Pharmacological induction of chromatin remodeling drives chemosensitization in triple-negative breast cancer

Targeted therapies have improved outcomes for certain cancer subtypes, but cytotoxic chemotherapy remains a mainstay for triple-negative breast cancer (TNBC). The epithelial-to-mesenchymal transition (EMT) is a developmental program co-opted by cancer cells that promotes metastasis and chemoresistance. There are no therapeutic strategies specifically targeting mesenchymal-like cancer cells. We report that the US Food and Drug Administration (FDA)-approved chemotherapeutic eribulin induces ZEB1-SWI/SNF-directed chromatin remodeling to reverse EMT that curtails the metastatic propensity of TNBC preclinical models. Eribulin induces mesenchymal-to-epithelial transition (MET) in primary TNBC in patients, but conventional chemotherapy does not. In the treatment-naive setting, but not after acquired resistance to other agents, eribulin sensitizes TNBC cells to subsequent treatment with other chemotherapeutics. These findings provide an epigenetic mechanism of action of eribulin, supporting its use early in the disease process for MET induction to prevent metastatic progression and chemoresistance. These findings warrant prospective clinical evaluation of the chemosensitizing effects of eribulin in the treatment-naive setting.

Alteration of DNA methyltransferases by eribulin elicits broad DNA methylation changes with potential therapeutic implications for triple-negative breast cancer

Background: Triple-negative breast cancer (TNBC) is an aggressive disease with limited treatment options. Eribulin, a chemotherapeutic drug, induces epigenetic changes in cancer cells, suggesting a unique mechanism of action. Materials & methods: MDA-MB 231 cells were treated with eribulin and paclitaxel, and the samples from 53 patients treated with neoadjuvant eribulin were compared with those from 14 patients who received the standard-of-care treatment using immunohistochemistry. Results: Eribulin treatment caused significant DNA methylation changes in drug-tolerant persister TNBC cells, and it also elicited changes in the expression levels of epigenetic modifiers (DNMT1, TET1, DNMT3A/B) in vitro and in primary TNBC tumors. Conclusion: These findings provide new insights into eribulin's mechanism of action and potential biomarkers for predicting TNBC treatment response.

TRIM33 Is a Co-Regulator of Estrogen Receptor Alpha

Estrogen receptor alpha (ER)-positive breast cancer is responsible for over 60% of breast cancer cases in the U.S. Among patients diagnosed with early-stage ER+ disease, 1/3 will experience recurrence despite treatment with adjuvant endocrine therapy. ER is a nuclear hormone receptor responsible for estrogen-driven tumor growth. ER transcriptional activity is modulated by interactions with coregulators. Dysregulation of the levels of these coregulators is involved in the development of endocrine resistance. To identify ER interactors that modulate transcriptional activity in breast cancer, we utilized biotin ligase proximity profiling of ER interactomes. Mass spectrometry analysis revealed tripartite motif containing 33 (TRIM33) as an estrogen-dependent interactor of ER. shRNA knockdown showed that TRIM33 promoted ER transcriptional activity and estrogen-induced cell growth. Despite its known role as an E3 ubiquitin ligase, TRIM33 increased the stability of endogenous ER in breast cancer cells. TRIM33 offers a novel target for inhibiting estrogen-induced cancer cell growth, particularly in cases of endocrine resistance driven by ER (ESR1) gene amplification or overexpression.

Estrogen Therapy Induces Receptor-Dependent DNA Damage Enhanced by PARP Inhibition in ER+ Breast Cancer

PURPOSE

Clinical evidence indicates that treatment with estrogens elicits anticancer effects in ∼30% of patients with advanced endocrine-resistant estrogen receptor α (ER)-positive breast cancer. Despite the proven efficacy of estrogen therapy, its mechanism of action is unclear and this treatment remains underused. Mechanistic understanding may offer strategies to enhance therapeutic efficacy.

EXPERIMENTAL DESIGN

We performed genome-wide CRISPR/Cas9 screening and transcriptomic profiling in long-term estrogen-deprived ER+ breast cancer cells to identify pathways required for therapeutic response to the estrogen 17β-estradiol (E2). We validated findings in cell lines, patient-derived xenografts (PDX), and patient samples, and developed a novel combination treatment through testing in cell lines and PDX models.

RESULTS

Cells treated with E2 exhibited replication-dependent markers of DNA damage and the DNA damage response prior to apoptosis. Such DNA damage was partially driven by the formation of DNA:RNA hybrids (R-loops). Pharmacologic suppression of the DNA damage response via PARP inhibition with olaparib enhanced E2-induced DNA damage. PARP inhibition synergized with E2 to suppress growth and prevent tumor recurrence in BRCA1/2-mutant and BRCA1/2-wild-type cell line and PDX models.

CONCLUSIONS

E2-induced ER activity drives DNA damage and growth inhibition in endocrine-resistant breast cancer cells. Inhibition of the DNA damage response using drugs such as PARP inhibitors can enhance therapeutic response to E2. These findings warrant clinical exploration of the combination of E2 with DNA damage response inhibitors in advanced ER+ breast cancer, and suggest that PARP inhibitors may synergize with therapeutics that exacerbate transcriptional stress.

Alternating 17β-Estradiol and Aromatase Inhibitor Therapies Is Efficacious in Postmenopausal Women with Advanced Endocrine-Resistant ER+ Breast Cancer

PURPOSE

Strategies to implement estrogen therapy for advanced estrogen receptor-positive (ER+) breast cancer are underdeveloped. Preclinical data suggest that cycling treatment with 17β-estradiol followed by estrogen deprivation can control tumor growth long-term.

PATIENTS AND METHODS

Postmenopausal women with advanced ER+/HER2- breast cancer with recurrence or progression on ≥ 1 antiestrogen or aromatase inhibitor (AI)-based therapy were eligible. Patients received 17β-estradiol (2 mg orally, three times a day) for 8 weeks followed by AI (physician's choice) for 16 weeks, alternating treatments on an 8-week/16-week schedule until disease progression. Patients then optionally received continuous single-agent treatment until a second instance of disease progression. Endpoints included 24-week clinical benefit and objective response per RECIST, and tumor genetic alterations.

RESULTS

Of 19 evaluable patients, clinical benefit rate was 42.1% [95% confidence interval (CI), 23.1%-63.9%] and objective response rate (ORR) was 15.8% (95% CI, 5.7%-37.9%). One patient experienced a grade 3 adverse event related to 17β-estradiol. Among patients who received continuous single-agent treatment until a second instance of disease progression, clinical benefit was observed in 5 of 12 (41.7%) cases. Tumor ER (ESR1) mutations were found by whole-exome profiling in 4 of 7 (57.1%) versus 2 of 9 (22.2%) patients who did versus did not experience clinical benefit from alternating 17β-estradiol/AI therapy. The only two patients to experience objective responses to initial 17β-estradiol had tumor ESR1 mutations.

CONCLUSIONS

Alternating 17β-estradiol/AI therapy may be a promising treatment for endocrine-refractory ER+ breast cancer, including following progression on CDK4/6 inhibitors or everolimus. Further study is warranted to determine whether the antitumor activity of 17β-estradiol differs according to ESR1 mutation status.

Alteration of DNMT1/DNMT3A by eribulin elicits global DNA methylation changes with potential therapeutic implications for triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive disease subtype with limited treatment options. Eribulin is a chemotherapeutic approved for the treatment of advanced breast cancer that has been shown to elicit epigenetic changes. We investigated the effect of eribulin treatment on genome-scale DNA methylation patterns in TNBC cells. Following repeated treatment, The results showed that eribulin-induced changes in DNA methylation patterns evident in persister cells. Eribulin also affected the binding of transcription factors to genomic ZEB1 binding sites and regulated several cellular pathways, including ERBB and VEGF signaling and cell adhesion. Eribulin also altered the expression of epigenetic modifiers including DNMT1, TET1, and DNMT3A/B in persister cells. Data from primary human TNBC tumors supported these findings: DNMT1 and DNMT3A levels were altered by eribulin treatment in human primary TNBC tumors. Our results suggest that eribulin modulates DNA methylation patterns in TNBC cells by altering the expression of epigenetic modifiers. These findings have clinical implications for using eribulin as a therapeutic agent.

Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression

The epithelial-mesenchymal transition (EMT) is a developmental program co-opted by tumor cells that aids the initiation of the metastatic cascade. Tumor cells that undergo EMT are relatively chemoresistant, and there are currently no therapeutic avenues specifically targeting cells that have acquired mesenchymal traits. We show that treatment of mesenchymal-like triple-negative breast cancer (TNBC) cells with the microtubule-destabilizing chemotherapeutic eribulin, which is FDA-approved for the treatment of advanced breast cancer, leads to a mesenchymal-epithelial transition (MET). This MET is accompanied by loss of metastatic propensity and sensitization to subsequent treatment with other FDA-approved chemotherapeutics. We uncover a novel epigenetic mechanism of action that supports eribulin pretreatment as a path to MET induction that curtails metastatic progression and the evolution of therapy resistance.

Estrogen therapy induces receptor-dependent DNA damage enhanced by PARP inhibition in ER+ breast cancer

Purpose

Clinical evidence indicates that treatment with estrogens elicits anti-cancer effects in ∼30% of patients with advanced endocrine-resistant estrogen receptor alpha (ER)-positive breast cancer. Despite the proven efficacy of estrogen therapy, its mechanism of action is unclear and this treatment remains under-utilized. Mechanistic understanding may offer strategies to enhance therapeutic efficacy.

Experimental Design

We performed genome-wide CRISPR/Cas9 screening and transcriptomic profiling in long-term estrogen-deprived (LTED) ER+ breast cancer cells to identify pathways required for therapeutic response to the estrogen 17β-estradiol (E2). We validated findings in cell lines, patient-derived xenografts (PDXs), and patient samples, and developed a novel combination treatment through testing in cell lines and PDX models.

Results

Cells treated with E2 exhibited replication-dependent markers of DNA damage and the DNA damage response prior to apoptosis. Such DNA damage was partially driven by the formation of DNA:RNA hybrids (R-loops). Pharmacological suppression of the DNA damage response via poly(ADP-ribose) polymerase (PARP) inhibition with olaparib enhanced E2-induced DNA damage. PARP inhibition synergized with E2 to suppress growth and prevent tumor recurrence in BRCA1/2 -mutant and BRCA1 /2-wild-type cell line and PDX models.

Conclusions

E2-induced ER activity drives DNA damage and growth inhibition in endocrine-resistant breast cancer cells. Inhibition of the DNA damage response using drugs such as PARP inhibitors can enhance therapeutic response to E2. These findings warrant clinical exploration of the combination of E2 with DNA damage response inhibitors in advanced ER+ breast cancer, and suggest that PARP inhibitors may synergize with therapeutics that exacerbate transcriptional stress.

Alpelisib Efficacy without Cherry-PI3King Mutations

The PI3K inhibitor alpelisib is clinically approved for the treatment of metastatic estrogen receptor-positive breast cancers harboring hotspot mutations in PIK3CA, which encodes a subunit of PI3K. Prospective clinical trial results demonstrated benefit from alpelisib for the treatment of advanced ER+ breast cancers harboring PIK3CA mutations in the hotspots of exons 7, 9, and 20. However, 20% of PIK3CA mutations occur in non-hotspot regions. A recent article demonstrated that patients with cancers bearing non-hotspot PIK3CA mutations also derived benefit from alpelisib, which will inform clinical decision-making moving forward. See related article by Rugo et al., p. 1056.

Tumour, whole-blood, plasma and tissue concentrations of metformin in lung cancer patients

AIM

Metformin is used for the management of type 2 diabetes mellitus (T2DM) and is being tested clinically as an anticancer agent. Metformin concentrations safely achievable in human solid tissues including tumours are unknown. This study was designed to determine metformin concentration in tissue compartments as a function of dose to inform rational dosing in preclinical models and interpretation of clinical results."

METHODS

Subjects with solid tumours to be treated by resection and either (A) willingness to take metformin for 7-10 days before surgery or (B) taking metformin for T2DM were eligible. Whole blood, plasma, tumour, tumour-adjacent uninvolved tissue and subcutaneous adipose tissue were obtained for liquid chromatography with tandem mass spectrometry to measure metformin concentrations.

RESULTS

All subjects had primary lung tumours. Metformin dose was significantly correlated with drug concentrations in all tissues analysed. Intersubject metformin concentrations varied by over two orders of magnitude. Metformin concentrations were significantly higher in tumour tissues and lower in adipose tissues compared to other tissues. Concentrations in blood and plasma were significantly correlated with concentrations in solid tissues.

CONCLUSION

Metformin accumulates in cellular compartments. Concentrations observed in plasma, blood, lung and tumour tissues in subjects treated with US Food and Drug Administration-approved doses for T2DM are lower than those typically used in tissue culture studies. However, such tissue concentrations are in line with those found within cultured cells treated with supra-pharmacological doses of metformin. Given the large intersubject variability in metformin concentrations, it is imperative to determine whether there is an association between tissue metformin concentration and anticancer activity in humans.

The role of cancer cell bioenergetics in dormancy and drug resistance

While anti-cancer drug treatments are often effective for the clinical management of cancer, these treatments frequently leave behind drug-tolerant persister cancer cells that can ultimately give rise to recurrent disease. Such persistent cancer cells can lie dormant for extended periods of time, going undetected by conventional clinical means. Understanding the mechanisms that such dormant cancer cells use to survive, and the mechanisms that drive emergence from dormancy, is critical to the development of improved therapeutic strategies to prevent and manage disease recurrence. Cancer cells often exhibit metabolic alterations compared to their non-transformed counterparts. An emerging body of evidence supports the notion that dormant cancer cells also have unique metabolic adaptations that may offer therapeutically targetable vulnerabilities. Herein, we review mechanisms through which cancer cells metabolically adapt to persist during drug treatments and develop drug resistance. We also highlight emerging therapeutic strategies to target dormant cancer cells via their metabolic features.

Abstract P4-02-12: Oxidative phosphorylation and NRF2 activation mediate resistance to estrogen deprivation in ER+ breast cancer

Despite the success of adjuvant endocrine therapy in the treatment of ER+ breast cancer, recurrences occur in ~1/3 of patients with most becoming metastatic and ultimately fatal. Recurrence can be traced to drug-tolerant persister cancer cells (DTPs) that can survive years of endocrine therapy. Targeting DTPs is an attractive therapeutic approach to prevent cancer recurrence, but it has been hampered by a lack of understanding of DTP biology. We observed that subpopulations of ER+ breast cancer cells persist when challenged with estrogen deprivation and exhibit slower cell cycling, which is reversed when estrogen is restored. A CRISPR/Cas9 knock-out screen in MCF-7 DTPs identified genes that modulate fitness and survival during estrogen deprivation. Pathways analysis of the genes most essential for estrogen-independent growth revealed that mitochondrial function and oxidative phosphorylation (OXPHOS) was a top enriched pathway. Validation experiments revealed that knock-out of Mitochondrial Complex I genes conferred sensitivity to estrogen deprivation. We measured the extent of metabolic reprogramming in ER+ breast cancer cells induced by estrogen deprivation. A global proteomics study revealed widespread changes in the abundance of proteins involved in metabolism; specifically, estrogen deprivation decreased levels of glycolytic proteins while maintaining high levels of Complex I and mitoribosome proteins. Following 3 weeks of estrogen deprivation, restoration of estrogen remediated metabolic reprogramming from estrogen deprivation with higher levels of glycolysis proteins and lower mitochondrial Complex I and mitoribosome proteins. MitoTracker dye staining for mitochondria revealed increased mitochondrial content in estrogen-deprived cells, reversed by estrogen restoration in both MCF-7 and T47D DTPs. Measurement of oxygen consumption and extracellular acidification rate by Seahorse assay confirmed a shift towards greater ATP productivity by mitochondria in the setting of estrogen deprivation. The therapeutic potential of targeting mitochondrial function in DTPs was tested with the Complex I inhibitor IACS-010759. Greater drug sensitivity occurred with longer periods of estrogen deprivation in DTPs, with increased cell death at 14 and 28 days of estrogen deprivation compared to cells without previous hormone deprivation. We postulated that increased mitochondrial oxidative phosphorylation subsequently increases reactive oxygen species and oxidative stress. Indeed, DTPs exhibited an anti-oxidant stress response driven by the transcription factor nuclear factor erythroid 2-related factor 2 (NRF2), a signature exhibited by ER+ tumors undergoing neoadjuvant endocrine therapy. Knock-down of NRF2 decreased survival in estrogen-deprived DTPs but not in estrogen-replete cells. The survival of NRF2-deficient DTPs was rescued by the antioxidant N-acetyl cysteine (NAC), affirming the role of an anti-oxidative stress response in preserving DTP survival. Decreased DTP survival was concomitant with an increase in ROS. These findings establish the scope of metabolic reprogramming in DTPs and offer Mitochondrial Complex I and NRF2 inhibition as novel therapeutic strategies for eradicating DTPs in ER+ breast cancer.

Citation Format: Steven Tau, Todd W. Miller. Oxidative phosphorylation and NRF2 activation mediate resistance to estrogen deprivation in ER+ breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-02-12.

Identification of Let-7f-5p as a novel biomarker of recurrence in non-muscle invasive bladder cancer

BACKGROUND

Among patients diagnosed with non-muscle invasive bladder cancer (NMIBC), 30% to 70% experience recurrences within 6 to 12 years of diagnosis. The need to screen for these events every 3 to 6 months and ultimately annually by cystoscopy makes bladder cancer one of the most expensive malignancies to manage.

OBJECTIVE

The purpose of this study was to identify reproducible prognostic microRNAs in resected non-muscle invasive bladder tumor tissue that are predictive of the recurrent tumor phenotype as potential biomarkers and molecular therapeutic targets.

METHODS

Two independent cohorts of NMIBC patients were analyzed using a biomarker discovery and validation approach, respectively.

RESULTS

miRNA Let-7f-5p showed the strongest association with recurrence across both cohorts. Let-7f-5p levels in urine and plasma were both found to be significantly correlated with levels in tumor tissue. We assessed the therapeutic potential of targeting Lin28, a negative regulator of Let-7f-5p, with small-molecule inhibitor C1632. Lin28 inhibition significantly increased levels of Let-7f-5p expression and led to significant inhibition of viability and migration of HTB-2 cells.

CONCLUSIONS

We have identified Let-7f-5p as a miRNA biomarker of recurrence in NMIBC tumors. We further demonstrate that targeting Lin28, a negative regulator of Let-7f-5p, represents a novel potential therapeutic opportunity in NMIBC.

Pan-Cancer Transcriptional Models Predicting Chemosensitivity in Human Tumors

MOTIVATION

Despite increasing understanding of the molecular characteristics of cancer, chemotherapy success rates remain low for many cancer types. Studies have attempted to identify patient and tumor characteristics that predict sensitivity or resistance to different types of conventional chemotherapies, yet a concise model that predicts chemosensitivity based on gene expression profiles across cancer types remains to be formulated. We attempted to generate pan-cancer models predictive of chemosensitivity and chemoresistance. Such models may increase the likelihood of identifying the type of chemotherapy most likely to be effective for a given patient based on the overall gene expression of their tumor.

RESULTS

Gene expression and drug sensitivity data from solid tumor cell lines were used to build predictive models for 11 individual chemotherapy drugs. Models were validated using datasets from solid tumors from patients. For all drug models, accuracy ranged from 0.81 to 0.93 when applied to all relevant cancer types in the testing dataset. When considering how well the models predicted chemosensitivity or chemoresistance within individual cancer types in the testing dataset, accuracy was as high as 0.98. Cell line-derived pan-cancer models were able to statistically significantly predict sensitivity in human tumors in some instances; for example, a pan-cancer model predicting sensitivity in patients with bladder cancer treated with cisplatin was able to significantly segregate sensitive and resistant patients based on recurrence-free survival times (P = .048) and in patients with pancreatic cancer treated with gemcitabine (P = .038). These models can predict chemosensitivity and chemoresistance across cancer types with clinically useful levels of accuracy.

Changes in Peripheral and Local Tumor Immunity after Neoadjuvant Chemotherapy Reshape Clinical Outcomes in Patients with Breast Cancer

PURPOSE

The recent approval of anti-programmed death-ligand 1 immunotherapy in combination with nab-paclitaxel for metastatic triple-negative breast cancer (TNBC) highlights the need to understand the role of chemotherapy in modulating the tumor immune microenvironment (TIME).

EXPERIMENTAL DESIGN

We examined immune-related gene expression patterns before and after neoadjuvant chemotherapy (NAC) in a series of 83 breast tumors, including 44 TNBCs, from patients with residual disease (RD). Changes in gene expression patterns in the TIME were tested for association with recurrence-free (RFS) and overall survival (OS). In addition, we sought to characterize the systemic effects of NAC through single-cell analysis (RNAseq and cytokine secretion) of programmed death-1-high (PD-1^HI) CD8⁺ peripheral T cells and examination of a cytolytic gene signature in whole blood.

RESULTS

In non-TNBC, no change in expression of any single gene was associated with RFS or OS, while in TNBC upregulation of multiple immune-related genes and gene sets were associated with improved long-term outcome. High cytotoxic T-cell signatures present in the peripheral blood of patients with breast cancer at surgery were associated with persistent disease and recurrence, suggesting active antitumor immunity that may indicate ongoing disease burden.

CONCLUSIONS

We have characterized the effects of NAC on the TIME, finding that TNBC is uniquely sensitive to the immunologic effects of NAC, and local increases in immune genes/sets are associated with improved outcomes. However, expression of cytotoxic genes in the peripheral blood, as opposed to the TIME, may be a minimally invasive biomarker of persistent micrometastatic disease ultimately leading to recurrence.

Abstract 4359: Rational development of novel treatment regimens to improve the efficacy of estrogen therapy in anti-estrogen-resistant ER+ breast cancer

We hypothesize that the viability of estrogen receptor-positive (ER+) breast cancer cells that acquire resistance to anti-estrogens can be controlled through oscillation of ER stimulation and inhibition. Although anti-estrogen therapy has been highly successful in treating ER+ breast cancer, approximately one third of patients experience recurrent disease and progressively develop resistance to all available anti-estrogen therapies. Paradoxically, treatment with estrogens can elicit anti-cancer effects in tumors with acquired resistance to anti-estrogens. However, the clinical use of estrogen therapy is limited by the lack of a known mechanism of action and a predictive marker of response. In this study, we delineate the context-dependent effects of ER overexpression and use these results to rationally develop novel estrogen therapy treatment regimens to improve tumor response. Using cellular models of ER+ breast cancer, we demonstrate that ER overexpression is a mechanism of resistance to estrogen deprivation, resulting in estrogen-independent ER transcriptional activity. However, ER overexpression is also required for therapeutic response to estrogen. Upon treatment with the endogenous estrogen 17b-estradiol, ER overexpression results in hyperactivation of ER transcriptional activity, DNA damage, and subsequent cell death. DNA damage is ER-dependent, and cell death can be abrogated by knockdown of ER. Additionally, the combination of estrogen therapy with poly (ADP-ribose) polymerase (PARP) inhibition enhances DNA damage and cell death. Using a patient-derived xenograft (PDX) model of therapeutic response to 17b-estradiol, we serially profiled ER expression and transcriptional activity during treatment response and the subsequent development of treatment resistance. Tumors from mice treated with 17b-estradiol exhibit a phenotypic shift between sensitivity to estrogen therapy and estrogen deprivation therapy over the course of treatment. Based on these results, we developed novel treatment schedules and regimens to improve the anti-tumor effects of estrogen therapy. We demonstrate that short-term treatment with 17b-estradiol followed by estrogen deprivation can improve long-term anti-tumor effects, as compared to continuous treatment with 17b-estradiol. In conclusion, we demonstrate the differential effects of ER overexpression in estrogen-depleted vs. estrogen-replete environments, and translate this mechanistic understanding into novel treatment regimens to improve response to estrogen therapy.

Citation Format: Nicole A. Traphagen, Amanda Jiang, Sarah R. Hosford, Todd W. Miller. Rational development of novel treatment regimens to improve the efficacy of estrogen therapy in anti-estrogen-resistant ER+ breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4359.

AMPK Activation by Metformin Promotes Survival of Dormant ER+ Breast Cancer Cells

PURPOSE

Despite adjuvant endocrine therapy for patients with estrogen receptor alpha (ER)-positive breast cancer, dormant residual disease can persist for years and eventually cause tumor recurrence. We sought to deduce mechanisms underlying the persistence of dormant cancer cells to identify therapeutic strategies.

EXPERIMENTAL DESIGN

Mimicking the aromatase inhibitor-induced depletion of estrogen levels used to treat patients, we developed preclinical models of dormancy in ER⁺ breast cancer induced by estrogen withdrawal in mice. We analyzed tumor xenografts and cultured cancer cells for molecular and cellular responses to estrogen withdrawal and drug treatments. Publicly available clinical breast tumor gene expression datasets were analyzed for responses to neoadjuvant endocrine therapy.

RESULTS

Dormant breast cancer cells exhibited upregulated 5' adenosine monophosphate-activated protein kinase (AMPK) levels and activity, and upregulated fatty acid oxidation. While the antidiabetes AMPK-activating drug metformin slowed the estrogen-driven growth of cells and tumors, metformin promoted the persistence of estrogen-deprived cells and tumors through increased mitochondrial respiration driven by fatty acid oxidation. Pharmacologic or genetic inhibition of AMPK or fatty acid oxidation promoted clearance of dormant residual disease, while dietary fat increased tumor cell survival.

CONCLUSIONS

AMPK has context-dependent effects in cancer, cautioning against the widespread use of an AMPK activator across disease settings. The development of therapeutics targeting fat metabolism is warranted in ER⁺ breast cancer.

Abstract P3-08-15: Immunologic correlates of long-term outcome in the residual disease of triple-negative breast cancer after neoadjuvant chemotherapy

The recent approval of anti-PD-L1 immunotherapy in combination with nAB-paclitaxel for metastatic triple-negative breast cancer (TNBC) highlights the need to understand the role of chemotherapy in modulating the tumor-immune microenvironment (TIME). Patients with TNBC are routinely treated with neoadjuvant chemotherapy (NAC). Stromal tumor-infiltrating lymphocytes (sTILs) in the pre-treatment diagnostic biopsy are predictive of pathologic complete response (pCR). In patients with residual disease (RD) at surgery, sTILs confer good prognosis. However, the effect of chemotherapy on sTILs and how it influences the TIME are poorly understood. We examined immune-gene expression patterns before and after NAC in a series of 83 breast tumors, including 44 TNBCs, from patients with RD. sTILs were enumerated by standardized guidelines. Gene expression patterns were tested for association with recurrence-free (RFS) and overall survival (OS). T cell receptor sequencing (TCRseq) was performed on a subset (n=15) of tumors. In 4 patients undergoing NAC, PD-1-high and -negative CD8+ peripheral blood mononuclear cells (PBMCs) were profiled using single-cell RNAseq and multiplexed cytokine secretion assays. Post-NAC sTILs (≥30%) were only predictive of outcome (RFS p=0.019; OS p=0.05) in TNBC patients, but not in non-TNBC patients (RFS p=0.28; OS p=0.78) confirming that the prognostic capacity of sTILs is confined to TNBC. Pre-NAC sTILs were not predictive of outcome in either group, likely due to exclusion of patients experiencing pCR. The change in sTILs during NAC did not prognosticate outcome in TNBC, suggesting that in the post-NAC setting, only the most proximal measurement of sTILs is meaningful. However, these results did suggest that NAC alters the TIME. To examine the interplay among NAC, the TIME, and clinical outcomes, we tested the change in expression of 770 immune-related genes during NAC in univariate cox-proportional hazards models. In non-TNBC, no change in expression of any single gene was associated with RFS or OS at a false-discovery rate (FDR) of 10%. In TNBC, individual changes in 12 genes and 204 genes were identified as associated with RFS and OS, respectively (FDR<10%). Interestingly, in nearly all cases, upregulation of these genes during NAC was associated with improved outcome, with only 1 and 15 genes being associated with poor RFS and OS, respectively. Collapsing genes to functional and cell-type specific signatures gave similar insights: T cell, NK cell, TNF-superfamily, and toll-like receptor signatures were highly prognostic. Surprisingly, NAC did not alter T cell clonality in TNBC. Thus, the immunologic impact of chemotherapy appears to be specific to TNBC and is primarily a beneficial effect but does not appear to appreciably expand the clonality of tumor-infiltrating T cells. Using fresh PD-1HI CD8+ T cells isolated from PBMCs of patients undergoing NAC, we detected a significant increase in cytolytic and inflammatory cytokines secreted in 2 TNBC patients after chemotherapy, but not in 2 non-TNBC patients, which was particularly dramatic in one TNBC patient who experienced a pCR. A further characterization of PD-1HI CD8+ cells by single-cell RNAseq identified a sizeable expansion of cytolytic gene (granulysin, Ksp37, granzyme) expressing cells in the TNBC patient with pCR compared to the TNBC patient with RD. In conclusion, we have characterized the effects of NAC on the TIME. TNBC appears to be uniquely sensitive to the immunologic effects of NAC, and most of these effects are primarily stimulatory, rather than repressive. Finally, these changes can be observed in the PD-1HI CD8+ peripheral T cell compartment and appeared to co-occur with pCR.

Citation Format: Justin M Balko, Mellissa Nixon, Paula I Gonzalez-Ericsson, Mark A Pilkinton, Wyatt J McDonnell, Violeta Sanchez, Susan R Opalenik, Sherene Loi, Brent Rexer, Vandana Abramson, Valerie Jansen, Simon Mallal, Jonathan D Marotti, Kevin Shee, Todd W Miller, Melinda E Sanders, Ingrid A Mayer, Roberto Salgado. Immunologic correlates of long-term outcome in the residual disease of triple-negative breast cancer after neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-08-15.

Endocytosis of very low-density lipoproteins: an unexpected mechanism for lipid acquisition by breast cancer cells

We previously described the expression of CD36 and LPL by breast cancer (BC) cells and tissues and the growth-promoting effect of VLDL observed only in the presence of LPL. We now report a model in which LPL is bound to a heparan sulfate proteoglycan motif on the BC cell surface and acts in concert with the VLDL receptor to internalize VLDLs via receptor-mediated endocytosis. We also demonstrate that gene-expression programs for lipid synthesis versus uptake respond robustly to triglyceride-rich lipoprotein availability. The literature emphasizes de novo FA synthesis and exogenous free FA uptake using CD36 as paramount mechanisms for lipid acquisition by cancer cells. We find that the uptake of intact lipoproteins is also an important mechanism for lipid acquisition and that the relative reliance on lipid synthesis versus uptake varies among BC cell lines and in response to VLDL availability. This metabolic plasticity has important implications for the development of therapies aimed at the lipid dependence of many types of cancer, in that the inhibition of FA synthesis may elicit compensatory upregulation of lipid uptake. Moreover, the mechanism that we have elucidated provides a direct connection between dietary fat and tumor biology.-.

Statistical determination of synergy based on Bliss definition of drugs independence

Although synergy is a pillar of modern pharmacology, toxicology, and medicine, there is no consensus on its definition despite its nearly one hundred-year history. Moreover, methods for statistical determination of synergy that account for variation of response to treatment are underdeveloped and if exist are reduced to the traditional t-test, but do not comply with the normal distribution assumption. We offer statistical models for estimation of synergy using an established definition of Bliss drugs’ independence. Although Bliss definition is well-known, it remains a theoretical concept and has never been applied for statistical determination of synergy with various forms of treatment outcome. We rigorously and consistently extend the Bliss definition to detect statistically significant synergy under various designs: (1) in vitro, when the outcome of a cell culture experiment with replicates is the proportion of surviving cells for a single dose or multiple doses, (2) dose-response methodology, (3) in vivo studies in organisms, when the outcome is a longitudinal measurement such as tumor volume, and (4) clinical studies, when the outcome of treatment is measured by survival. For each design, we developed a specific statistical model and demonstrated how to test for independence, synergy, and antagonism, and compute the associated p-value.

A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition

PURPOSE

We hypothesized that integrated analysis of cancer types from different lineages would reveal novel molecularly defined subgroups with unique therapeutic vulnerabilities. On the basis of the molecular similarities between subgroups of breast and ovarian cancers, we analyzed these cancers as a single cohort to test our hypothesis.

EXPERIMENTAL DESIGN

Identification of transcriptional subgroups of cancers and drug sensitivity analyses were performed using mined data. Cell line sensitivity to Hsp90 inhibitors (Hsp90i) was tested in vitro. The ability of a transcriptional signature to predict Hsp90i sensitivity was validated using cell lines, and cell line- and patient-derived xenograft (PDX) models. Mechanisms of Hsp90i sensitivity were uncovered using immunoblot and RNAi.

RESULTS

Transcriptomic analyses of breast and ovarian cancer cell lines uncovered two mixed subgroups comprised primarily of triple-negative breast and multiple ovarian cancer subtypes. Drug sensitivity analyses revealed that cells of one mixed subgroup are significantly more sensitive to Hsp90i compared with cells from all other cancer lineages evaluated. A gene expression classifier was generated that predicted Hsp90i sensitivity in vitro, and in cell line- and PDXs. Cells from the Hsp90i-sensitive subgroup underwent apoptosis mediated by Hsp90i-induced upregulation of the proapoptotic proteins Bim and PUMA.

CONCLUSIONS

Our findings identify Hsp90i as a potential therapeutic strategy for a transcriptionally defined subgroup of ovarian and breast cancers. This study demonstrates that gene expression profiles may be useful to identify therapeutic vulnerabilities in tumor types with limited targetable genetic alterations, and to identify molecularly definable cancer subgroups that transcend lineage.

Tumor pharmacokinetics and pharmacodynamics of the CDK4/6 inhibitor ribociclib in patients with recurrent glioblastoma

INTRODUCTION

We conducted a phase Ib study (NCT02345824) to determine whether ribociclib, an inhibitor of cyclin-dependent kinases 4 and 6 (CDK4/6), penetrates tumor tissue and modulates downstream signaling pathways including retinoblastoma protein (Rb) in patients with recurrent glioblastoma (GBM).

METHODS

Study participants received ribociclib (600 mg QD) for 8-21 days before surgical resection of their recurrent GBM. Total and unbound concentrations of ribociclib were measured in samples of tumor tissue, plasma, and cerebrospinal fluid (CSF). We analyzed tumor specimens obtained from the first (initial/pre-study) and second (recurrent/on-study) surgery by immunohistochemistry for Rb status and downstream signaling of CDK4/6 inhibition. Participants with Rb-positive recurrent tumors continued ribociclib treatment on a 21-day-on, 7-day-off schedule after surgery, and were monitored for toxicity and disease progression.

RESULTS

Three participants with recurrent Rb-positive GBM participated in this study. Mean unbound (pharmacologically active) ribociclib concentrations in plasma, CSF, MRI-enhancing, MRI-non-enhancing, and tumor core regions were 0.337 μM, 0.632 μM, 1.242 nmol/g, 0.484 nmol/g, and 1.526 nmol/g, respectively, which exceeded the in vitro IC₅₀ (0.04 μM) for inhibition of CDK4/6 in cell-free assay. Modulation of pharmacodynamic markers of ribociclib CDK 4/6 inhibition in tumor tissues were inconsistent between study participants. No participants experienced serious adverse events, but all experienced early disease progression.

CONCLUSIONS

This study suggests that ribociclib penetrated recurrent GBM tissue at concentrations predicted to be therapeutically beneficial. Our study was unable to demonstrate tumor pharmacodynamic correlates of drug activity. Although well tolerated, ribociclib monotherapy seemed ineffective for the treatment of recurrent GBM.

Estrogen therapy induces an unfolded protein response to drive cell death in ER+ breast cancer

Estrogens have been shown to elicit anticancer effects against estrogen receptor α (ER)-positive breast cancer. We sought to determine the mechanism underlying the therapeutic response. Response to 17β-estradiol was assessed in ER+ breast cancer models with resistance to estrogen deprivation: WHIM16 patient-derived xenografts, C7-2-HI and C4-HI murine mammary adenocarcinomas, and long-term estrogen-deprived MCF-7 cells. As another means to reactivate ER, the anti-estrogen fulvestrant was withdrawn from fulvestrant-resistant MCF-7 cells. Transcriptional, growth, apoptosis, and molecular alterations in response to ER reactivation were measured. 17β-estradiol treatment and fulvestrant withdrawal induced transcriptional activation of ER, and cells adapted to estrogen deprivation or fulvestrant were hypersensitive to 17β-estradiol. ER transcriptional response was followed by an unfolded protein response and apoptosis. Such apoptosis was dependent upon the unfolded protein response, p53, and JNK signaling. Anticancer effects were most pronounced in models exhibiting genomic amplification of the gene encoding ER (ESR1), suggesting that engagement of ER at high levels is cytotoxic. These data indicate that long-term adaptation to estrogen deprivation or ER inhibition alters sensitivity to ER reactivation. In such adapted cells, 17β-estradiol treatment and anti-estrogen withdrawal hyperactivate ER, which drives an unfolded protein response and subsequent growth inhibition and apoptosis. 17β-estradiol treatment should be considered as a therapeutic option for anti-estrogen-resistant disease, particularly in patients with tumors harboring ESR1 amplification or ER overexpression. Furthermore, therapeutic strategies that enhance an unfolded protein response may increase the therapeutic effects of ER reactivation.

Abstract P5-04-08: Timing provides context for the paradoxical effects of AMPK activation in ER+ breast cancer: Suppressing growing tumors, but promoting dormant tumor cell survival and recurrence

Precision oncology requires delivering the right drug to the right patient at the right time, but “time” is rarely studied preclinically before a drug enters a particular clinical setting. Despite showing efficacy against recurrent/metastatic solid tumors, drugs sometimes fail to prevent tumor recurrence when given (neo)adjuvantly. The biology and microenvironments of overt tumors likely differ substantially from dormant cancer cells. The development of preclinical models to investigate clinically dormant disease will increase understanding of residual tumor cell biology and enable the development of therapeutics for rational adjuvant trials.

Despite treatment with adjuvant anti-estrogen therapies, ˜30% of patients with ER+ breast cancer (BC) experience recurrence. In contrast to other BC subtypes, ER+ relapses occur late, often appearing years to decades after initial diagnosis and treatment. This delay suggests that ER+ BC cells can undergo extended periods of clinical dormancy. We developed novel, clinically relevant xenograft models of dormancy in ER+ BC. Low systemic levels of estrogens in mice can be further suppressed by ovariectomy, mimicking the effects of aromatase inhibitor (AI)-induced estrogen deprivation (ED) therapy. In ovariectomized mice, luciferase-labeled MCF-7, HCC-1428, HCC-1500, and MDA-MB-415 cells, as well as the HCI-017 PDX model, formed palpable orthotopic tumors upon 17b-estradiol supplementation. ED induced rapid tumor regression and decreased bioluminescent signal. However, a small proportion of ER+ BC cells survived ED for >1 year in a clinically dormant, growth-suppressed state. This residual cell population stabilized after ˜90 days of ED, as evidenced by stabilization of bioluminescent signal. Transcriptional and immunohistochemical analyses revealed significant upregulation of AMP-activated protein kinase (AMPK)-alpha-2 levels and activity in clinically dormant tumor cells compared to estrogen-driven or acutely ED xenografts. Dormant tumor cells were dependent upon AMPK activity for survival, as short-term pharmacologic inhibition of AMPK reduced residual bioluminescent signal.

Metformin is an AMPK-activating drug approved for the treatment of diabetes. Metformin is currently being tested as an anti-cancer agent in many clinical trials at various points in the disease progression of diverse cancer types. In our models of clinically dormant ER+ BC, AMPK activation via metformin slowed ED-induced tumor regression, promoted residual tumor cell survival, and caused earlier tumor regrowth. In vitro studies indicated that metformin promotes cell survival during ED by enhancing fatty acid β-oxidation. Conversely, metformin treatment slowed estrogen-driven tumor growth, in agreement with prior observations that metformin slows growth of various tumor subtypes. These findings suggest that AMPK activation may be efficacious against growing tumors, but deleterious when used in combination with drugs that suppress tumor growth and induce regression. More broadly, this work highlights the issue that the time in a disease course needs to be considered when testing potential anti-cancer agents such as AMPK modulators.

Citation Format: Miller TW, Hampsch RA, McCleery CF, Wells JD, Fields JL, Dillon LM, Shee K. Timing provides context for the paradoxical effects of AMPK activation in ER+ breast cancer: Suppressing growing tumors, but promoting dormant tumor cell survival and recurrence [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 P5-04-08.

Abstract P3-11-15: Development of pan-cancer transcriptional signatures that predict chemosensitivity

Background: Despite the increasing understanding of the molecular characteristics of cancer, chemotherapy success rates remain low for many cancer types. Studies have attempted to identify patient and tumor characteristics that predict sensitivity or resistance to different types of conventional chemotherapies, yet a concise model that predicts chemosensitivity based on gene expression signatures across cancer types remains to be formulated. We attempted to generate a pan-cancer chemosensitivity predictive model using publicly available data from multiple sources. Such a model may increase the likelihood of identifying the type of chemotherapy most likely to succeed for a given patient based on the gene expression signature of their tumor.

Methods: Data used to build the predictive model were obtained from the Genomics of Drug Sensitivity in Cancer (GDSC) database, consisting of gene expression profiles from 962 cancer cell lines via RNA sequencing (RNA-seq) and drug sensitivity profiles reported as ln(IC50). Predictive gene signatures were generated using a cross-validated generalized linear model (leave one out cross-validation) using elasticnet penalization parameters. Models were generated for each individual drug tested by the GDSC cohort, as well as different classes of chemotherapeutics (platinum agents, topoisomerase inhibitors, mustard agents, antibiotics and anti-fungals, anti-metabolites, and taxanes). Accuracy of the models was determined using normalized mean square error (nRMSE). Models were then validated using publicly available data from Cancer Cell Line Encyclopedia (CCLE), NCI-60, and the Patient-Derived Xenograft (PDX) Clinical Trial (PCT) database. Models were further validated using human tumor datasets available via the Gene Expression Omnibus (GEO). As the training data used to generate the models were from RNA-seq, and some of the testing and validation data were generated using microarray technology, feature-specific quantile normalization was used to enable cross-platform analyses.

Results: For most single-drug gene signatures, accuracy measured by nRMSE ranged from 0.10-0.20, which suggests that for any given model the root mean squared error is 10-20% of the range of actual ln(IC50) in the tested data. Chemotherapy class-level models yielded slightly less accuracy, with nRMSE ranging from 0.15-0.25 for most classes. When considering how well the models predicted chemosensitivity within cancer types, accuracy was improved in some cancer types (e.g., lung cancer and head and neck cancer), with more heterogeneous cancer types (e.g., breast cancer) giving less accuracy.

Conclusions: Our results show that the models generated can predict chemosensitivity across cancer types with clinical useful levels of accuracy, with some cancer types resulting in a high rate of accuracy across several classes of chemotherapy. The inclusion of future datasets, particularly from those cancer types in which chemosensitivity has been difficult to predict, may provide opportunities to strengthen model accuracy as well as decrease the numbers of genes needed to assess chemosensitivity.

Citation Format: Wells JD, Miller TW. Development of pan-cancer transcriptional signatures that predict chemosensitivity [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 P3-11-15.

Abstract P5-04-15: Enhancing response to estrogen therapy in ER+ breast cancer with novel scheduling and dosing regimens

Estrogen therapy was historically used as a standard breast cancer treatment from the 1940s until the introduction of tamoxifen in the 1970s. Although a clinical trial directly comparing the synthetic estrogen diethylstilbestrol and tamoxifen in post-menopausal patients demonstrated no significant difference in progression-free survival between the two, tamoxifen showed a more favorable toxicity profile and estrogens fell out of favor. However, 1 in 3 patients eventually recur and develop advanced disease that is resistant to all available anti-estrogens. Estrogen therapy is being resurrected in clinical trials for advanced, heavily pre-treated ER+ breast cancer. These studies demonstrate that ˜30% of patients respond to treatment with estrogens. However, little pharmacologic work has been done to optimize the schedule and method of hormone delivery.

Estrogen therapies such as 17b-estradiol (E2) and ethinylestradiol are typically administered orally several times daily. Toxicities have been observed with such regimens, and there is no evidence that the maximally efficacious doses or schedules are being used clinically. We used two in vivo tumor models to preclinically define the optimal dosing schedule and method of E2 delivery that maximizes response. WHIM16 patient-derived ER+ breast cancer xenografts (PDX) and C7-2-HI ER+ murine mammary adenocarcinoma allografts both grow in ovariectomized (“estrogen-deprived”) mice, and regress in response to E2 treatment.

We tested an array of E2 doses and delivery methods [e.g., oral gavage, subcutaneous (s.c.) injection, s.c. pellet, and s.c. osmotic pump] in mice bearing C7-2-HI and WHIM16 tumors to determine optimal methods for inducing maximal and sustained tumor regression. We found that oral dosing is less effective at inducing tumor regression than other methods. However, intermittent high-dose estrogen given as 1 mg of E2 orally every 14 days both prevented tumor growth and did not result in toxicity, suggesting that intermittent dosing should be further examined as a means to increase therapeutic index.

Although estrogen therapy induces clinical response in a subset of patients with ER+ disease, nearly all patients eventually experience disease progression and develop resistance to the therapeutic effects of estrogen. Clinical observations suggest that some cancers that progressed on estrogen therapy are re-sensitized to anti-estrogen treatment. We therefore examined whether resistance to estrogen therapy could be prevented by preemptively cycling estrogen therapy with estrogen deprivation in mice. Discontinuous scheduling of E2 and estrogen deprivation was tested with either 1 or 4 weeks on E2 treatment, followed by estrogen deprivation until tumors re-grew to baseline volume, then E2 treatment was repeated. In the WHIM16 tumor model, the 4-week E2 treatment cycle nearly doubled time to recurrence compared to mice treated continuously with E2. Surprisingly, there was no difference in time to recurrence between groups treated with the 1-week cycle vs. continuous E2. However, tumors that re-grew on continuous E2 were sensitized to estrogen deprivation. These collective findings warrant clinical testing of schedules of alternating estrogen and anti-estrogen therapies.

Citation Format: Traphagen NA, Hosford SR, Miller TW. Enhancing response to estrogen therapy in ER+ breast cancer with novel scheduling and dosing regimens [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 P5-04-15.

Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier

Background

BRCA1-mutated cancers exhibit deficient homologous recombination (HR) DNA repair, resulting in extensive copy number alterations and genome instability. HR deficiency can also arise in tumors without a BRCA1 mutation. Compared with other breast tumors, HR-deficient, BRCA1-like tumors exhibit worse prognosis but selective chemotherapeutic sensitivity. Presently, patients with triple negative breast cancer (TNBC) who do not respond to hormone endocrine-targeting therapy are given cytotoxic chemotherapy. However, more recent evidence showed a similar genomic profile between BRCA1-deficient TNBCs and hormone-receptor-positive tumors. Characterization of the somatic alterations of BRCA1-like hormone-receptor-positive breast tumors as a group, which is currently lacking, can potentially help develop biomarkers for identifying additional patients who might respond to chemotherapy.

Methods

We retrained and validated a copy-number-based support vector machine (SVM) classifier to identify HR-deficient, BRCA1-like breast tumors. We applied this classifier to The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) breast tumors. We assessed mutational profiles and proliferative capacity by covariate-adjusted linear models and identified differentially methylated regions using DMRcate in BRCA1-like hormone-receptor-positive tumors.

Results

Of the breast tumors in TCGA and METABRIC, 22% (651/2925) were BRCA1-like. Stratifying on hormone-receptor status, 13% (302/2405) receptor-positive and 69% (288/417) triple-negative tumors were BRCA1-like. Among the hormone-receptor-positive subgroup, BRCA1-like tumors showed significantly increased mutational burden and proliferative capacity (both P < 0.05). Genome-scale DNA methylation analysis of BRCA1-like tumors identified 202 differentially methylated gene regions, including hypermethylated BRCA1. Individually significant CpGs were enriched for enhancer regions (P < 0.05). The hypermethylated gene sets were enriched for DNA and chromatin conformation (all Bonferroni P < 0.05).

Conclusions

To provide insights into alternative classification and potential therapeutic targeting strategies of BRCA1-like hormone-receptor-positive tumors we developed and applied a novel copy number classifier to identify BRCA1-like hormone-receptor-positive tumors and their characteristic somatic alteration profiles.

Electronic supplementary material

The online version of this article (10.1186/s13058-018-1090-z) contains supplementary material, which is available to authorized users.

Ductal Carcinoma in Situ Biomarkers in a Precision Medicine Era: Current and Future Molecular-Based Testing

Historically, ductal carcinoma in situ (DCIS) of the breast has been managed aggressively with surgery and radiotherapy because of a risk of progression to invasive ductal carcinoma. However, this treatment paradigm has been challenged by overtreatment concerns and evidence that suggests that DCIS can be stratified according to risk of recurrence or risk of progression to invasive disease. Traditional methods of risk stratification include histologic grade and hormone receptor status. Recent technological advancements have enabled an era of precision medicine, where DCIS can be molecularly analyzed by tools, such as next-generation DNA and RNA sequencing, to identify molecular biomarkers for risk stratification. These findings have led to the development of tools such as the Oncotype DX Breast DCIS Score, a gene expression-based assay with the potential to prevent overtreatment in low-risk disease.

Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER+ breast cancer

Despite the success of approved systemic therapies for estrogen receptor α (ER)-positive breast cancer, drug resistance remains common. We hypothesized that secreted factors from the human tumor microenvironment could modulate drug resistance. We previously screened a library of 297 recombinant-secreted microenvironmental proteins for the ability to confer resistance to the anti-estrogen fulvestrant in 2 ER⁺ breast cancer cell lines. Herein, we considered whether factors that enhanced drug sensitivity could be repurposed as therapeutics and provide leads for drug development. Screening data revealed bone morphogenic protein (BMP)4 as a factor that inhibited cell growth and synergized with approved anti-estrogens and cyclin-dependent kinase 4/6 inhibitors (CDK4/6_i). BMP4-mediated growth inhibition was dependent on type I receptor activin receptor-like kinase (ALK)3-dependent phosphorylation (P) of mothers against decapentaplegic homolog (SMAD/P-SMAD)1 and 5, which could be reversed by BMP receptor inhibitors and ALK3 knockdown. The primary effect of BMP4 on cell fate was cell-cycle arrest, in which RNA sequencing, immunoblot analysis, and RNA interference revealed to be dependent on p21^WAF1/Cip1 upregulation. BMP4 also enhanced sensitivity to approved inhibitors of mammalian target of rapamycin complex 1 and CDK4/6 via ALK3-mediated P-SMAD1/5 and p21 upregulation in anti-estrogen-resistant cells. Patients bearing primary ER⁺ breast tumors, exhibiting a transcriptomic signature of BMP4 signaling, had improved disease outcome following adjuvant treatment with anti-estrogen therapy, independently of age, tumor grade, and tumor stage. Furthermore, a transcriptomic signature of BMP4 signaling was predictive of an improved biologic response to the CDK4/6_i palbociclib, in combination with an aromatase inhibitor in primary tumors. These findings highlight BMP4 and its downstream pathway activation as a therapeutic opportunity in ER⁺ breast cancer.-Shee, K., Jiang, A., Varn, F. S., Liu, S., Traphagen, N. A., Owens, P., Ma, C. X., Hoog, J., Cheng, C., Golub, T. R., Straussman, R., Miller, T. W. Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER⁺ breast cancer.

Abstract PD4-08: A microenvironment secretome screen reveals FGF2 as a mediator of resistance to anti-estrogens and PI3K/mTOR pathway inhibitors in ER+ breast cancer

Despite the clinical success of anti-estrogen therapies, phosphatidylinositol 3-kinase inhibitors (PI3Ki), and mechanistic target of rapamycin complex I inhibitors (mTORC1i) for the treatment of patients with ER+ breast cancer, disease recurrence and progression are common. We found that a tumor transcriptional profile reflecting high stromal fibroblast content was associated with poor outcome in 3 cohorts of patients with ER+ breast cancer. We hypothesized that individual factors in the tumor microenvironment (TME) significantly contribute to drug resistance.

To test this hypothesis, we screened 297 recombinant secreted proteins for ability to confer resistance to the anti-estrogen fulvestrant in MCF-7 and T47D ER+ breast cancer cells. Screen results were validated, and expansion screening included the anti-estrogen tamoxifen, the PI3Ki pictilisib, and the mTORC1i everolimus in 4 cell lines. To identify hits are most likely to be relevant to ER+ breast cancer, a bioinformatics filter was developed utilizing gene and protein expression in human tissues relevant to the TMEs of ER+ breast cancer. After filtering, the top screening hit was fibroblast growth factor 2 (FGF2), which confers resistance to anti-estrogens, PI3Ki, and mTORC1i, and is highly expressed in tissues and cell types associated with ER+ breast cancer. FGF2 did not rescue cells from the CDK4/6i palbociclib or the DNA-damaging agent doxorubicin, demonstrating pathway selectivity in the rescue phenotype. FGF2 rescued cells from anti-estrogen-, PI3Ki-, and mTORC1i-induced apoptosis and cell cycle arrest via activation of FGFR signaling through FRS2a, MEK1/2, ERK1/2, and downstream upregulation of cyclin D1 and degradation of Bim. FGF2-mediated anti-cancer effects were abrogated by co-treatment with the FGF2-neutralizing antibody GAL-F2, the pan-FGFR inhibitor PD-173074, the MEK inhibitor trametinib, or palbociclib. Cell cycle- and apoptosis-specific effects of FGF2 were abrogated by RNAi targeting cyclin D1 and Bim, respectively.

We generated a transcriptional signature of FGF2 response by RNA-seq of fulvestrant-treated MCF-7 and T47D cells treated +/- FGF2. In 3 cohorts of patients with ER+ breast cancer, a signature of FGF2 signaling was significantly associated with poor prognosis and predictive of anti-estrogen resistance, including in a multivariate analysis including age, tumor grade, tumor stage, and FGFR amplification status. Finally, the therapeutic potential of targeting FGF2 was confirmed in 3 mouse models of ER+ breast cancer: 1) FGF2 rescue MCF-7 xenografts from fulvestrant; 2) GAL-F2 synergized with fulvestrant to suppress growth of 59-2-HI murine mammary adenocarcinomas that recruit FGF2-secreting stroma; 3) GAL-F2 synergized with fulvestrant to induce regression of HCI-003 patient-derived xenografts. Therapeutic effects coincided with increased tumor cell apoptosis and decreased proliferation, but not changes in tumor vasculature. These findings warrant consideration of FGF2 as a novel therapeutic target in ER+ breast cancer.

Citation Format: Shee K, Hinds JW, Yang W, Hampsch RA, Patel K, Varn FS, Cheng C, Jenkins NP, Kettenbach AN, Demidenko E, Owens P, Lanari C, Faber AC, Golub TR, Straussman R, Miller TW. A microenvironment secretome screen reveals FGF2 as a mediator of resistance to anti-estrogens and PI3K/mTOR pathway inhibitors in ER+ 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 PD4-08.

Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer

Tumor microenvironment (TME) cytokine screening revealed FGF2 as a clinically relevant mechanism of resistance to anti-estrogens, mTORC1 inhibition, and PI3K inhibition in ER+ breast cancer. Shee et al. highlight an underdeveloped aspect of precision oncology: treating patients according to their TME constitution.

Drug resistance to approved systemic therapies in estrogen receptor–positive (ER+) breast cancer remains common. We hypothesized that factors present in the human tumor microenvironment (TME) drive drug resistance. Screening of a library of recombinant secreted microenvironmental proteins revealed fibroblast growth factor 2 (FGF2) as a potent mediator of resistance to anti-estrogens, mTORC1 inhibition, and phosphatidylinositol 3-kinase inhibition in ER+ breast cancer. Phosphoproteomic analyses identified ERK1/2 as a major output of FGF2 signaling via FGF receptors (FGFRs), with consequent up-regulation of Cyclin D1 and down-regulation of Bim as mediators of drug resistance. FGF2-driven drug resistance in anti-estrogen–sensitive and –resistant models, including patient-derived xenografts, was reverted by neutralizing FGF2 or FGFRs. A transcriptomic signature of FGF2 signaling in primary tumors predicted shorter recurrence-free survival independently of age, grade, stage, and FGFR amplification status. These findings delineate FGF2 signaling as a ligand-based drug resistance mechanism and highlights an underdeveloped aspect of precision oncology: characterizing and treating patients according to their TME constitution.

Trailblazing Precision Oncology for Rare Tumor Subtypes

Molecular Tumor Boards seek to recommend therapeutics to patients based on varying levels of evidence linking specific genetic alterations to treatment response. This commentary highlights the study by Kato and colleagues, which reports the usage of precision medicine approaches in rare and ultra‐rare tumor subtypes, as well as the need to discover effective drugs for tumor subtypes without known targetable genetic alterations.

Estrogen receptor alpha drives mTORC1 inhibitor-induced feedback activation of PI3K/AKT in ER+ breast cancer

The mTORC1 inhibitor RAD001 (everolimus) is approved for treatment of recurrent/metastatic estrogen receptor (ER)-positive breast cancer in combination with the aromatase inhibitor (AI) exemestane. The benefits of A) continued anti-estrogen therapy for anti-estrogen-resistant disease in the context of mTORC1 inhibition, and B) adjuvant everolimus in combination with anti-estrogen therapy for early-stage disease are being tested clinically, but molecular rationale remains unclear. We hypothesized that mTORC1 inhibition activates the IGF-1R/InsR/IRS-1/2 axis in an ER-dependent manner to drive PI3K/AKT and promote cancer cell survival, implicating ER in survival signaling induced by mTORC1 inhibition. Anti-estrogen treatment synergized with RAD001 to inhibit ER+ breast cancer cell growth. Inhibition of ER, IGF-1R/InsR, or IRS-1/2 suppressed AKT activation induced by mTORC1 inhibition. RAD001 primed IGF-1R/InsR for activation, which was enhanced by ER signaling. Post-menopausal patients with early-stage ER+ breast cancer were treated presurgically +/- the AI letrozole. Viable tumor fragments from surgical specimens were treated with RAD001 and/or OSI-906 ex vivo; RAD001 increased AKT activation, which was abrogated by presurgical letrozole. Letrozole decreased IGF-1R and IRS-1/2 tumor levels. These data suggest that ER drives PI3K/AKT activation in response to mTORC1 inhibition, providing molecular rationale for therapeutic combinations of anti-estrogens and mTORC1 inhibitors in endocrine-sensitive disease.

Autophagy promotes escape from phosphatidylinositol 3-kinase inhibition in estrogen receptor-positive breast cancer

Hyperactivation of the PI3K pathway has been implicated in resistance to antiestrogen therapies in estrogen receptor α (ER)-positive breast cancer, prompting the development of therapeutic strategies to inhibit this pathway. Autophagy has tumor-promoting and -suppressing roles and has been broadly implicated in resistance to anticancer therapies, including antiestrogens. Chloroquine (CQ) is an antimalarial and amebicidal drug that inhibits autophagy in mammalian cells and human tumors. Herein, we observed that CQ inhibited proliferation and autophagy in ER⁺ breast cancer cells. PI3K inhibition with GDC-0941 (pictilisib) induced autophagy. Inhibition of autophagy using CQ or RNA interference potentiated PI3K inhibitor-induced apoptosis. Combined inhibition of PI3K and autophagy effectively induced mitochondrial membrane depolarization, which required the BH3-only proapoptotic proteins Bim and PUMA. Treatment with GDC-0941, CQ, or the combination, significantly suppressed the growth of ER⁺ breast cancer xenografts in mice. In an antiestrogen-resistant xenograft model, GDC-0941 synergized with CQ to provide partial, but durable, tumor regression. These findings warrant clinical evaluation of therapeutic strategies to target ER, PI3K, and autophagy for the treatment of ER⁺ breast cancer.-Yang, W., Hosford, S. R., Traphagen, N. A., Shee, K., Demidenko, E., Liu, S., Miller, T. W. Autophagy promotes escape from phosphatidylinositol 3-kinase inhibition in estrogen receptor-positive breast cancer.

Therapeutic sensitivity to Rac GTPase inhibition requires consequential suppression of mTORC1, AKT, and MEK signaling in breast cancer

Rac GTPases have oncogenic roles in cell growth, survival, and migration. We tested response to the Rac inhibitor EHT1864 in a panel of breast cancer cell lines. EHT1864-induced growth inhibition was associated with dual inhibition of the PI3K/AKT/mTORC1 and MEK/ERK pathways. Breast cancer cells harboring PIK3CA mutations or HER2 overexpression were most sensitive to Rac inhibition, suggesting that such oncogenic alterations link Rac activation with PI3K/AKT/mTORC1 and MEK/ERK signaling. Interestingly, EHT1864 decreased activation of the mTORC1 substrate p70S6K earlier than AKT inhibition, suggesting that Rac may activate mTORC1/p70S6K independently of AKT. Comparison of the growth-inhibitory profile of EHT1864 to 137 other anti-cancer drugs across 656 cancer cell lines revealed significant correlation with the p70S6K inhibitor PF-4708671. We confirmed that Rac complexes contain MEK1/2 and ERK1/2, but also contain p70S6K; these interactions were disrupted by EHT1864. Pharmacokinetic profiles revealed that EHT1864 was present in mouse plasma at concentrations effective in vitro for approximately 1 h after intraperitoneal administration. EHT1864 suppressed growth of HER2+ tumors, and enhanced response to anti-estrogen treatment in ER+ tumors. Further therapeutic development of Rac inhibitors for HER2+ and PIK3CA-mutant cancers is warranted.

Molecular matching and treatment strategies for lung cancer at Dartmouth-Hitchcock Medical Center: A three year review of a molecular tumor board

e20585

Background: Matching of actionable tumor mutations with targeted therapy has been shown to increase response rates and prolong survival in lung cancer patients. Drug development and trials targeting genetic alterations are expanding rapidly. We describe the role of a Molecular Tumor Board (MTB) in the design of molecularly informed treatment strategies in our lung cancer patient population. Methods: DNA from tumor specimens was sequenced to identify coding mutations using a 50-gene targeted next-generation sequencing panel (Ampliseq v2). Cases were evaluated by a multidisciplinary MTB that included medical oncologists, hematologists, molecular and anatomic pathologists, genetic counselors, and basic science researchers who suggested a course of treatment based on the patient’s molecular findings. Results: During a three-year period, 88 patients were presented to the MTB. Of these, 21 patients had lung cancer (23.9%). All patients lacked common (indicated for FDA approved drug) activating EGFR and ALK mutations. One patient was stage IIIb, all others were stage IV; 18 had previously received at least one prior line of therapy (range 0-5). Suggestions for treatment with a targeted therapy were made for 19 of 21 (90.5%) and four patients underwent treatment with a MTB-suggested targeted agent (21.1%); two as part of a clinical trial. One patient received targeted therapy for 27 months before his disease eventually progressed. Barriers to treatment with targeted therapy included: ineligibility for study (n = 2), lack of interest in study/distance to travel (n = 2), lack of disease progression (n = 2), death/hospice enrollment (n = 5), decision to treat with immunotherapy (n = 3), and unknown (n = 1). Conclusions: For the majority of lung cancer patients, the MTB was able to provide suggestions based on targetable genetic alterations. The largest barriers to treatment were death and hospice enrollment indicating that molecular testing and presentation to the MTB at earlier stages of disease may increase the number of patients who ultimately are eligible for treatment with a targeted agent.

Abstract PD2-01: Clinically dormant ER+ breast tumors exhibit AMPK activation

While adjuvant anti-estrogen therapy has shown immense clinical benefit for patients with estrogen receptor-positive (ER+) breast cancer, &gt;30% of patients experience cancer recurrence within 15 years of initial diagnosis. Anti-estrogen therapies inhibit ER activity either directly (tamoxifen, fulvestrant) or by reducing systemic estrogen levels (aromatase inhibitors, AIs). Extending adjuvant anti-estrogen therapy from 5 to 10 years further prevents recurrence; however, with both 5- and 10-year treatment regimens, a large proportion of patients who relapse do so after cessation of therapy (“late recurrence”). Additionally, disseminated tumor cells in bone marrow have been found after 4 years of adjuvant anti-estrogen therapy in “disease-free” patients. These data collectively indicate that anti-estrogens elicit clinical benefit as adjuvant therapies, in part, by maintaining a population of residual micrometastatic cancer cells in a “clinically dormant” state (i.e., undetectable by routine clinical methods). Understanding how such dormant cancer cells survive will enable the development of more effective adjuvant therapies.

We developed several luciferase-labeled xenograft models of ER+ breast cancer that recapitulate clinical dormancy in vivo. Low systemic levels of estrogen in mice can be further suppressed by ovariectomy, mimicking the effects of AI-induced estrogen deprivation seen in patients. In ovariectomized mice, palpable tumors form upon 17b-estradiol supplementation, but quickly regress upon estrogen withdrawal. While regressed tumors become non-palpable within 2 wk, a small proportion of cancer cells survive these estrogen-deprived conditions for &gt;4 months in a clinically dormant, growth-suppressed state. This estrogen deprivation-induced clinically dormant cell population retains tumorigenic potential, as 17b-estradiol retreatment induces tumor recurrence. RNA expression profiling revealed AMPK alpha 2 as one of the most highly expressed genes in clinically dormant residual tumor cells compared to acutely estrogen-withdrawn tumors. Increased AMPK kinase activity was confirmed through immunohistochemical analysis of phospho-ACC, and AMPK substrate.

AMPK activation using glucose deprivation or the anti-diabetes drug metformin promoted estrogen-independent survival and growth of ER+ breast cancer cells in vitro. Metformin treatment may also slow estrogen withdrawal-induced tumor regression and promote tumor cell survival in ER+ breast cancer xenografts. As a cellular energy sensor, AMPK has been shown to promote autophagy, a process linked with anti-estrogen resistance. Immunofluorescent staining of estrogen deprivation-induced clinically dormant residual tumor cells revealed decreased levels of the autophagy marker p62 compared to 17b-estradiol-driven tumors. Early data suggest that inhibition of autophagy with hydroxychloroquine abrogates cell survival conferred by metformin in estrogen-depleted conditions. Thus, AMPK may be promoting the survival of ER+ breast cancer cells in estrogen-deprived conditions by increasing autophagic flux. These data have implications for the interpretation of data from ongoing clinical studies testing metformin for the treatment of cancer.

Citation Format: Hampsch RA, Dillon LM, Miller TW. Clinically dormant ER+ breast tumors exhibit AMPK activation [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 PD2-01.

Abstract P1-07-04: Unique overlapping subtypes of triple-negative breast and ovarian cancers and sensitivity of “mesenchymal-like” cancers to HSP90 inhibition is revealed by integrated gene expression and drug sensitivity profiling

Next-generation sequencing and gene expression signature analysis of primary tumors from The Cancer Genome Atlas (TCGA) revealed striking similarities between triple-negative breast cancer (TNBC) and ovarian cancer (OVCA). We hypothesized that these similarities may reveal transcriptionally-identifiable subgroups within a mix of TNBC and OVCA that are uniquely sensitive to certain drugs.

To test this hypothesis, gene expression profiles for TNBC and OVCA cell lines in the Cancer Cell Line Encyclopedia were analyzed by unsupervised hierarchical clustering, which revealed two major unique subgroups containing both TNBC and OVCA cell lines that clustered according to the previously defined Mesenchymal and Basal subclasses of TNBC. Differential gene expression between “Mesenchymal-like” and “Basal-like” TNBC/OVCA cell lines was used to generate a gene signature that was subsequently validated using gene expression data in the Genomics of Drug Sensitivity in Cancer (GDSC) database. Drug sensitivity data from GDSC was then utilized to profile differential sensitivity of “Mesenchymal-like” and “Basal-like” cell lines to the 99 anti-cancer drugs with coverage of &gt;50 breast and ovarian cell lines. Mesenchymal-like TNBC/OVCA cells were uniquely sensitive to HSP90 inhibition compared to Basal-like TNBC/OVCA cells for both HSP90 inhibitors in GDSC: CCT018159 (p&lt;0.001) and 17-AAG (p=0.012). Strikingly, Mesenchymal-like TNBC/OVCA cells were most sensitive to HSP90 inhibition among all 33 solid tumor cancer lineages in GDSC, as well as other subgroups of breast and ovarian cancers.

Differential sensitivity of Mesenchymal-like and Basal-like TNBC/OVCA cells to HSP90 inhibition with 4 agents (CCT018159, 17-AAG, AT13387, PU-H71) was validated using growth assays for 12 cell lines (6 of each subgroup) previously characterized in GDSC. To further validate the predictive value of our gene signature, gene expression data for 6 TNBC/OVCA cell lines with uncharacterized drug sensitivity was used to classify cell lines as “Mesenchymal-like” (n=4) or “Basal-like” (n=2). Our gene signature successfully predicted differential sensitivity to HSP90 inhibition, with the 4 Mesenchymal-like cell lines displaying greater sensitivity to HSP90 inhibition. The gene signature has been used to select PDX models with predicted differential sensitivity to HSP90 inhibition, and treatment studies are ongoing.

In summary, we developed a novel approach to generate a gene expression signature that robustly predicts sensitivity to HSP90 inhibitors in preclinical models of TNBC and OVCA. HSP90 thus represents a therapeutic opportunity in an overlapping subpopulation of TNBC and OVCA. Our approach to identify novel combinations of drugs and histology/lineage-independent cancer subgroups may be used to discover new therapeutic opportunities in other cancer types.

Citation Format: Shee K, Ung MH, Cheng C, Miller TW. Unique overlapping subtypes of triple-negative breast and ovarian cancers and sensitivity of “mesenchymal-like” cancers to HSP90 inhibition is revealed by integrated gene expression and drug sensitivity profiling [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 P1-07-04.

Abstract P3-04-06: ER reactivation rapidly elicits cell death effects in anti-estrogen-resistant breast cancer

Antagonism of estrogen receptor (ER) transcriptional activity using adjuvant anti-estrogen therapies has improved disease outcomes in many patients with ER+ breast cancer. However, cancer recurs in 1/3 of patients within 15 years of follow-up. While anti-estrogens can slow the progression of metastatic disease, this disease is almost uniformly fatal. Prior to the development of tamoxifen, high-dose estrogens were used to treat late stage breast cancer with response rates similar to those achieved with tamoxifen. Increased efficacy of estrogen therapy was observed in women who were farther past menopause, suggesting that tumor adaptation to low-estrogen conditions is associated with response to estrogen therapy. Similarly, withdrawal of anti-estrogen therapy in patients with anti-estrogen-resistant disease has shown clinical benefit.

MCF-7 cells with acquired resistance to fulvestrant (fulv; FR), and long-term estrogen-deprived (LTED) MCF-7 and HCC-1428 cells overexpress ER compared to parental controls. Upon withdrawal of fulv in FR cells or treatment with 17b-estradiol in LTED cells, ER transcriptional activity is re-engaged at higher levels than in parental cells, concomitant with drastically decreased cell proliferation and increased apoptosis in endocrine-resistant lines. ER reactivation coincides with an unfolded protein response (UPR) following fulv withdrawal (FR) or E2 treatment (LTED). However, treatment of LTED cells with a proteasome inhibitor protects against apoptosis induced by E2 treatment. Prior studies in other cancer subtypes have shown that proteasome inhibitor treatment can prevent expression of pro-apoptotic FasL, which is upregulated following ER reactivation in FR and LTED cells. Alternatively, inhibition of the proteasome may prevent degradation of anti-apoptotic Bcl-2 family proteins including Mcl-1, which is downregulated following FW in FR cells.

The WHIM16 PDX model was derived from a post-menopausal patient with anti-estrogen-resistant ER+/PR+ breast cancer that responded to 17b-estradiol therapy. WHIM16 PDX tumors grown in ovariectomized mice rapidly, completely regress upon 17b-estradiol treatment. Tumor regression is paralleled by increased Src activation, which is associated with ER turnover and has been implicated in 17b-estradiol-induced apoptosis. Src activation is also observed in FR cells following fulv withdrawal, and in LTED cells treated with E2. Treatment of LTED cells with the Src inhibitor dasatinib protects against E2-induced apoptosis, indicating Src activity may be required for the anti-cancer effects of 17b-estradiol.

Upon withdrawal of 17b-estradiol, clinically silent (non-palpable) WHIM16 tumors resume growth; however, tumors remain sensitive to repeat administration of 17b-estradiol. Long-term fulv-withdrawn FR cells show restored sensitivity to fulv, indicating that cycling of estrogen and anti-estrogen therapies may be an effective treatment strategy.

Citation Format: Hosford SR, Kettenbach AN, Varn FS, Cheng C, Miller TW. ER reactivation rapidly elicits cell death effects in anti-estrogen-resistant 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 P3-04-06.

Abstract P3-03-01: A novel high-throughput secreted factor screen and bioinformatics pipeline identifies microenvironment-derived FGF2 as a mechanism of resistance to anti-estrogens, PI3K, and mTOR inhibitors in ER+ breast cancer

Resistance to anti-estrogen therapy is a serious obstacle to the treatment of patients with ER+ breast cancer. Unlike the majority of preclinical studies that focus on cancer cell-intrinsic mechanisms of resistance, we hypothesized that the tumor microenvironment significantly contributes to drug resistance, and that individual factors present in the microenvironment differentially modulate response to therapy.

To systematically test this hypothesis, high-throughput screens were performed in which 297 unique secreted proteins (cytokines, growth factors, and extracellular matrix) were tested on ER+ breast cancer cell lines (MCF-7 and T47D) treated +/- anti-estrogen fulvestrant or the PI3K inhibitor GDC-0941 (pictilisib). Cytokines that rescued cells (hits) were validated in two additional ER+ breast cancer cell lines (ZR75-1 and HCC-1500), and expanded to include the anti-estrogen tamoxifen and the mTORC1 inhibitor everolimus. Hits were also found to rescue from combinations of fulvestrant/GDC-0941 and fulvestrant/everolimus in models with acquired resistance to fulvestrant. Multiple factors, such as ErbB family ligands and fibroblast growth factors (FGFs), were among the top validated hits.

To parse out which hits are most likely to be relevant in the setting of the ER+ breast tumor microenvironment, a bioinformatics filter was developed to incorporate gene and protein expression data for secreted proteins in non-cancer human tissues relevant to ER+ breast cancer. These tissues include primary breast tissue components (breast mammary, adipose, primary fibroblasts) and common metastatic sites (bone marrow, lung, liver). After filtering, the top hit was fibroblast growth factor 2 (FGF2), which significantly drives resistance to anti-estrogens, PI3K, and mTOR inhibitors, and is highly expressed in non-cancer tissues relevant to ER+ breast cancer.

FGF2-mediated rescue was completely abrogated by the ATP-competitive pan-FGFR inhibitor PD173074, confirming FGFR kinase specificity of the rescue phenotype. Immunoblot data confirmed that FGF2 induced phosphorylation of FGFR and the FGFR effector FRS2, and a consistent pattern of downstream MEK-ERK-Rsk90 activation for rescue to all drugs. Flow cytometry data showed that FGF2-mediated rescue leads to decreases in drug-induced apoptosis and G1 cell cycle arrest, which correspond at the protein level to increased degradation of the pro-apoptotic protein Bim and upregulation of the cell cycle driver cyclin D1, respectively.

Mice bearing MCF-7 xenografts were treated with vehicle, FGF2 (20 ug/kg/d, s.c.), fulvestrant (5 mg/wk, s.c.), or the combination. Vehicle-treated and FGF2-treated mice showed similar rates of tumor growth. Single-agent fulvestrant significantly suppressed tumor growth, while the addition of FGF2 rescued from the growth-inhibitory effect of fulvestrant. Studies in other tumor models are ongoing. These data collectively suggest that stroma-derived FGF2-mediated drug resistance is a novel therapeutic opportunity in ER+ breast cancer.

Citation Format: Shee K, Hinds JW, Hampsch RA, Golub TR, Straussman R, Miller TW. A novel high-throughput secreted factor screen and bioinformatics pipeline identifies microenvironment-derived FGF2 as a mechanism of resistance to anti-estrogens, PI3K, and mTOR inhibitors in ER+ 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 P3-03-01.

Abstract P3-04-11: ER is required for mTORC1 inhibitor-induced feedback activation of PI3K/AKT in ER+ breast cancer cells and patients' tumors

The mTORC1 inhibitor everolimus (afinitor) is approved for the treatment of patients with advanced/metastatic ER+/HER2- breast cancer in combination with the steroidal aromatase inhibitor exemestane following progression on a non-steroidal aromatase inhibitor. The BOLERO-2 and TAMRAD studies demonstrated that combined everolimus/anti-estrogen therapy provided longer PFS compared to anti-estrogen alone. However, it has not been clarified whether continued treatment with an anti-estrogen backbone is beneficial in the setting of mTORC1 inhibition.

Upon activation by mTORC1, p70S6K phosphorylates the insulin-like growth factor-1 receptor (IGF-1R)/insulin receptor (InsR) effector IRS-1 to promote IRS-1 degradation, which in turn decreases activation of phosphatidylinositol 3-kinase (PI3K), AKT, and mTORC1. IGF1R, IRS1, and IRS2 are ER-inducible genes, and crosstalk between the ER and IGF-1R pathways has been described. We hypothesized that mTORC1 inhibition with everolimus will upregulate IGF-1R/InsR/IRS-1/2 signaling to activate PI3K/AKT and promote cancer cell survival, while combined inhibition of ER and mTORC1 will block PI3K/AKT activation by decreasing IGF-1R and IRS-1/2, providing rationale for combined targeting of ER and mTORC1.

In 3 ER+ breast cancer cell lines, everolimus treatment increased phospho-AKT levels. ER inhibition with fulvestrant suppressed the induction of P-AKT by everolimus. IGF-1R/InsR inhibition with OSI-906, and RNAi-mediated knockdown of IGF-1R, InsR, or IRS-1/2, decreased everolimus-induced P-AKT. Everolimus sensitized IGF-1R/InsR to IGF-1 that was suppressed by fulvestrant but enhanced by 17b-estradiol. Although fulvestrant decreased IGF-1R and InsR protein levels, phospho-receptor tyrosine kinase profiling showed that fulvestrant increased P-IGF-1R and P-InsR. Acting downstream of IGF-1R/InsR, fulvestrant prevented everolimus-induced PI3K/AKT activation by blocking binding between the p85 regulatory subunit of PI3K and IRS-1, possibly by decreasing IRS-1/2 levels. In summary, everolimus-induced activation of PI3K/AKT requires IGF-1R/InsR/IRS-1/2 signaling facilitated by ER. Combined treatment with fulvestrant and everolimus synergistically inhibited growth in 4 ER+ cell lines.

To determine whether ER promotes PI3K/AKT activation induced by mTORC1 inhibition in patients' tumors without exposing patients to everolimus, we analyzed live tumor tissues from post-menopausal patients with ER+/HER2- breast cancer treated +/- letrozole for 10-21 d before surgical tumor resection. Tumor cores (1 mm diameter) were used for ex vivo culture in DMEM +/- everolimus +/- OSI-906 for 1 h, and lysates were analyzed by immunoblot. Everolimus significantly increased P-AKT in tumors from untreated patients (n=10). OSI-906 did not affect P-AKT, but OSI-906 suppressed everolimus-induced P-AKT. In tumors from letrozole-treated patients (n=7), neither everolimus nor OSI-906 affected P-AKT. These data collectively suggest that ER activation is required for activation of PI3K/AKT induced by mTORC1 inhibition, and provide rationale for therapeutic combinations of anti-estrogens and mTORC1 inhibitors.

Citation Format: Yang W, Chen VS, Schwartz GN, Marotti JD, Rosenkranz KM, Gui J, Miller TW. ER is required for mTORC1 inhibitor-induced feedback activation of PI3K/AKT in ER+ breast cancer cells and patients' tumors [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 P3-04-11.

Maximizing the Benefit-Cost Ratio of Anthracyclines in Metastatic Breast Cancer: Case Report of a Patient with a Complete Response to High-Dose Doxorubicin

Despite the clinical efficacy of anthracycline agents such as doxorubicin, dose-limiting cardiac toxicities significantly limit their long-term use. Here, we present the case of a 33-year-old female patient with extensive metastatic ER+/PR+/HER2– mucinous adenocarcinoma of the breast, who was started on doxorubicin/cyclophosphamide therapy after progressing on paclitaxel and ovarian suppressor goserelin with aromatase inhibitor exemestane. The patient was comanaged by cardiology, who carefully monitored measures of cardiac function, including EKGs, serial echocardiograms, and profiling of lipids, troponin, and pro-BNP every 2 months. The patient was treated with the cardioprotective agent dexrazoxane, and changes in cardiac markers [e.g. decreases in ejection fraction (EF)] were immediately addressed by therapeutic intervention with the ACE inhibitor lisinopril and beta-blocker metoprolol. The patient had a complete response to doxorubicin therapy, with a cumulative dose of 1,350 mg/m², which is significantly above the recommended limits, and to our knowledge, the highest dose reported in literature. Two and a half years after the last doxorubicin cycle, the patient is asymptomatic with no cardiotoxicity and an excellent quality of life. This case highlights the importance of careful monitoring and management of doxorubicin-mediated cardiotoxicity, and that higher cumulative doses of anthracyclines can be considered in patients with ongoing clinical benefit.

Combined Inhibition of Both p110α and p110β Isoforms of Phosphatidylinositol 3-Kinase Is Required for Sustained Therapeutic Effect in PTEN-Deficient, ER+ Breast Cancer

Purpose: Determine the roles of the PI3K isoforms p110α and p110β in PTEN-deficient, estrogen receptor α (ER)-positive breast cancer, and the therapeutic potential of isoform-selective inhibitors.Experimental Design: Anti-estrogen-sensitive and -resistant PTEN-deficient, ER⁺ human breast cancer cell lines, and mice bearing anti-estrogen-resistant xenografts were treated with the anti-estrogen fulvestrant, the p110α inhibitor BYL719, the p110β inhibitor GSK2636771, or combinations. Temporal response to growth factor receptor-initiated signaling, growth, apoptosis, predictive biomarkers, and tumor volumes were measured.Results: p110β primed cells for response to growth factor stimulation. Although p110β inhibition suppressed cell and tumor growth, dual targeting of p110α/β enhanced apoptosis and provided sustained tumor response. The growth of anti-estrogen-sensitive cells was inhibited by fulvestrant, but fulvestrant inconsistently provided additional therapeutic effects beyond PI3K inhibition alone. Treatment-induced decreases in phosphorylation of AKT and Rb were predictive of therapeutic response. Short-term drug treatment induced tumor cell apoptosis and proliferative arrest to induce tumor regression, whereas long-term treatment only suppressed proliferation to provide durable regression.Conclusions: p110β is the dominant PI3K isoform in PTEN-deficient, ER⁺ breast cancer cells. Upon p110β inhibition, p110α did not induce significant reactivation of AKT, but combined targeting of p110α/β most effectively induced apoptosis in vitro and in vivo and provided durable tumor regression. Because apoptosis and tumor regression occurred early but not late in the treatment course, and proliferative arrest was maintained throughout treatment, p110α/β inhibitors may be considered short-term cytotoxic agents and long-term cytostatic agents. Clin Cancer Res; 23(11); 2795-805. ©2016 AACR.

Clinical Implementation of Novel Targeted Therapeutics in Advanced Breast Cancer

The majority of advanced breast cancers have genetic alterations that are potentially targetable with drugs. Through initiatives such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), data can be mined to provide context for next-generation sequencing (NGS) results in the landscape of advanced breast cancer. Therapies for targets other than estrogen receptor alpha (ER) and HER2, such as cyclin-dependent kinases CDK4 and CDK6, were recently approved based on efficacy in patient subpopulations, but no predictive biomarkers have been found, leaving clinicians to continue a trial-and-error approach with each patient. Next-generation sequencing identifies potentially actionable alterations in genes thought to be drivers in the cancerous process including phosphatidylinositol 3-kinase (PI3K), AKT, fibroblast growth factor receptors (FGFRs), and mutant HER2. Epigenetically directed and immunologic therapies have also shown promise for the treatment of breast cancer via histone deacetylases (HDAC) 1 and 3, programmed T cell death 1 (PD-1), and programmed T cell death ligand 1 (PD-L1). Identifying biomarkers to predict primary resistance in breast cancer will ultimately affect clinical decisions regarding adjuvant therapy in the first-line setting. However, the bulk of medical decision-making is currently made in the secondary resistance setting. Herein, we review the clinical potential of PI3K, AKT, FGFRs, mutant HER2, HDAC1/3, PD-1, and PD-L1 as therapeutic targets in breast cancer, focusing on the rationale for therapeutic development and the status of clinical testing. J. Cell. Biochem. 117: 2454-2463, 2016. © 2016 Wiley Periodicals, Inc.

Abstract P6-13-22: Pharmacodynamics and consequences of PI3K inhibition in ER+ breast tumors

PI3K inhibitors have shown promise for the treatment of anti-estrogen-resistant ER+ breast cancers. Current PI3K inhibitor treatment regimens may incompletely and transiently inhibit the pathway in carcinomas, and are accompanied by significant adverse effects in patients. We hypothesized that short-term, complete inhibition of PI3K will have a greater anti-tumor effect and reduce systemic toxicity compared to chronic, partial inhibition.

Pharmacokinetic analysis of the orally available pan-PI3K inhibitor GDC-0941 at low (100 mg/kg) and high (800 mg/kg) doses in mice revealed that plasma levels peaked after 15-30 min, and decreased below the limit of detection within 24 h (low dose) and 72 h (high dose), respectively. Administering 2 doses at 100 mg/kg 12 h apart provided continuous drug exposure. Drug pharmacokinetics in MCF-7 tumors was similar.

Mice bearing s.c. MCF-7 tumors were treated with the anti-estrogen fulvestrant (fulv; 5 mg/wk) three days before GDC-0941 treatment to assess pharmacodynamic effects. Phospho-AKT and -S6 levels (markers of PI3K and mTORC1 activities, respectively) were inversely correlated with tumor drug concentrations. Mice bearing MCF-7, fulv-resistant T47D/FR, or HCC-003 patient-derived xenografts were treated with vehicle, fulv, GDC-0941 (100 mg/kg QD 5 d/wk; 100 mg/kg BID 3 d on/4 d off; 800 mg/kg QW), or combinations. Tumor growth curves indicated that different schedules of PI3K inhibition with fulv similarly induced tumor regression. Molecular analysis of MCF-7 tumors showed that fulv plus GDC-0941 QW induced 30.14% apoptosis (assessed by TUNEL) at 48 h, which dropped to baseline (2.72%) at 72 h. Fulv plus GDC-0941 BID induced 18.27% apoptosis at 24 h, and maintained apoptosis rate near 10% until 96 h (when GDC-0941 washed out), which is a rate similar to that observed with fulv plus GDC-0941 QD. Fulv plus GDC-0941 QW decreased cell proliferation (assessed by geminin and Ki67 staining) from 34.89% (baseline) to 11.46%, which rebounded to 60.54% at the time of GDC-0941 washout (at 96 h). Fulv plus GDC-0941 QD or BID modestly decreased cell proliferation to 28.84% and 24.32%, respectively, after 24 h, which returned to baseline after 36 h and 72 h, respectively, then maintained the level for a week. Temporal analysis of PI3K signaling revealed that fulv plus GDC-0941 QW and BID maximally decreased phospho-AKT levels after 3 h, which returned to baseline within 48 h and 72 h, respectively. With fulv + GDC-0941 QD, phospho-AKT levels decreased after 3 h, but rebounded to baseline within 24 h. These results indicate that 2 approaches to PI3K inhibition provide similar anti-tumor efficacy: 1) complete/intermittent (QW) PI3K inhibition induces a burst of apoptosis with a rebound in cell proliferation after drug clearance; and 2) metronomic/repeated (QD) PI3K inhibition repeatedly induces a smaller amount of apoptosis without significantly affecting cell proliferation. These findings may inform clinical testing of PI3K inhibitors to maximize therapeutic index.

Citation Format: Yang W, Bean J, Hosford S, Lloye D, Liu S, Salphati L, Pang J, Zhang X, Nannini M, Miller TW. Pharmacodynamics and consequences of PI3K inhibition in ER+ breast tumors. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-13-22.

Abstract P3-05-03: Estrogen receptor alpha reactivation for the treatment of anti-estrogen-resistant breast cancer

Adjuvant anti-estrogen therapies that antagonize ER transcriptional activity have improved outcome in many patients, yet resistance to anti-estrogen therapies is common, resulting in disease recurrence in 1/3 of patients within 15 years of follow-up. However, prior to the introduction of tamoxifen, estrogens were used for treatment of breast cancer with response rates similar to those obtained by anti-estrogens in the advanced setting. Similarly, withdrawal of anti-estrogen therapy has shown anti-tumor effects, indicating that reactivation of ER may elicit therapeutic benefit.

MCF-7 cells with long-term (&gt;1 yr) acquired resistance to the selective ER downregulator fulvestrant (fulv; MCF-7/FR) retain ER expression and harbor ESR1 (ER) gene amplification. Upon withdrawal of fulv, these cells re-engage ER as demonstrated by increased luciferase transcriptional reporter activity and re-expression of proteins encoded by ER-inducible genes. Following fulv withdrawal, MCF-7/FR cells show drastically decreased proliferation and increased apoptosis that are temporally correlated with ER reactivation. Protein levels of the anti-senescence protein FoxM1 decline following ∼12 d of fulv withdrawal, paralleled by increased staining for senescence-associated β-galactosidase. Transcriptomic analyses confirmed that fulv withdrawal progressively induces gene expression patterns indicative of stress and senescence. Similar effects were observed in long-term estrogen-deprived (LTED) MCF-7 cells treated with 17b-estradiol. Prospective studies characterizing the development of acquired anti-estrogen resistance have demonstrated the MCF-7 cells at 9 months of fulv resistance do not respond to fulv withdrawal, contrasting the long-term (&gt;1 yr) MCF-7/FR cells. Additionally, withdrawal of fulv from T47D/FR, ZR75-1/FR, or HCC-1428/FR cells did not induce cell death or re-engage ER activity, confirming that ER reactivation is required for anti-cancer effects. Ongoing studies are characterizing the temporal changes in ER transcriptional activity during 1) development of acquired anti-estrogen resistance, and 2) 17b-estradiol treatment of mice bearing WHIM16 patient-derived xenografts (regress in response to 17b-estradiol) to elucidate the mechanism underlying sensitivity of anti-estrogen resistant cells to ER reactivation.

While estrogen therapies have shown clinical efficacy for decades, biomarkers to identify patients with tumors likely to respond to estrogen remain undefined. We are conducting a Phase II clinical trial [Pre-emptive OsciLLation of ER activitY levels through alternation of estradiol/anti-estrogen therapies prior to disease progression in ER+/HER2- metastatic breast cancer (POLLY); NCT02188745] that will use tumor biopsy tissues to identify baseline and pharmacodynamic biomarkers that predict response to 17b-estradiol therapy.

Citation Format: Hosford SR, Kaufman PA, Miller TW. Estrogen receptor alpha reactivation for the treatment of anti-estrogen-resistant breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-05-03.

Abstract P5-03-01: Therapeutic targeting of Rac GTPases in ER+ and HER2+ breast cancer

As crucial regulators of cell motility, survival, and proliferation, Rac GTPases (Rac1/2/3) have been implicated in cancer. We previously found that P-REX1, a guanine nucleotide exchange factor that activates Rac GTPases, forms a PI3K-driven positive feedback loop to promote activation of Rac enzymes, receptor tyrosine kinases, PI3K/AKT/mTOR, and MEK/ERK in ER+ breast cancer cells. Importantly, inhibition of Rac GTPases with a small molecule (EHT1864) simultaneously suppressed activation of both the PI3K/AKT/mTOR and MEK/ERK pathways. While co-targeting of the PI3K/AKT/mTOR and MEK/ERK pathways with drug combinations has anti-tumor activity in preclinical models and is being tested in ongoing clinical trials, targeting Rac as a common upstream signaling node may be a more efficient means of simultaneously targeting these two oncogenic pathways.

In breast cancer cell lines, treatment with EHT1864 decreased activation of AKT, mTOR, p70S6K, and S6 in a dose-dependent manner. Pulldown of activated Rac from cell lysates revealed that GTP-bound Rac1 and/or Rac3 bind MEK1/2, ERK1/2, p70S6K, S6, Raptor, Rictor, and mTOR. Temporal analysis indicated that EHT1864 inhibits phosphorylation of p70S6K (an mTORC1 substrate) before AKT is inhibited, suggesting that Rac may directly activate p70S6K and/or mTORC1. Mining of sensitivity data from ∼700 cell lines to a panel of 138 drugs (COSMIC/GDSC database) revealed that the growth-suppressive effects of EHT1864 correlate most strongly with growth-suppressive patterns induced by a p70S6K inhibitor, supporting the notion that Rac directly activates p70S6K. Additionally, EHT1864 treatment dose-dependently decreased phosphorylation of ERK1/2 and MEK1/2, and induced apoptosis in breast cancer cell lines. In a panel of 16 breast cancer lines, cells with activating mutations in PIK3CA (encodes the p110-alpha subunit of PI3K) exhibit increased EHT1864 sensitivity. Pharmacokinetic analysis of EHT1864 (100 mg/kg, i.p.) in plasma in NSG mice revealed that drug was present at &gt;50 uM for 1 h after administration. In mice bearing s.c. ER+/HER2+ BT-474 breast cancer xenografts, EHT1864 (100 mg/kg BID) significantly slowed tumor growth compared to vehicle control. Thus, therapeutically targeting Rac could be an effective means of reducing cancer cell proliferation and survival by simultaneously suppressing both the PI3K/AKT/mTOR and MEK/ERK signaling pathways in ER+ and HER2+ breast cancers.

Citation Format: Hampsch RA, Shee K, Miller TW. Therapeutic targeting of Rac GTPases in ER+ and HER2+ breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-03-01.

Abstract P4-09-20: Plasma DNA as a surrogate for tumor biopsy to identify genetic alterations in patients with metastatic breast cancer

Precision medicine requires that a patient's tumor be accurately genotyped to identify a potentially effective targeted therapy. However, genotyping a tumor in patients with oligometastatic disease is complicated by the potential for intratumor and intertumor heterogeneity, and the requirement for sufficient tumor tissue obtained by invasive biopsy for genetic profiling. We sought to determine whether circulating tumor DNA in plasma provides a surrogate for solid tumor biopsy, and captures the genetic heterogeneity of tumors in patients with metastatic breast cancer. We hypothesized that genetic mutations detected in plasma DNA are reflective of the genetic mutations present in all tumors within a patient.

Eight patients with advanced/metastatic breast cancer have thus far been enrolled in an ongoing clinical study (NCT01836640). Tumor specimens from two (n=4) or three (n=4) tumor sites and blood were obtained with one month. Blood was separated into plasma and buffy coat fractions. DNA extracted from tissue, buffy coat, and plasma samples was used for massively parallel DNA sequencing using the Ion Proton platform with a custom TargetSeq capture probe set covering all exons of 196 genes (4.1 Mb). All tumor and buffy coat samples, and plasma samples from three patients have thus far been analyzed. Tumor mutations were identified by comparison to buffy coat DNA sequences. We achieved sequencing coverage of ∼100-fold for tumor and buffy coat DNA samples, and ∼1,000-fold for plasma DNA samples. In Patient #1, we obtained 14 tumor nodules from a mastectomy specimen and used 3 nodules for DNA sequencing; Among the 73 point mutations detected in DNA from at least one tumor nodule, 29 mutations (40%) were detected in plasma DNA, and 10 mutations were found in plasma but not in tumors. In Patient #5, we analyzed bilateral breast tumors and a brain metastasis; among 151 mutations detected in at least one tumor, 80 (53%) were found in plasma, and an additional 18 mutations were found in plasma but not tumors; mutations specific to the brain tumor were less likely to be found in plasma; interestingly, the bilateral breast tumors showed genetic and histologic similarity, and so were likely derived from a single clone. Patient #6 had only one lung metastasis evaluable by DNA sequencing; 64/125 (51%) tumor-derived mutations were detected in plasma, and an additional 26 mutations were found in plasma but not the tumor.

Preliminary ResultsMutationsTumorPlasma (Plasma only)TotalPlasma concordance with tumorPlasma concordance with totalTumor concordance with totalPatient #17329 (10)8339.7%46.9%87.9%Patient #515180 (18)16952.9%57.9%89.3%Patient #612564 (26)15151.2%59.6%82.8%

These data suggest that, although challenging to get multiple biopsies for comparison, plasma is a promising surrogate for solid tumor biopsy to identify potentially targetable mutations. However, the ability of plasma DNA to genetically reflect all tumors in a patient with oligometastatic disease remains to be clarified through further analysis.

Citation Format: Chamberlin MD, Shee K, Varn FS, Bean JR, Marotti JD, Gui J, Gemery JM, Barth RJ, Rosenkranz KM, Tsapakos MJ, McNulty NJ, Cheng C, Miller TW. Plasma DNA as a surrogate for tumor biopsy to identify genetic alterations in patients with metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-09-20.