERRα-induced metabolic reprogramming promotes survival of lapatinib-resistant cancer cells and demonstrates the potential of ERRα inhibition as an effective adjuvant therapy in poor outcome HER2-positive breast cancer.