ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials

Matching patients to optimal treatment is challenging, in part due to the limited availability of real-world clinical datasets for predictive biomarker identification. The growing integration of omics profiling into clinical trials presents a new opportunity to tackle this challenge. Here, we introduce ClinicalOmicsDB, a web application for exploring molecular associations of oncology drug responses in clinical trials. This database includes transcriptomic data from 40 clinical trial studies, with 5913 patients spanning 11 cancer types. These studies include 67 treatment arms with a variety of chemotherapy, targeted therapy and immunotherapy drugs, and their combinations, which we organize based on an established ontology for easier navigation. The web application provides users with three options to explore molecular associations of oncology drug responses, focusing on studies, treatments or genes, respectively. Gene set analysis further connects treatment response to pathway activity and tumor microenvironment attributes. The user-friendly web interface of ClinicalOmicsDB streamlines interactive analysis. A Rust-based backend speeds up response time, and application programming interfaces and an R package enable programmatic access. We use three case studies to demonstrate the utility of this resource in human cancer studies. ClinicalOmicsDB is freely available at http://trials.linkedomics.org/.

Targeting kinome reprogramming in ESR1 fusion-driven metastatic breast cancer

1085

Background: Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor-alpha positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain is replaced by C-terminal sequences from many different gene partners. Transcriptionally active ESR1 fusions promoted hormone-independent cell growth, motility and resistance to endocrine therapy. The diversity of partner genes creates a considerable diagnostic challenge and no targeted treatments exist for ESR1 translocated tumors. Thus, we have established a transcriptional signature to diagnose the presence of an active ESR1 fusion (PMID: 34711608) and developed novel targeted therapies against ESR1 fusion-driven biology. Methods: Fifteen ESR1 fusion cDNA constructs were expressed in ER+ breast cancer cell lines by lentiviral transduction. Cell growth was assayed by Alamar blue assay. A mass spectrometry (MS)-based Kinase Inhibitor Pulldown Assay (KIPA) and tandem mass tag-based proteomics were performed to identify ESR1 fusion-driven druggable kinases for subsequent pharmacological inhibition. Results: KIPA profiling demonstrated an increase of multiple receptor tyrosine kinases including RET in T47D cells expressing active ESR1 fusions. Inhibition of RET by repurposing an FDA-approved drug significantly suppressed ESR1 fusion-driven cell growth in vitro, suggesting that despite marked diversity in the 3’ partners, common kinase activities were elevated and targetable. Proteogenomic profiling, including whole exome sequencing, RNA sequencing, and MS-based proteomics and phosphoproteomics were further performed on 22 ER+ patient-derived xenograft (PDX) tumors, which demonstrated different degrees of estradiol dependence. These integrated “omic” profiles defined targetable genes/pathways and predict tumor subsets that could be responsive to kinase inhibition therapy from this biologically heterogeneous panel of PDX tumors. WHIM18, a PDX naturally harboring the ESR1-YAP1 fusion showed elevated level of RET and CDK4/6 pathways. The tumor volumes were significantly reduced by the RET inhibitor. CDK4/6 inhibitor treatment showed similar tumor reductions to RET inhibition. Interestingly, WHIM9 PDX that expressed wild-type ESR1 conferred a comparable kinome profile to WHIM18. The tumor growth was significantly suppressed by RET or CDK4/6 inhibition. Therefore, pharmacological experiments validated proteogenomics-predicted drug response in two tested ER+ PDX models. Conclusions: Proteogenomics characterization of PDX tumors can drive clinical trial hypotheses. Here, we reveal therapeutic kinase vulnerabilities in ESR1 fusion-driven tumors as exemplified by RET inhibition, which will lay the framework for future clinical trials.

Abstract P6-17-15: Evaluating preclinical efficacy of anti-HER2 drug combinations using ER+/HER2 mutant models

Background

Until recently, HER2 gene amplification was the only mechanism of HER2 activation recognized. However, activating HER2 mutations have been noted in different cancer types. A trials of HER2 mutant breast cancer and the subsequent SUMMIT trial data have shown that monotherapy with the pan-HER drug neratinib as showed clinical efficacy, but with poor response durability. This study therefore investigates the preclinical efficacy of anti HER2 agents alone or in combination with endocrine therapy agents or in combination with CDK4/6 inhibitors using ER+/HER2 mutant cell lines and ex vivo HER2 mutant patient derived xenograft (PDX) model to define a more effective treatment approach.

Methods

ER+ breast cancer cell lines (T47D and MCF7) stably expressing HER2V777L, and ER+/HER2 mutant PDX model (HER2G778_P780 dup) were used to examine HER2 signaling and drug responses. Signaling downstream mutant HER2 was examined by immunoblot analysis. Effects of neratinib alone, neratinib + fulvestrant, and neratinib + abemaciclib on cell growth were examined in ER+/HER2 mutant cell lines and in an ex vivo HER2G778_P780 dup.

Results

We found that MCF7/T47D cells expressing HER2V777L and HER2G778_P780 dup PDX tumors showed strongly activated autophosphorylation of HER2 and increased expression of CDK4, CDK6, phospho-Rb, and cyclin D1 as compared to MCF7/T47D cells expressing HER2WT or ER+/non-HER2mut PDX modes, suggesting that HER2 mutations preferentially depend on CDK4/6 signaling for cell growth. Additionally, we showed that activating MCF7 HER2 V777L cause resistance to endocrine therapy treatment (fulvestrant IC50 >5μM). Further, we show that neratinib alone is effective at higher concentrations (IC50 < 2μM) in MCF7/HER2 V777L cells. We also demonstrate that abemaciclib alone exhibited moderate activity against MCF7 HER2 V777L cells (IC50 < 0.4μM) and additional activity in combination with neratinib (IC50 < 0.06μM) was seen. Moreover, ex vivo HER2 G778_P780 dup cells are relatively resistant to fulvestrant alone (IC50 < 0.2μM), neratinib alone (IC50 < 0.006μM), abemaciclib alone (IC50 < 0.04μM), and neratinib in combination with abemaciclib (IC50 < 0.005μM), suggesting that patients harboring ER+/HER2-mutant tumors may benefit from neratinib in combination with abemaciclib.

Conclusion

These preclinical data suggest that neratinib monotherapy may not be effective to treat ER+/HER2 mutant patients and we propose that simultaneous targeting of both HER2 and the CDK4/6 axis will be required for effective treatment of ER+ breast cancers harboring HER2 activating mutations.

Citation Format: Kavuri SM, Devarakonda V, Williams LC, Seker S, Lei JT, Singh P, Han A, Anurag M, Holloway KR, Welm AL, Ellis MJ. Evaluating preclinical efficacy of anti-HER2 drug combinations using ER+/HER2 mutant models [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-17-15.

Abstract P5-04-01: Functional and therapeutic significance of ESR1 fusions in metastatic ER+ breast cancer

Background. Next-generation sequencing methods have identified several ESR1 fusion genes in treatment refractory ER+ breast cancer, however detailed functional studies in experimental models are lacking and how they might be targeted remains poorly understood. We recently reported two transcriptionally active, in-frame ESR1 fusions, ESR1-YAP1 and ESR1-PCDH11X, identified in a small cohort of metastatic ER+ cases, that induce not only pan-endocrine therapy resistance but also metastatic disease progression (Lei et al., Cell Reports, in press). Limited characterization of ESR1-DAB2 and ESR1-GYG1, also identified in metastatic ER+ disease from a recent study, suggests these two ESR1 fusions also drive estrogen-independent gene activation (Hartmaier et al., Annals of Oncology, 2018). Here, we functionally characterize ESR1-DAB2 and ESR1-GYG1 along with additional ESR1 fusions discovered in metastatic ER+ breast tumors to further support a causal role for in-frame ESR1 fusions in driving endocrine therapy resistance and promoting metastasis-associated biology, and explore therapeutic vulnerabilities induced by ESR1 fusion gene formation.

Methods. RNA-seq identified ESR1 fusions from treatment refractory, ER+ metastatic breast tumors. In-frame ESR1 fusions constructs were generated and stably expressed in ER+ breast cancer cell lines: T47D, MCF7, and ZR75-1. Estrogen-independent and fulvestrant-resistant growth was monitored in hormone-deprived stable cell lines. mRNA-qPCR was performed to examine expression of estrogen responsive and epithelial-to-mesenchymal transition (EMT) genes. In vitro sensitivity to CDK4/6 inhibition was tested with palbociclib and abemaciclib.

Results. In addition to previously described ESR1-YAP1, ESR1-PCDH11X, ESR1-DAB2, and ESR1-GYG1, that follow a pattern retaining the first 6 exons of ESR1 (ESR1-e6) fused in-frame to C-terminal sequences provided by the partner gene, additional in-frame ESR1-e6 fusions, ESR1-PCMT1, ESR1-ARNT2, and ESR1-ARID1B, all identified in metastatic ER+ samples, were found to follow the same fusion pattern. ESR1-DAB2 and ESR1-GYG1 produced stable ESR1 fusion proteins in ER+ breast cancer cell lines. In T47D, these two fusions drove estrogen-independent and fulvestrant-resistant growth. In addition, T47D and ZR75-1 models revealed that ESR1-DAB2 drove estrogen-independent expression of estrogen responsive genes and also EMT genes, including SNAI1, suggesting this fusion, like ESR1-YAP1 and ESR1-PCDH11X, could also drive metastasis. Treatment with CDK4/6 inhibitors suppressed growth induced by ESR1-DAB2 and ESR1-GYG1.

Conclusion. The majority of in-frame ESR1 exon 6 fusions found in metastatic ER+ breast are transcriptionally active, drive endocrine therapy resistant proliferation, and induce an EMT-like transcriptional program. The ability to block ESR1 fusion induced growth with a CDK4/6 inhibitor is clinically significant as ESR1 fusion gene formation renders ER insensitive to all endocrine therapies that target the ligand binding domain. Furthermore, clinical diagnosis of an active ESR1 fusion could potentially stratify patients for CDK4/6 inhibitor treatment. This presentation is the most complete description of the role for ESR1 fusions in endocrine therapy resistance and metastasis described to date.

Citation Format: Lei JT, Gou X, Seker S, Haricharan S, Lee AV, Robinson DR, Ellis MJ. Functional and therapeutic significance of ESR1 fusions in metastatic ER+ breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-01.

Abstract P5-08-01: DPYSL3 modulates mitosis, migration and epithelial to mesenchymal transition in claudin-low breast cancer

Proteogenomics is the field of integrating data from mass spectrometry-based shotgun proteomics, and phosphoproteomics into next-generation RNA and DNA sequencing data analysis pipelines that promises new insights into cancer biology and therapeutic targeting. As well as analyses of clinical samples for disease phenotype association analysis, the application of proteogenomics to model systems also has considerable potential. A Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomic analysis prioritized dihydropyrimidinase-like-3 (DPYSL3) as a multi-level (RNA/Protein/Phosphoprotein) expression outlier specific to the Claudin-Low (CLOW) subset of triple negative breast cancers. A Pubmed informatics tool indicated a paucity of data in the context of breast cancer which further prioritized DPYSL3 for study.

DPYSL3 was identified as a protein that is regulated during neuronal differentiation in the cerebral cortex and in neuronal cell lines and plays a role in regulating neurite outgrowth somehow through an association with vesicles in the growth cone. In addition, DPYSL3 expression has been observed in several malignant tumors, including prostate cancer, pancreatic cancer, gastric cancer and neuroblastoma. DPYSL3 is reported to play a role in cell migration and metastasis suppression in prostate cancer. However, in pancreatic cancer, DPYSL3 is positively associated with liver metastasis and poor outcome.

DPYSL3 knock-down in DPYSL3 (+) CLOW cell lines demonstrated reduced proliferation, yet enhanced motility and increased expression of Epithelial to Mesenchymal Transition (EMT) markers suggesting that DPYSL3 is a multi-functional signaling modulator. Slower proliferation in DPYSL3 (-) CLOW cells was associated with accumulation of multi-nucleated cells indicating a mitotic defect that was associated with a collapse of the vimentin (VIM) microfilament networkinduced by VIM hyperphosphorylation. On the other hand, DPYSL3 suppressed the expression of EMT regulators TWIST and SNAIL and opposed p21 activated kinase 2 (PAK2) dependent migration, but these EMT regulators in turn induced DPYSL3 expression, suggesting DPYSL3 participates in negative feedback in EMT. Cell migration in DPYSL3 (-) cells correlated with increased phosphorylation of PAK2 on Ser20 and was sensitive to PAK2 siRNA and pharmacological PAK inhibition.Immunoprecipitation and mass spectrometry-based proteomics or western blotting strongly suggests that PAKs interact such that DPYSL3 may function as a direct negative regulator of PAK family kinases. Thus, a PAK inhibitor could potentially mitigate increase migration as an adverse effect of DPYSL3 suppression.

In conclusion, DPYSL3 is a remarkable multifunctional signaling scaffold that should be examined further to provide insights into the stem cell-like state of claudin-low breast cancers, particularly in terms of their cell cycle dependencies, migratory activity and capacity for EMT.

Citation Format: Matsunuma R, Chan DW, Kim B-J, Singh P, Han A, Saltzman A, Cheng C, Lei JT, Sahin E, Leng M, Fan C, Perou CM, Malovannaya A, Ellis MJ. DPYSL3 modulates mitosis, migration and epithelial to mesenchymal transition in claudin-low breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-08-01.

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 P1-08-07: Assessing the impact of loss of NF1 protein on endocrine therapy resistance

Background: The vast majority of breast cancers belong to the luminal subtype, which expresses the estrogen receptor-α (ER). Although great strides have been made in targeting the ER pathway for treating the ER+ tumors, relapse and death is common and ongoing. In order to identify the cause for treatment resistance, we have conducted a retrospective analyses on the tumor ge­nomes of >600 patients treated by tamoxifen monotherapy in the adjuvant setting with a median follow-up of 10.4 years. Our data have revealed that NF1 (Neuro­fibromatosis type 1) gene loss of function mutations were greatly associated with poor prognosis. NF1 is a tumor suppressor acting mostly as a GAP (GTP ase activating protein) to switch off acti­vated Ras. We aim to define the impact of loss of NF1 protein on patient outcome in ER+ breast cancer patients by establishing an immunohistochemistry (IHC) protocol to detect NF1.

Method and results: We have first surveyed commercially available antibodies by Western blot and found one that could efficiently detect endogenous NF1. We then use this to validate inducible shRNA clones against NF1, as well as a breast cancer cell line that is NF1-null. This antibody has high background. We have thus partially purified a commercially available NF1 antibody by preclearing using NF1-null cell lysate. We then performed immunostaining using NF1-silenced and null cells as control and found that NF1 is mostly cytoplasmic and nuclear. To get antibody of high quality, we have decided to make our own antibody by expressing a C-terminal fragment of NF1 as a GST-tagged protein (GST-NF1c). Production of polyclonal and monoclonal antibody is in progress.

Conclusion: Our clinical profiling data suggest that loss of NF1 protein, a very common event in a wide range of other cancers, promotes endocrine therapy resistance. An efficient IHC protocol will enable us to firmly validate whether loss of the NF1 protein indeed correlates with poor patient outcome. This method will ultimately enable us to identify high risk NF1 deficient patients and to properly treat them.

Citation Format: Cakar B, Chan D, Yan P, Zheng Z, Singh P, Lei JT, Haricharan S, Ellis M, Chang E. Assessing the impact of loss of NF1 protein on endocrine therapy resistance [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 P1-08-07.

Abstract P1-08-01: Regulation of estrogen receptor-α by NF1

Background. Although great strides have been made in targeting the ER pathway for treating ER+ breast cancer, relapse and death is common and is closely linked to resistance to ER-targeting agents. As a result, the majority of deaths from breast cancer still come from ER+ tumors. To discover drivers for endocrine resistance, we have sequenced tumor DNAs from a cohort of >600 patients treated with 5-year tamoxifen (Tam) monotherapy with a median 10.4 years follow up. Our preliminary data show that the worst outcome mutations (Hazard Ratio of ∼3 for relapse) were mostly those of the Neurofibromatosis type 1 (NF1) gene (encoding Neurofibromin), with nonsense/frame shift mutations creating early stop codons.

Germline NF1mutations cause neurofibromatosis type 1, a common inherited disorder that predisposes individuals to both benign and malignant tumors of the nervous system, as well as an increased risk for breast cancer. Analysis of DNA sequencing data has also shown that the NF1 gene is mutated in a wide range of common cancers (e.g., melanoma, lymphoma, and cancers of the lung, breast, and colon). Thus, NF1-deficiency underlies the formation and/or progression of a large number of cancers, so that the development of therapies targeted to NF1-deficient malignancies would have broad impact.

These observations support the hypothesis that NF1 gene inactivation is associated with aggressive tumor behaviors, such as endocrine therapy resistance in breast cancer. The key focus of this study is to define how the NF1 protein neurofibromin, regulates endocrine therapy resistance. Although neurofibromin is best known as a negative regulator for Ras, our data show that it may have other functions.

Method. Our data suggest that many of the identified nonsense/frame shift create a NF1 null state; thus, we have used gene-silencing to recapitulate the effects of such NF1 mutations on the activities of ER+ breast cancer cells. NF1+ and NF1– ER+ breast cancer cells were grown in defined media to measure how estradiol (E2) and Tam impact their growth, transforming activities, and gene expression. The binding between neurofibromin and components of the ER transcriptional pathway was measured biochemically and using the mammalian two-hybrid system.

Results. Our data showed that NF1-silenced cells use Tam as an agonist and can grow with very little E2, and these activities are driven by enhanced recruitment of ER to the ERE, leading to efficient expression of many classic ER-responsive genes. Expressing the NF1-GAP domain does not restore normal responses to Tam and E2 in NF1-silenced cells, suggesting that neurofibromincan regulate ER activity in a Ras-independent manner. To investigate the possibility that neurofibromin can directly regulate ER, we found that it can bind ER; furthermore, neurofibromin was more strongly recruited to the ERE by Tam than by E2.

Conclusion. Our data support a model whereby neurofibromin acts like a co-repressor for ER. As such,NF1 loss may result in more aggressive tumor behaviors by activating, not only the Ras pathways, but also the ER transcriptional pathways. Simultaneous activation of two powerful oncogenic pathways by the loss of a single tumor suppressor may explain why neurofibromin is such a potent tumor suppressor lost in a wide range of cancers.

Citation Format: Zheng Z-Y, Cakar B, Lavere P, Cao J, Yao J, Singh P, Lei JT, Toonen JA, Haricharan S, Anurag M, Shah K, Kavuri M, Chan DW, Chen X, Gutmann DH, Foulds CE, Ellis MJ, Chang EC. Regulation of estrogen receptor-α by NF1 [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 P1-08-01.