Abstract PD8-03: ESR1 gene fusions drive endocrine therapy resistance and metastasis in breast cancer

Background. Dysregulation of the estrogen receptor gene (ESR1) is an established mechanism of inducing endocrine therapy resistance. We previously discovered a chromosomal translocation event generating an estrogen receptor gene fused in-frame to C-terminal sequences of YAP1 (ESR1-YAP1) that contributed to endocrine therapy resistance in estrogen receptor positive (ER+) breast cancer models. This study compares functional, transcriptional, and pharmacological properties of additional ESR1 gene fusion events of both early stage (ESR1-NOP2) late stage (ESR1-YAP1 and ESR1-PCDH11x) breast cancers to gain a better understanding of therapeutic resistance and metastasis. Understanding the role of ESR1 fusions in inducing metastasis is critical, since the primary cause of death in breast cancer patients is through metastasis to distant sites.

Methods. RNA-seq screens identified ESR1 fusions from early and late stage, endocrine therapy resistant breast tumor samples. Functional experiments were conducted using ER+ breast cancer cell lines, xenograft, and PDX models to test the ability of ESR1 fusions to induce therapeutic resistance and metastasis. ChIP-seq and RNA-seq were performed to examine transcriptional properties and differential gene expression induced by the fusions which directed subsequent pharmacological experiments with a CDK4/6 inhibitor.

Results. ESR1-YAP1 and ESR1-PCDH11x promoted estrogen-independent and fulvestrant-resistant growth in vitro and induced greater tumor growth and increased metastatic capacity to the lungs of xenografted mice. In contrast, the ESR1-NOP2 fusion was sensitive to low estrogen conditions in vitro, and did not promote tumor growth. RNA-seq profiling revealed E2F targets pathway as the most highly enriched pathway induced by the ESR1 fusions. IHC revealed higher levels of pRb in ESR1-YAP1 and ESR1-PCDH11x xenograft tumors and subsequent CDK4/6 inhibition completely blocked tumor growth in an ESR1-YAP1 PDX model. Integrating RNA-seq with ChIP-seq data, we discovered a set of EMT and metastasis genes bound by all ESR1 fusions and WT-ER, but whose expression was strongly and uniquely up-regulated only by the ESR1-YAP1 and ESR1-PCDH11x fusions. These studies also revealed gained sites bound only by the ESR1-YAP1 and ESR1-PCDH11x fusions, not bound by WT-ER nor ESR1-NOP2. Genes mapping to these sites have a role in metastatic biology and were highly up-regulated by the YAP1 and PCDH11x fusions, potentially mediated by long range transcriptional activation.

Conclusion. ESR1-YAP1 and ESR1-PCDH11x are driver fusions that occur in drug-resistant, advanced stage breast cancer and are a new class of recurrent somatic mutation that can cause acquired endocrine therapy resistance, yet can be treated with CDK4/6 inhibition. These driver fusions also confer increased metastatic ability through their ability to drive expression of genes that contribute to EMT and metastasis. In contrast, ESR1-NOP2 did not produce functional protein and appears to be a passenger event. These studies may provide pre-clinical rationale for targeting ESR1 translocated breast tumors, since the presence of an ESR1 driver fusion places a patient in a therapeutic category where none of the currently available endocrine therapies are likely to be effective.

Citation Format: Lei JT, Shao J, Zhang J, Iglesia M, Chan DW, Cao J, Anurag M, Singh P, Haricharan S, Kavuri SM, Matsunuma R, Schmidt C, Kosaka Y, Crowder R, Hoog J, Phommaly C, Goncalves R, Ramalho S, Rodrigues-Peres RM, Lai W-C, Hampton O, Rogers A, Tobias E, Parikh P, Davies S, Ma C, Suman V, Hunt K, Watson M, Hoadley KA, Thompson A, Perou CM, Creighton CJ, Maher C, Ellis MJ. ESR1 gene fusions drive endocrine therapy resistance and metastasis in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-03.

Abstract PD2-03: Recurrent functionally diverse in-frame ESR1 gene fusions drive endocrine resistance in breast cancer

Background. We previously reported an alternative ESR1 somatic gain-of-function chromosomal translocation event in a patient presenting with aggressive, endocrine therapy resistant estrogen receptor (ER) positive disease, producing an in-frame fusion gene consisting of N-terminal ESR1 and the C-terminus of the Hippo pathway coactivator YAP1 (ESR1-YAP1). We recently identified another ESR1 fusion through RNA sequencing (RNA-seq) in advanced stage ER+ disease from a chest wall recurrence in a male patient that was refractory to multiple lines of treatment. Two examples of fusions discovered in primary breast cancer samples include ESR1 fused in-frame to C-terminal sequences from NOP2 (ESR1-NOP2), identified in a resistant cohort from a RNA-seq screen focused on 81 primary breast cancers from aromatase inhibitor clinical trials, and a second ESR1 fusion, fused in-frame to the entire coding sequence of POLH (ESR1-POLH), that was identified from RNA-seq analysis of 728 Cancer Genome Atlas breast samples. This current study extends our previous characterization of ESR1-YAP1 by comparing functional and pharmacological properties of these three additional ESR1 gene fusion events of both early stage and advanced breast cancers.

Methods. In vitro and in vivo experiments were conducted to test ESR1 fusions to induce therapeutic resistance, and metastasis. The transcriptional and binding properties of each fusion was also examined. Pharmacological inhibition with Palbociclib, a cyclin-dependent kinase 4/6 inhibitor, was utilized to assess drug sensitivity in ESR1 fusion containing breast cancer cells and in a patient derived xenograft (PDX) model expressing ESR1-YAP1 (WHIM18).

Results. The YAP1 and PCDH11x fusions conferred estrogen-independent and fulvestrant-resistant growth. Immunohistochemistry revealed significantly higher numbers of ER+ cells in lungs of mice xenografted with T47D cells expressing the YAP1 and PCDH11x fusions compared to YFP control, NOP2 and POLH fusions. Results from ChIP-seq and microarray studies suggest that these two fusions promote proliferation and metastasis through genomic action by binding estrogen response elements (ERE) and subsequent gene activation. We thereby define these fusions as “canonical” fusions compared to “non-canonical” NOP2 and POLH fusions, which demonstrated dramatically decreased genomic binding ability. The non-canonical fusions induced genes associated with basal-like breast cancer and promoted HER2, EGFR, and MAPK gene expression signatures in contrast to genes associated with cell cycle/proliferation induced by canonical fusions. The proliferative ability of canonical fusion-containing ER+ cells was inhibited by Palbociclib in a dose-dependent manner. In vivo WHIM18 tumors in mice fed with Palbociclib-containing chow demonstrated significantly reduced tumor volume, growth rate, and weight compared to tumors in mice on control chow.

Conclusions. In-frame ERE activating canonical fusions occur in end-stage drug resistant advanced breast cancer and can be added to ESR1 point mutations as a class of recurrent somatic mutation that may cause acquired resistance. Growth induced by these fusions can be antagonized by Palbociclib and is potentially clinically helpful.

Citation Format: Lei JT, Shao J, Zhang J, Iglesia M, Cao J, Chan DW, He X, Kosaka Y, Schmidt C, Matsunuma R, Haricharan S, Crowder R, Hoog J, Phommaly C, Goncalves R, Ramalho S, Lai W-C, Hampton O, Rogers A, Tobias E, Parikh P, Davies S, Ma C, Suman V, Hunt K, Watson M, Hoadley KA, Thompson A, Chen X, Perou CM, Creighton CJ, Maher C, Ellis MJ. Recurrent functionally diverse in-frame ESR1 gene fusions drive endocrine resistance in breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD2-03.

Abstract P2-19-01: Modulating Response to Phosphoinositol-3-Kinase/mTOR Inhibition in ER Positive Breast Cancer Cell Lines after Acquired Resistance to Estrogen Deprivation

Background: We have recently shown that acquired resistance to aromatase inhibitors (AI) can, in some instances, be reversed low-dose estradiol treatment until progression followed by repeat treatment with an aromatase inhibitor (Ellis, M. JAMA 302:774, 2009). We have also demonstrated that simultaneous inhibition of phosphoinositol-3-kinase (PI3K) and ER (though estrogen deprivation) activates cell death through apoptosis, which is reversed by estradiol, revealing a link between ER activation and the efficacy of PI3 kinase inhibition (Crowder, R. Cancer Res 69:3955, 2009). Consistent with this concept we have also shown that long term estrogen deprived (LTED) cells are co-resistant to both classes of agent (SABCS 2009 Abs#3131). We therefore studied ways to overcome resistance to PI3 kinase inhibitors in LTED cell lines using second line endocrine therapy strategies that could be offered to patients with AI resistant advanced disease.

Methods: ER+ MCF7 and T47D (PIK3CA mutant) cells were cultured in phenol-red free media containing charcoal-stripped serum for 12 months to create long term estrogen deprivation (LTED) variants that mimicked clinical endocrine therapy resistance. A variant of the MCF7 LTED line that regained estrogen-dependent proliferation was created by re-exposure to estradiol for 4 months (MCF7 LTED-R). The effects of the PI3K isoform inhibitor BKM120, the mTOR inhibitor RAD001 and the dual PI3K/mTOR inhibitor BGT226 in MCF7 LTED and T47D LTED were assessed in combination with estrogen deprivation and fulvestrant. MCF7 LTED-R cells were treated with PI3 kinase pathway inhibitors after acute estradiol withdrawal. Apoptosis was measured using TUNEL flow cytometry. Results: MCF7 LTED were resistant to all three PI3 kinase inhibitors, but combination treatment with fulvestrant restored apoptosis to levels seen with parental MCF7 cells after acute estrogen-deprivation. Acute estrogen deprivation in MCF7 LTED-R cells was also effective in restoring an apoptotic response to BGT226. T47D LTED cells, which, unlike MCF7 cells, have markedly down-regulated ER expression, become more sensitive to PI3 kinase monotherapy than the parental T47D cell line, particularly in response to BKM120, and fulvestrant did not increase the apoptotic response.

Conclusions: The MCF7 cell results suggest that PI3 kinase inhibitors will be effective in endocrine therapy resistant advanced breast cancer if these agents are administered with appropriate second line endocrine strategies. Potentially efficacious approaches include fulvestrant combinations and second-line aromatase inhibition, but only after restoration of AI sensitivity with estradiol. The T47D experiments suggest that in the setting of ER+ tumors that lose ER upon disease progression PI3 kinase inhibitors may be very effective.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-19-01.

The Effect of the IGF1R Antibody R1507 on ER Positive Breast Cancer Cell Lines Growth and Survival

Background: The insulin-like growth factor-1 receptor (IGF1R) mediates the biological actions of IGF-1 and IGF-2 and is expressed in most breast cancer cells, where receptor activation induces proliferative, cell-survival, and transforming activities. Because crosstalk exists between ER and IGF1R blockade of both pathways could increase antitumor activity. Further, IGF signaling may be enhanced in ER+ cells that have become refractory to long term estrogen deprivation (LTED) explaining resistance to aromatase inhibitor therapy. The effect of the selective IGF1R antibody (R1507) was therefore assessed in a series of breast cancer cell lines in both estrogen-dependent and estrogen-independent growth phases.Methods: The ER positive breast cancer cells lines MCF7, T47D and HCC712 were kept in phenol red-free medium containing 5% charcoal-stripped serum. Several doses of R1507 were used to evaluate effects on cell proliferation, signaling and apoptosis. Western blotting with phospho-specific antibodies was used to observe effects on cell signaling, cell growth was measured using resazurin reduction and apoptosis was quantified by flow cytometry using the TUNEL assay. STED (short-term estrogen deprived) cells were treated with R1507 between 2 and 3 weeks after estrogen depletion and LTED were treated with R1507 after 6+ months of estrogen depletion.Results: R1507 suppressed IGF1R expression and inhibited IGF-1 stimulated IGF1R and AKT phosphorylation in all cell lines. R1507 had anti-proliferative effects in MCF7 cells in both estrogen-dependent and independent growth phases and the magnitude of the effect was similar to fulvestrant. R1507 had a smaller effect on cell proliferation in HCC712 cells and no effects on proliferation were observed in T47D cells. Antibody treatment resulted in significant induction of apoptosis in MCF7 STED but MCF7 LTED cells were resistant to the apoptotic effects of IGF1R blockade.Conclusions: R1507 had an inhibitory effect on IGF1R signaling and an anti-proliferative effect in two of the three cell lines tested. In addition R1507 induced synthetic lethality in combination with acute estrogen deprivation in MCF7 cells, an effect we have recently reported for direct PI3 kinase inhibitors under the same circumstances (1). While the proapoptotic effects of R1507 were lost in the estrogen-independent growth phase of MCF7 cells, the anti-proliferative effect was not, indicating that R1507 might have efficacy in patients with endocrine therapy resistant tumors. In other cell lines the efficacy of R1507 was variable and synthetic lethality was not observed, suggesting that the development of predictive biomarkers for R1507 should be a priority. We are currently addressing the activity of R1507 in a clinical trial with two cohorts, one with acquired resistance to letrozole, where the antibody is added to continued letrozole treatment and a second group of patients with stable disease on letrozole to determine if R1507 can induce tumor regression under these circumstances.1. Crowder et al Cancer Research 69:3955-62, 2009

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3126.

Phosphoinositide-3-Kinase Catalytic Subunit Inhibition Does Not Produce Synthetic Lethality in Estrogen Receptor Positive Breast Cancer Cells with Acquired Resistance to Estrogen Deprivation

Background: Several phosphoinositide-3-kinase (PI3K) catalytic subunit inhibitors are currently in clinical development. However, targeting strategies for PI3K catalytic subunits for treatment in estrogen receptor positive (ER+) disease have not been fully developed. We have recently reported that targeted inhibition of the two major PI3K catalytic subunits, p110α and p110β, using RNA interference (RNAi) induces apoptosis in short term estrogen-deprived ER+ breast cancer cells. Similarly, treatment with BEZ235, a clinical grade p110α/mammalian target of rapamycin (mTOR)-selective inhibitor, also promoted apoptosis in estrogen-deprived ER+ breast cancer cells. Importantly, we found that estradiol significantly suppressed death in ER+ cells induced by inhibition of PI3K catalytic subunits through both RNA interference and BEZ235. In contrast estrogen deprivation or PI3K inhibition individually caused little or no increase in apoptosis, indicating that there is a synthetic lethal interaction with estrogen deprivation/PI3K inhibitor combination treatment in ER+ breast cancer. These data suggest that combining estrogen deprivation with PI3K inhibition may improve clinical outcome by eradicating ER+ cells through increased tumor cell kill. We have extended these studies in order to determine the effect of PI3K catalytic subunit inhibition in long-term estrogen deprived (LTED) cells, a model for acquired resistance to endocrine therapy.Methods: LTED sub-lines of the ER+ MCF7 and T47D breast cancer cell lines were derived by depriving cells of estrogen for 6–9 months in phenol red-free medium containing charcoal-stripped serum after which time cells grow readily without supplemental estrogen. The effects of PI3K inhibition using RNAi and treatment with BEZ235 or BGT226, a p110α-selective inhibitor, were compared in short-term estrogen deprived MCF7 and T47D cells and their LTED derivatives by measuring effects on cell signaling, growth and apoptosis. Cell signaling was evaluated through western blotting, cell growth was measured using resazurin reduction and apoptosis was quantified by flow cytometry using the TUNEL assay.Results: PI3K inhibition using p110α RNAi or treatment with BEZ235 inhibited the growth of MCF7 LTED cells in the absence of supplemental estrogen. However, p110α RNAi or treatment with BEZ235 or the clinical grade p110α-selective inhibitor BGT226 failed to significantly induce apoptosis in MCF7 LTED cells. The effects of PI3K inhibition in T47D LTED cells are under investigation and will be presented.Conclusions: These results suggest that that the efficacy of PI3K inhibitors will be blunted after the onset of acquired resistance to estrogen deprivation through treatment with aromatase inhibitors and that a combined ER/PI3K targeting strategy in ER+ breast cancer treatment should be employed in the endocrine therapy sensitive phase of the disease.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3131.