O43: CLINICAL IMPACT OF GENE FUSIONS IN BREAST CANCER BRAIN METASTASES

Introduction

The incidence of brain metastases is increasing despite longer survival rates for patients with advanced breast cancer. The identification of novel therapeutic targets for these patients is an urgent unmet clinical need. Sequencing of metastatic tumours have largely focused on mutations however gene fusions have an important, yet underappreciated role in tumorigenesis and disease progression. In this study, we investigate the role of gene fusions in brain metastatic disease and their impact on altered therapeutic responses.

Method

RNA sequencing was performed on the largest reported cohort of patient matched primary and resected brain metastatic tumours (45 patients n=90 samples). Expressed gene fusions were detected computationally using STAR-Fusion and Arriba.

Result

We identified differential gene fusion burden in brain metastatic tumours (medium of 58) vs. primary breast tumours (medium of 38) (p < 0.05). Enrichment for fusions in pathways associated with tumour cell plasticity and proliferation with recurrent fusions in known cancer driver genes related to MAPK, HER signaling identified. Of note, a fusion in CDK12 is of clinical importance. Increased genomic alterations and over expression of CDK12 is associated with brain metastases free survival in an independent cohort of primary breast tumours with a recorded history of brain metastases. It has been proposed that inhibition of CDK12 may induce BRCAness in tumours making them sensitive to PARP inhibition.

Conclusion

These results highlight the significant role of gene fusions in breast cancer brain metastases.

Abbreviations

MAPK Mitogen Activated Protein Kinase, HER Human Epidermal Receptor, CDK12 Cyclin Dependent Kinase 12

Take-home message

We highlight the significant role of gene fusions in breast cancer brain metastases and offer specific actionable genomic alterations to be exploited.

Quality improvement during the COVID-19 pandemic

In response to the COVID-19 pandemic, quality improvement teams at Cleveland Clinic initiated a number of measures to guide the care of patients with suspected or confirmed COVID-19 infection and protect care givers. This included increasing the frequency of team meetings from monthly to daily or weekly and creating task forces to create protocols for patient transport, airway management, and management of personal protective equipment and medications in short supply. Enterprise wide, we postponed non-essential surgeries, set up an overflow intensive care unit onsite, created a web-based COVID-19 toolkit for all care givers, and sent daily emails about the most recent developments, decisions, and recommendations from national and international societies.

Loss of function of NF1 is a mechanism of acquired resistance to endocrine therapy in lobular breast cancer

Background

Invasive lobular carcinoma (ILC) as a disease entity distinct from invasive ductal carcinoma (IDC) has merited focused studies of the genomic landscape, but those to date are largely limited to the assessment of early-stage cancers. Given that genomic alterations develop as acquired resistance to endocrine therapy, studies on refractory ILC are needed.

Patients and methods

Tissue from 336 primary-enriched, breast-biopsied ILC and 485 estrogen receptor (ER)-positive IDC and metastatic biopsy specimens from 180 ILC and 191 ER-positive IDC patients was assayed with hybrid-capture-based comprehensive genomic profiling for short variant, indel, copy number variants, and rearrangements in up to 395 cancer-related genes.

Results

Whereas ESR1 alterations are enriched in the metastases of both ILC and IDC compared with breast specimens, NF1 alterations are enriched only in ILC metastases (mILC). NF1 alterations are predominantly under loss of heterozygosity (11/14, 79%), are mutually exclusive with ESR1 mutations [odds ratio = 0.24, P < 0.027] and are frequently polyclonal in ctDNA assays. Assessment of paired specimens shows that NF1 alterations arise in the setting of acquired resistance. An in vitro model of CDH1 mutated ER-positive breast cancer demonstrates that NF1 knockdown confers a growth advantage in the presence of 4-hydroxy tamoxifen. Our study further identified a significant increase in tumor mutational burden (TMB) in mILCs relative to breast ILCs or metastatic IDCs (8.9% >20 mutations/mb; P < 0.001). Most TMB-high mILCs harbor an APOBEC trinucleotide signature (14/16; 88%).

Conclusions

This study identifies alteration of NF1 as enriched specifically in mILC. Mutual exclusivity with ESR1 alterations, polyclonality in relapsed ctDNA, and de novo acquisition suggest a role for NF1 loss in endocrine therapy resistance. Since NF1 loss leads to RAS/RAF kinase activation, patients may benefit from a matched inhibitor. Moreover, for an independent subset of mILC, TMB was elevated relative to breast ILC, suggesting possible benefit from immune checkpoint inhibitors.

Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer

Background

Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer.

Patients and methods

To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots.

Results

We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations.

Conclusions

Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.

Abstract P5-04-21: FGFR4 is a novel druggable target for recurrent ER-positive breast cancers

Background

Breast cancer recurrence is a major clinical problem for estrogen receptor positive (ER+) disease, even decades after initial surgery. These long-term recurrences are a challenge for invasive ductal carcinoma (IDC), and are particularly frequent for the histological subtype of invasive lobular carcinoma (ILC). To study the long-term endocrine resistance seen in ILC patients, our lab recently generated six long-term estrogen deprivation (LTED) models of ILC cells and performed RNA-Sequencing to identify differentially expressed genes that ostensibly allow these cells to grow in the absence of estrogen. We overlapped these results with a previously published microarray dataset of tamoxifen-resistant cells, and found that FGFR4 is the most consistently overexpressed gene in the setting of acquired resistance to endocrine therapy in ILC cells. From a recent publication of RNA-Seq from other LTED models, FGFR4 RNA overexpression is also seen in all five IDC cell lines.

Hypothesis

FGFR4 is an important mediator of acquired endocrine resistance in breast cancer.

Methods

To study the role of FGFR4 in vitro, we used multiple shRNAs and specific small molecule inhibition for growth assays. To study the role of FGFR4 in de novo resistance to endocrine therapy, we collected 129 well curated ER+ ILC tumor specimens and performed gene expression analysis on the pre-treatment samples using a custom NanoString panel. To study the role of FGFR4 in acquired resistance, we collected over 50 pairs of primary-metastatic ER+ tumors and performed exon capture based RNA-Sequencing.

Results

FGFR4 inhibition decreases parental and LTED cell growth in classic 2D conditions and in colony formation assays. The LTED cells, with higher FGFR4 expression, are more sensitive to its inhibition. For the parental cells, combination FGFR4 and ER-targeting drugs results in synergistic decreases in growth. In our database of primary ILC clinical samples, increased expression of FGFR4 is predictive of shorter time to distant recurrence. Among primary-recurrent tumor pairs, FGFR4 is an outlier expression gain in 20/50 (40%), spanning all recurrence sites studied (i.e. local recurrences, and metastases to the brain, bone, ovaries, and GI tract). Finally, in analyzing large cohorts of metastatic tumors, there is a significant enrichment of hotspot FGFR4 mutations in tumors originating in the breast, with &gt;2% of metastatic ILC tumors containing such a mutation.

Conclusion/Future studies

FGFR4 may play an important role in de novo resistance to endocrine therapy in ILC and acquired resistance in both ILC and IDC. Ongoing studies include overexpression of wild-type and FGFR4 hotspot mutations in ILC and IDC cell lines to determine growth and metastatic phenotypes.

Citation Format: Levine KM, Ding K, Priedigkeit N, Sikora MJ, Tasdemir N, Zhu L, Tseng GC, Jankowitz RC, Dabbs DJ, McAuliffe PF, Lee AV, Oesterreich S. FGFR4 is a novel druggable target for recurrent ER-positive breast cancers [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 P5-04-21.

Abstract P2-01-09: ESR1 mutations drive breast cancer metastasis by context-dependent alterations in adhesive and migratory properties

Background: Estrogen receptor alpha (ERα/ESR1) is mutated in 30-40% of endocrine resistant ER+ breast cancer. These mutations, primarily located in the ligand binding domain, are associated with worse outcome in patients, and preclinical studies have shown that they cause ligand independent growth. An open question is whether these mutations contribute to actual metastatic process, or merely endocrine resistance.

Methods: Using Y537S and D538G genome-edited MCF7 and T47D cells, 3D growth was assessed in ultralow attachment plates. Cell-cell adhesion was determined using calcein-labelled adhesion assay and quantitative microfluidic fluorescence microscope (qMFM). Collagen-based adhesion and spheroid invasion assays were used to test adhesive and invasive properties. Wound scratching, spheroid collective migration and Boyden chamber transwell assays were applied to monitor cell migratory phenotypes. Mutated ER cistromes were profiled using ChIP-sequencing. ESR1 mutations in clinical samples were characterized using ddPCR.

Results: Visual inspection of cells grown in suspension culture revealed more compressed multicellular spheroids in ESR1 mutant cells, indicative of increased cell-cell interactions. This observation was confirmed in both static and microfluidic conditions. This effect was more pronounced in MCF7 than T47D cells, correlating with increased expression of desmosome and gap junction genes. Pharmacological blockade of gap junctions decreased cell-cell adhesion. Decreased attachment and increased invasion to collagen were discerned in all mutant cell types. Further functional analysis identified alterations in the TIMP3-MMP axis causing these phenotypes. The cell-cell adhesion phenotypes were restricted to MCF7-Y537S/D538G and T47D-Y537S, whereas T47D-D538G cells showed significantly increased migration. A GSEA screen identified Wnt signaling as uniquely induced in this context, and combination treatment using the Wnt inhibitor LGK974 and Fulvestrant led to synergistic inhibition of migration. ChIP-seq identified mutation-specific cistromes with an overall increased ligand-independent ER binding. However, it did not reveal binding sites in any candidate metastases genes, suggesting secondary epigenetic mechanisms. The motif analysis revealed the enrichment of FOXA1 motifs in mutated ER cistromes except T47D-D538G cells. However, knockdown of FOXA1 induced significantly higher inhibition of T47D-D538G migration than Fulvestrant treatment alone, indicating a FOXA1-dominated mechanism. Collectively, these data show that ESR1 mutant cells gain metastatic properties, in addition to endocrine resistance. To prove this using clinical samples, we measured ESR1 mutations in a well-defined cohort of endocrine resistant local or distant recurrence. Significant enrichment of ESR1 mutations in distant (9/55) vs local (0/27) recurrences confirms critical role of mutant ERα in metastases.

Conclusion: Further analysis of context dependent changes in cell-cell adhesion and migration of ESR1 mutant cells might guide the design and development of drugs targeting ERα-mutant tumors, such as inhibitors of gap junction, FOXA1, MMP, and Wnt signaling pathways.

Disclosure: The authors declare no conflict of interest.

Citation Format: Li Z, Bahreini A, Levine KM, Wang P, Tasdemir N, Montanez MA, Sundd P, Wallace CT, Watkins SC, Chu D, Park BH, Hou W, Mooring MS, Zhu L, Tseng GC, Carroll JS, Atkinson JM, Lee AV, Oesterreich S. ESR1 mutations drive breast cancer metastasis by context-dependent alterations in adhesive and migratory properties [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 P2-01-09.

Abstract P3-10-05: BRCA1/2 alterations are present at significant rates across breast cancer subtypes and are associated with a high genome-wide loss of heterozygosity signature

Background

The recent approval of PARP inhibitor, olaparib, in HER2-negative breast cancer expands the therapeutic options for patients with germline BRCA1/2 alterations. The role of somatic BRCA alteration as a predictive biomarker in breast cancer is currently unclear. NCCN guidelines call for germline testing in all young patients (&lt;46 yrs) and patients with triple negative breast cancer (TNBC) (&lt; 61 yrs) with a personal history of breast cancer. Here we examined the landscape of BRCA mutations to assess whether additional populations may have potential benefit from PARP inhibitors.

Methods

Hybrid-capture based comprehensive genomic profiling of 395 cancer-related genes using the FoundationOne assay (Foundation Medicine, MA) was performed on 12,508 breast carcinomas. Somatic/germline/zygosity status for BRCA1/2 variants was analyzed as described in Sun, 2018 (PMID: 29415044). High genome-wide loss-of-heterozygosity (gLOH) was classified as ≥16% LOH. Subgroups were analyzed on histological {Invasive Ductal Carcinoma (IDC), Invasive Lobular Carcinoma (ILC)} and molecular subtypes [ER-positive (ER+), HER2-amplified (HER2+), TNBC], patient age [≤45, 46-60, 61+], and gender.

Results

Consistent with previous reports, the frequency of BRCA1/2 alterations was highest in young patients (&lt;46; 15%), TNBC (10%), and male breast cancer (14%); BRCA1/2 alterations were also identified in HER2+, ILC, and ER+ tumors (5.3%, 6.5%, 8.3%). Overall, BRCA1 was more frequently mutated in TNBC and young patients (67%), whereas BRCA2 was more frequently mutated in ER+, HER2+, ILC, and male breast cancer (63%, 57%, 79%, 100%).

The fraction of somatic BRCA mutations (sBRCA) was 38%, with the lowest fraction of sBRCA in TNBC and young patients (30%, 30% overall, 36%, 42% for BRCA1) and highest in HER2+, ILC, and older patients (46%, 52%, 51%); the absolute frequency of sBRCA is approximately 3.5%. In tumors with ESR1 mutations, we detected concurrent BRCA mutation in 6.4% (85/1319), with 48% predicted somatic.

Almost all tumors with BRCA mutations had biallelic inactivation, with LOH of the second allele irrespective of predicted germline status (90% of gBRCA and 86% of sBRCA under LOH). gLOH score was used as a phenotypic measure of homologous recombination deficiency (HRD): patients harboring biallelic BRCA alterations had elevated rates of gLOH with 89% of gBRCA and 84% of sBRCA tumors harboring a high gLOH score, vs 47% with heterozygous BRCA, 34% with no BRCA alteration, and 80% for patients with BRCA deletion.

Conclusions

Thirty-eight percent of deleterious BRCA alterations in breast are predicted somatic, including 36% of BRCA1 alterations in TNBC. Germline testing would miss these alterations even though they are frequently under LOH and are associated with high gLOH, a biomarker with predictive value in ovarian cancer. While patients with ER+ and HER2+ tumors have low rates of gBRCA alterations, the overall BRCA mutation rate, including somatic alterations, is appreciable at 8.3% and 5.3%. Our findings demonstrate that sBRCA alterations are associated with a comparable HRD phenotype to gBRCA altertions and suggests that PARP inhibitors may have potential value for a wider range of breast cancer patients.

Citation Format: Sokol ES, Frampton GM, Ross J, Ali S, Chung J, Oesterreich S. BRCA1/2 alterations are present at significant rates across breast cancer subtypes and are associated with a high genome-wide loss of heterozygosity signature [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 P3-10-05.

Abstract P6-12-01: Withdrawn

This abstract was withdrawn by the authors.

Citation Format: Palliyaguru DL, Chartoumpekis DV, Skoko JJ, Wendell SG, Woodcock SR, Wakabayashi N, Yagishita Y, Oesterreich S, Michalopoulos GK, Kensler TW. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-12-01.

Abstract P3-06-03: Copy number analysis identifies ESR1 and MDM4 as drivers of progression in invasive lobular breast carcinoma

Background: Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer after invasive ductal carcinoma (IDC). While specific clinical and pathological features differ between ILC and IDC, both histologies are treated the same, due to a lack of knowledge of targetable pathways underlying the observed differences. To identify potential genetic drivers of ILC progression, we set out to identify genes with copy number (CN) alterations, comparing tumors with good outcome to those with poor outcome.

Method: We designed probes for a total of 67 genes known to be frequently altered in breast cancer and used sensitive nanoString technology to comprehensively investigate CN alterations of these genes in 70 well-curated primary ILCs. ILC cell lines MDA-MB-134-VI, SUM44PE, and BCK4 were used for functional studies including proliferation, apoptosis, colony formation, and analysis of gene expression.

Results: Our studies reveal that ESR1 is frequently amplified in primary ILC (14% gains and 10% amplification), and that tumors with amplified ESR1 are more likely to recur compared to those with normal CN. Our analysis also identified a subset of ILCs with HER2 amplification (19%) despite a negative clinical IHC score, and these tumors expressed high HER2 mRNA, protein, and demonstrated enrichment of a molecular HER2 signature. The other most frequently amplified genes included CCND1 (33%), MDM4 (17%), and MYC (17%), and most frequently lost genes were NCOR2 (7%), FGFR4 (6%) and TP53 (6%). MDM4, a negative regulator of p53, has previously been reported to play a role in breast cancer, though little is known about its role in ILC. We demonstrate that decreasing MDM4 levels in p53 wild type ILC cell lines results in increased apoptosis, decreased proliferation associated with cell cycle arrest, and activation of p53 target genes. Intriguingly, a similar induction of G0/G1 cell cycle arrest and increase in apoptosis was observed in p53 mutant ILC cells after MDM4 downregulation, suggesting a p53-independent function of MDM4.

Conclusion: Sensitive detection of CN changes identified amplifications of ESR1 and MDM4 as potential drivers of ILC. Functional studies demonstrate that MDM4 has both p53 dependent and independent functions that warrant further study.

Citation Format: Atkinson JM, Cao L, Basudan A, Sikora MJ, Bahreini A, Tasdemir N, Jankowitz RC, McAuliffe PF, Dabbs D, Haupt S, Haupt Y, Peter Lucas PC, Lee AV, Oesterreich S. Copy number analysis identifies ESR1 and MDM4 as drivers of progression in invasive lobular breast carcinoma [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 P3-06-03.

Etiology of Acute Coronary Syndrome after Noncardiac Surgery

BACKGROUND

The objective of this investigation was to determine the etiology of perioperative acute coronary syndrome with a particular emphasis on thrombosis versus demand ischemia.

METHODS

In this retrospective cohort study, adult patients were identified who underwent coronary angiography for acute coronary syndrome within 30 days of noncardiac surgery at a major tertiary hospital between January 2008 and July 2015. Angiograms were independently reviewed by two interventional cardiologists who were blinded to clinical data and outcomes. Acute coronary syndrome was classified as ST-elevation myocardial infarction, non-ST-elevation myocardial infarction, or unstable angina; myocardial infarctions were adjudicated as type 1 (plaque rupture), type 2 (demand ischemia), or type 4b (stent thrombosis).

RESULTS

Among 215,077 patients screened, 146 patients were identified who developed acute coronary syndrome: 117 were classified as non-ST-elevation myocardial infarction (80.1%); 21 (14.4%) were classified as ST-elevation myocardial infarction, and 8 (5.5%) were classified as unstable angina. After coronary angiography, most events were adjudicated as demand ischemia (type 2 myocardial infarction, n = 106, 72.6%) compared to acute coronary thrombosis (type 1 myocardial infarction, n = 37, 25.3%) and stent thrombosis (type 4B, n = 3, 2.1%). Absent or only mild, nonobstructive coronary artery disease was found in 39 patients (26.7%). In 14 patients (9.6%), acute coronary syndrome was likely due to stress-induced cardiomyopathy. Aggregate 30-day and 1-yr mortality rates were 7 and 14%, respectively.

CONCLUSIONS

The dominant mechanism of perioperative acute coronary syndrome in our cohort was demand ischemia. A subset of patients had no evidence of obstructive coronary artery disease, but findings were consistent with stress-induced cardiomyopathy.

Abstract PD8-08: ESR1 mutations confer novel metastatic functions in genome-edited breast cancer cell models

Background: Estrogen receptor alpha (ERα), encoded by the ESR1 gene, is expressed in approximately 70% of breast cancers. Recent studies conducted by us and others have shown that somatic mutations in ESR1 gene play a key role in conferring endocrine resistance in ER+ breast cancer. These hotspot mutations mainly occur on the ligand binding domain of ERα, leading to poor outcomes in 25-30% of patients with ER+ metastatic breast cancer in clinic. The mechanisms behind the potential enhanced metastasis of these mutations have become an urgent issue to be addressed, but they are not well understood due to a lack of ESR1 mutant models.

Methods: We generated and characterized genome-edited T47D and MCF7 breast cancer cell lines with the two most common ESR1 mutations (Y537S and D538G), using CRIPSR/Cas9 and rAAV systems respectively. Multiple clones for each mutant were sorted and the mutation frequencies were detected using digital droplet PCR (ddPCR). We subsequently performed an RNA-sequencing to deeply differentiate the gene expression patterns in these mutants. The growth of these pooled mutant-cells was determined in both 2D and 3D plates. The cell-matrix adhesions were measured based on ECM array, and 84-ECM adhesion related genes were further tested by qPCR array. IncuCyte real-time image system and boyden chamber transwell assays were used to monitor the cell migration and chemotaxis. Tail vein injection were performed on nude mice, and immunofluorescent staining of lung tissues with human specific cytokeratin 19 were utilized to evaluate in vivo metastatic capacities of the mutant cell models.

Results: We first identified the robust mutation frequencies at both RNA and DNA levels in our cell models. The RNA-seq exhibits multiple ligand-independent genes overlapping between either cell lines or mutants, which were further conformed by qPCR. We also found that both Y537S and D538G mutants present ligand-independent growth in 2D and 3D ultra-low attachment plates. Using wound-scratching assay, we observed significant higher migration rate in D538G mutant of T47D cell lines on both matrigel and type I collagen, indicating a cell-line and mutant-specific phenotype. We also detected lower attachment of both mutants on type I collagen in both cell lines, and our qPCR array revealed that alterations in the MMP pathways could be one of the major mechanism causing this phenotype. Finally, tail vein injection of T47D mutant-cells in nude mice derived more micrometatsatic spots in the lung tissues.

Conclusion: In sum, our study presents the first in-depth metastatic functional analysis of the biology of ESR1 mutations in genomic knock-in cell models, pointing out the enhanced migration and decreased cell-matrix adhesion as a potential novel gain-of-function of the Y537S and D538G mutant-cells in vitro and in vivo. These findings suggest the potential role of enhanced metastasis of these ESR1 mutations through remodeling of transcriptional profiles, shedding lights towards the development of efficient therapies of ESR1 mutant breast cancer.

Citation Format: Oesterreich S, Li Z, Bahreini A, Wang P, Levine KM, Tasdemir N, Chu D, Park BH, Lee AV. ESR1 mutations confer novel metastatic functions in genome-edited breast cancer cell models [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-08.

Abstract PD8-05: Genomic profiling of metastatic invasive lobular carcinoma reveals unique genomics and therapeutic opportunities

Background

Invasive lobular carcinoma (ILC) is a common breast cancer histological subtype comprising ˜10-15% of all cases. ILC possesses many unique features when compared to invasive ductal carcinoma (IDC). First, ILC has distinct genomic alterations expanding beyond the defining event of CDH1 loss to other genes such as TBX3, FOXA1, and AKT signaling related genes. Second, ILC responds differently to chemotherapeutics and endocrine therapies despite similar clinical staging. Third, ILC tumors spread to a distinct set of organs compared to IDC tumors, commonly forming distant metastases in the ovary, colon, omentum, and stomach. However, the genomics of metastatic ILC have yet to be fully explored.

Methods

Comprehensive hybrid-capture based genomic analysis of 286-395 cancer related genes was performed on 5523 histologically defined ILC (n=613) and IDC (n=4910) tumors. Of these, 29% and 21% were from distant metastatic sites for ILC and IDC, respectively. Additionally, histology based ER-status was available for a subset of tumors allowing a subgroup of ER-positive, HER2-negative IDC (ER-IDC) samples to be identified (n=655).

Results

We examined the genetic differences between ILC and IDC in the context of both local and metastatic disease. Overall, the genomic profiles of ILC are enriched for alterations in CDH1, TBX3, PIK3CA, and RUNX1 in agreement with previous studies. Alterations in genes involved in AKT signaling (PIK3CA, PTEN, and AKT1) are also enriched in ILC (64% v. 49%; p&lt;10-7). Interestingly, NF1 loss of function alterations are enriched in metastatic ILC compared to ER-IDC (12.2% v. 3.6%, p&lt;0.001) but not in local disease (4.8% v. 4.1%, p=0.72). NF1 is a negative regulator of RAS-cyclic AMP pathway and suggests that NF1 driven RAS signaling is an important driver of metastasis in ILC.

We next examined metastatic ILC samples for alterations enriched at specific metastatic tissue sites. Two metastatic sites were exclusive to ILC samples compared to ER-IDC: GI (19.4%) and the female reproductive tract (11.7%). Within metastatic ILC, alterations in ESR1 showed strong tissue site bias towards liver metastases with 29% harboring an alteration in ESR1 (range: 8-13% in other sites, excluding ovary). Interestingly, ESR1 alterations were never observed in 14 ovary metastases, potentially reflecting an effect of local estrogen production on ILC ovarian metastases. In support of this, ILC ovarian metastases occur in younger women with a median age of 53.5 compared to 63.5 across all other sites.

Lastly, high tumor mutation burden (TMB) is strongly associated with metastatic ILC with 8.9% of metastatic ILC classified as TMB-high (320 mutations/Mb) compared to 2.1% of ILC in the breast. A similar but less pronounced finding was also observed for ER-IDC (1.6% versus 0.8%). This suggests that checkpoint blockage therapies may be a more common option in metastatic ILC than previously appreciated.

Conclusions

Genomic profiling of metastatic ILC reveals numerous potential therapeutic options enriched in this disease. Inhibition of RAS signaling driven by NF1 loss and TMB-high directed immunotherapeutics may be potential therapeutic options for a substantial portion of metastatic ILC patients.

Citation Format: Sokol ES, Basudan A, Lee AV, Stephens PJ, Frampton GM, Oesterreich S, Hartmaier RJ. Genomic profiling of metastatic invasive lobular carcinoma reveals unique genomics and therapeutic opportunities [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-05.

Abstract PD4-09: Combination FGFR4 and ER-targeted therapy for invasive lobular carcinoma

Background

Invasive Lobular Carcinoma (ILC) is an understudied subtype of breast cancer that requires novel therapies in the advanced setting. Distinctive properties of ILC include growth patterns, metastatic behavior, and receptor status (almost universally estrogen receptor (ER) positive). Our lab recently generated six long-term estrogen deprivation (LTED) models of ILC cells and performed RNA-Sequencing to identify differentially expressed genes compared to their parental cells cultured with estrogen. We overlapped these results with a previously published microarray dataset and found that FGFR4 is the most consistently overexpressed gene in the setting of acquired resistance to endocrine therapy in ILC cells.

Hypothesis

FGFR4 is an important mediator of resistance to endocrine therapy in ILC.

Methods

To study the role of FGFR4 in vitro, we used multiple shRNAs and specific small molecule inhibition for growth assays of ILC cells. To study the role of FGFR4 in de novo resistance to endocrine therapy, we collected 129 well curated ER+ ILC tumor specimens and performed gene expression analysis on the pre-treatment samples using a custom NanoString panel. To study the role of FGFR4 in acquired resistance, we collected over 50 pairs of primary-metastatic ER+ tumors and performed exon capture based RNA-Sequencing.

Results

FGFR4 inhibition decreases parental and LTED ILC cell growth in classic 2D conditions, in the setting of ultra-low attachment, and in colony formation assays. The LTED cells, with higher FGFR4 expression, are more sensitive to its inhibition. For the parental cells, combination FGFR4 and ER-targeting drugs results in synergistic decreases in growth. In our database of primary ILC clinical samples, increased expression of FGFR4 is predictive of shorter time to distant recurrence. For our collection of 50 paired, primary-metastatic ER+ tissues, FGFR4 expression increases on average &gt;2.5 fold in the metastatic setting, with large gains even in ductal carcinoma cases. Finally, in analyzing recently published cohorts of metastatic tumors, there is a significant enrichment of hotspot FGFR4 mutations in tumors originating in the breast, with &gt;2% of metastatic ILC tumors containing such a mutation.

Conclusion

FGFR4 may play an important role in both acquired and de novo resistance to endocrine therapy in ILC.

Citation Format: Levine KM, Chen J, Sikora MJ, Tasdemir N, Priedigkeit N, Tseng GC, Puhalla SL, Jankowitz RC, Dabbs DJ, McAuliffe PF, Lee AV, Oesterreich S. Combination FGFR4 and ER-targeted therapy for invasive lobular carcinoma [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 PD4-09.

Abstract P1-01-07: Clinical and histological characteristics of peritoneal metastases of invasive lobular breast cancer

Introduction: In previously reported autopsy series, peritoneal metastases have been detected in up to 40% of patients with invasive lobular breast cancer (ILC). Despite modern diagnostic techniques such as high-resolution ultrasound, it remains a challenge to differentiate ovarian cancer from metastatic breast cancer with peritoneal manifestation before or during surgery. The goal of this analysis was to determine typical clinical and immunohistological features of peritoneal metastasis of ILC. Specifically, we asked the question whether there are predictive factors in primary breast cancer associated with subsequent development of peritoneal metastasis. Patients and methods: We identified 58 patients with ovarian metastases in the Charité cancer register (4,792 breast cancer patients from 2003 to 2015). We looked for clinical and pathological differences between breast cancer patients with (N=58) and without (N=4734) peritoneal metastases and between ILC and non-ILC breast cancer subtypes. Imaging and surgical reports of these 58 patients with ILC intraperitoneal metastases were reviewed. Results: The majority (84.7%) of primary breast cancers consisted of subtypes other than ILC and only 15.3% were histologically characterized as ILC. In contrast, 63.6% of patients with peritoneal metastases had histologically proven ILC in the metastatic tissue. Other subtypes where found in the 36.4% of the metastatic tissue (p&lt;0.001). The Odds ratio for peritoneal metastases for ILC was 2.35 (95% CI 1.655-3.332) and for Non-ILC 0.23 (0.185-0.284). There were no significant differences in receptor status between primary and peritoneal metastatic ILC. Comparing ER/PR expressions levels on primary tumor versus metastasis, while statistically not significant (p= 0.805), showed a rise in ER expression in 42.95% in the metastatic tissue while PR expression remained stable with no difference in 53.3% and a rise in the metastatic site in only 26.7% (p= 0.715). Median age of all patients with primary breast cancer was 60 years (10%-90%: 41-75). There was a significant difference in age at diagnosis of metastasis between patients with (50.5 years) and without peritoneal metastases (59 years) (p= 0.002). Median time to development of peritoneal metastases for all patients was 48.5 months (10%-90%: 0-191.7), for ILC 44 months (0-198.2) and for Non-ILC 56.5 months (6.7-206.4) (p= 0.487). Median survival time for patients with ILC and peritoneal metastases was 56 months, for Non-ILC 53 months (p=0.759). 33 of 58 patients had radiologic evidence of disease, 26 with ILC and 7 with Non-ILC. An ovarian mass was detected by imaging in 15/26 patients with ILC and 4/7 patients with non-ILC. Ascites and diffuse peritoneal metastases were seen in 18/26 patients with detectable ILC and in 4/7 patients with Non-ILC.

Conclusion: This is the first comprehensive analysis of clinical and pathological characteristics of peritoneal metastases showing ILC is more frequent than other histologic subtypes. Patients with peritoneal metastasis are significantly younger (median 50.5y.) than patients without. The clinical signs are similar to those of ovarian cancer except and therefore the diagnosis of metastatic ILC must be taken into consideration as a differential diagnosis.

Citation Format: Karsten MM, Ingold-Heppner B, Oesterreich S, Sander S, Machleidt A, von Waldenfels G, Denkert C, Blohmer JU. Clinical and histological characteristics of peritoneal metastases of invasive lobular 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 P1-01-07.

Abstract P4-05-02: Differential regulation of ER protein-turnover in invasive lobular carcinoma cells

Background: Invasive lobular breast carcinoma (ILC) accounts for 10-15% of breast cancers diagnosed annually. ILCs are more likely to be positive (90-95%) for ER compared to IDC (60-70%), and there is some evidence that endocrine treatment response might be different in patients with IDC vs ILC. We asked the question whether there were differences in ER protein steady state levels, and/or turn-over rates.

Methods: We utilized TCGA dataset to compare ESR1 mRNA and ER protein levels between ER+ ILC (n=137) and IDC (n=554). ER H-scores and ESR1 mRNA levels were analyzed from patients with ER+ ILC (n=143) and IDC (n=877) seen at UPMC Magee Women's Hospital. Correlation analysis with Pearson's (r) and Spearman's rank order coefficient (ρ) was used to study the relationship between mRNA and protein levels. Basal and ligand induced ESR1 mRNA and ER protein expression and turn-over were determined in a panel of estrogen responsive ER+ IDC (MCF-7, T47D and ZR75-1) and ILC (BCK-4, MDA-MB-134 VI (MM134), SUM44PE) cell lines to identify potential mechanisms that can contribute to differential expression of ERα protein.

Results: TCGA database analysis revealed significantly lower ESR1 mRNA and ER protein levels in ER+ ILC compared to IDC tumors. Analysis of data from our Magee hospital showed similar ER IHC H-scores for ER+ ILCs and IDCs despite having significantly lower ESR1 mRNA in ILC. In both the study sets, the correlation between ER mRNA and protein levels were found to be significantly weaker in ER+ ILC than IDC suggesting subtype specific increased synthesis and/or stability of the receptor protein. ILC cell lines MM134 and SUM44 have increased levels of ER protein compared to IDC cell lines. Estradiol decreased the levels and half-life of ER protein in all IDC cell lines tested. In MM134 and SUM44PE ILC cell lines, estradiol decreased the rate of degradation of ER and increased its half-life. In MM134 cells, treatment with estradiol induced a dose- and time-dependent increase in ER, which is associated with a sustained level of elevated phosphorylation at Ser 118.

Conclusions and ongoing/future studies: The estradiol-induced ER protein stability in a subset of ILC cell lines suggest a possible mechanism leading to weaker ER mRNA-protein correlation in ILC tumors. We currently do not know if and how this observation might be linked to antiestrogen response in ILC. We have recently initiated a TBCRC-supported trial in which we will compare the effect of different endocrine therapies in patients with ILC. Access to pre and post therapy samples will provide the opportunity to study ER levels and its downstream signaling as a function of antiestrogen treatment.

Citation Format: Jankowitz RC, Sreekumar S, Levine KM, Meier C, Sikora MJ, Basudan A, Boone D, Dabbs DJ, Jacobsen B, Lee AV, Oesterreich S. Differential regulation of ER protein-turnover in invasive lobular carcinoma cells [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 P4-05-02.

Abstract GS2-03: Highly recurrent transcriptional remodeling events in advanced endocrine resistant ER-positive breast cancers

BACKGROUND: Although individual cancers are driven by heterogeneous processes, cancer mortality has a near universal cause—therapy resistance, recurrence and metastasis to vital organs. Characterizing more advanced tumors has borne valuable insight into cancer progression, yet studies of longitudinally collected breast cancer specimens are scarce given lengthy periods of cancer dormancy. In this study, we aimed to create the most comprehensive characterization of gene expression alterations to date between patient-matched pairs of primary and advanced ER-positive breast cancers.

MATERIALS/METHODS: Hybrid-capture RNA-sequencing was performed on 50 patient-matched pairs of primary and advanced ER-positive tumors from various recurrence sites (9 brain, 11 bone, 3 GI, 10 ovary, 17 local). Time to recurrence was up to 14.1 years with a median of 3.4 years. A shared variant analysis confirmed all paired samples were patient-matched. 1,380 cancer-related genes were analyzed for outlier expression fold-changes in matched recurrences versus primary tumors. Pair-specific, outlier fold-change thresholds were defined as Q1/Q3 +/- [1.5 X IQR]; using each pairs' fold-change values across all genes as the distribution. These discrete, longitudinal transcriptional remodeling events (LTREs) were assessed for recurrence across all sites and analyzed for enrichments within specific cohorts (Fisher's exact tests), such as locoregional vs. distant recurrences. To determine if LTREs represent acquired vulnerabilities, ex vivo and in vivo experiments targeting a recurrent, druggable LTRE gain of RET was performed.

RESULTS: The majority of advanced cancers were transcriptionally similar to patient-matched primaries with 23 of 33 distant metastases retaining PAM50 assignments of the matched primary—shifts to HER2 (n=4, 12%) or Luminal B (n=5, 15%) subtypes accounted for most metastatic discordances. Despite this intrinsic conservation, remarkably recurrent gene-level LTRE gains and losses were observed in advanced disease. Recurrent LTRE gains included NCAM1 [42%], FGFR4 [40%], IBSP [36%], ROBO2 [36%] and SPP1 [30%]. Notable LTRE losses included RELN [42%] and ESR1 [26%]. NCAM1 LTREs showed the most significant enrichments (p &lt; 0.001) in distant disease (20 of 33, 61%) versus locoregional disease (1 of 17, 6%). A prominent LTRE enriched in brain metastasis (BrM) was RET (p-value = 0.003), expression of which showed outlier gains in 56% of ER-positive BrM. Marked anti-tumor activity was demonstrated with the RET inhibitor cabozantinib in ex vivo explant cultures of patient resected BrMs (n=3) and a BrM patient-derived xenograft.

CONCLUSIONS: Taken together, these results demonstrate profound, recurrent and metastatic site-specific LTREs in advanced breast cancers, which may be essential to our understanding of endocrine-therapy resistance and metastasis. Although current emphasis for longitudinal clinical profiling of tumors is on DNA-level alterations, these results suggest LTREs as a compelling, shared mechanism of cancer progression. Given remarkably high recurrence rates of specific LTREs across multiple cohorts, further preclinical and clinical investigations of LTREs are demanded, especially considering some (i.e. FGFR4 and RET) are readily druggable.

Citation Format: Priedigkeit N, Vareslija D, Basudan A, Watters RJ, Lucas PC, Davidson NE, Blohmer J-U, Denkert C, Machleidt A, Heppner BI, Brufsky AM, Oesterreich S, Young L, Lee AV. Highly recurrent transcriptional remodeling events in advanced endocrine resistant ER-positive breast cancers [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 GS2-03.

Abstract P1-03-03: Invasive lobular carcinoma and invasive ductal carcinoma differ in immune response, translation efficiency and metabolic rate

Background

Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer after invasive ductal carcinoma (IDC). ILC differs from IDC in pathologic, molecular, and clinical features. ILC tumors are most often characterized as luminal A by PAM50 analysis, suggestive of an indolent disease. Yet, when matched for receptor status and tumor grade, patients with ILC tend to have worse long-term outcomes than patients with IDC. The main distinguishing molecular feature of ILC is the loss of functional E-cadherin, and yet, beyond that loss, the mechanisms underlying the differences between ILC and IDC are largely unknown. We examined the RNA expression profiles of ILC and IDC tumors to assess if there may be underlying vulnerabilities of ILC tumors to novel therapeutic strategies.

Methods

Differential expression analysis was performed on 159 luminal A (LumA) ILC tumors versus 311 LumA IDC tumors from The Cancer Genome Atlas (TCGA). The METABRIC cohort (65 LumA ILC and 533 LumA IDC) was used as a validation dataset. Pathway enrichment analysis was performed to identify potential differences in biological processes, and these potential differences were then tested in a series of in vitro experiments, using 3 ER+ ILC (MDA-MB-134VI, SUM44PE, and MDA-MB-330) and 3 ER+ IDC (MCF7, T47D, and ZR75.1) cell lines.

Results

Pathway analysis led to the identification of three main signaling differences between LumA ILC and LumA IDC: immune regulation, translation, and metabolism. A series of immune pathways, including Immunological Synapse, Biocarta IL17 pathway, and Response to Wounding were up-regulated in ILC tumors. We examined specific cell type markers, and found that ILC tumors have a higher activity of nearly all immune cell types, including CD4+ T cells, CD8+ T cells, B cells, NK cells, dendritic cells, M1 macrophages, and M2 macrophages. These results were surprising, since ILC tumors have a lower incidence of stromal inflammation, as defined by H&E staining, suggesting a unique immune regulatory mechanism in ILC.

Next, we examined the translational regulation in ILC vs IDC tumors by comparing RNA expression and protein quantities as determined by RPPA analysis. ILC tumors have a lower protein:RNA ratio, suggesting a lower translation efficiency. This was reflected in the RPPA data by lower protein expression of eIF4G, ribosome protein S6 (S6) and p70-S6K in ILC tumors. Phosphorylation of 4E-BP1 (Ser65), eEF2, S6 (Ser235/236, Ser240/244), and mTOR (Ser2448) were also significantly lower in LumA ILCs. This lower translation efficiency was then validated in cell lines by O-propargyl-puromycin treatment.

Finally, the pathway analysis suggested lower rates of metabolism in lobular tumors. Comparative studies of OXPHOS and glycolysis with a Seahorse analyzer confirmed this finding.

Conclusions

ILC tumors have a higher immune activity than IDC tumors, even with lower rates of stromal inflammation, suggesting a potential for differential response to immunotherapy. The lower rates of translation and metabolism, which are general identifiers of tumor dormancy, could enable ILC to escape from cytotoxic therapies, and may play an important role in the late recurrence of ILC.

Citation Format: Levine KM, Du T, Zhu L, Tasdemir N, Lee AV, Van Houten B, Tseng GC, Oesterreich S. Invasive lobular carcinoma and invasive ductal carcinoma differ in immune response, translation efficiency and metabolic rate [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 P1-03-03.

Abstract MS2-2: Understanding the unique biology of ILC

Invasive lobular breast cancer (ILC) is characterized by distinct etiological, pathological, and clinical features, yet the underlying biology is poorly understood. To extend the molecular determinants of ILC beyond the well-known loss of E-cadherin, we combined a plethora of in silico and wet-bench approaches, and comprehensively characterized ILC tumor models and clinical samples.

In support of recent data from The Cancer Genome Atlas on differences in mutations in critical ER co-factors between invasive lobular and ductal cancers, we have identified distinct ER signaling pathways, and mechanisms of endocrine resistance in ILC. These include the acquisition of unique ER target genes, activation of IGF and FGFR signaling, and changes in metabolic pathways. As part of our efforts to elucidate mediators of ILC progression, transcriptomic analysis of primary tissue from patients with and without disease recurrence identified potential genetic drivers, including Cortactin, an actin binding protein with a known role in metastasis. To further identify genes that mediate the unique metastatic properties of ILC cells, we sequenced metastases to the ovary and the gastrointestinal tract, and uncovered pathways that might serve as critical vulnerabilities and therapeutic opportunities. In this lecture, I will review our progress, and discuss the potential clinical significance and implications of these findings.

Citation Format: Oesterreich S. Understanding the unique biology of ILC [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 MS2-2.

Abstract P5-17-01: Lobular breast cancer alliance - Advocates advancing research, screening, treatment and follow-up care for lobular breast disease

Introduction

Thirty patient advocates attended the First International Invasive Lobular Breast Cancer Symposium in 2016 at the University of Pittsburgh Cancer Center. The conference underscored that invasive lobular breast cancer (ILC) and other lobular pathologies are understudied. Specifically:

ILC is the sixth most prevalent cancer of women and the second most frequently diagnosed histological subtype of breast cancer impacting up to 34,000 patients a year in the US.

ILC is a molecularly distinct breast cancer with unique subtypes and variants with differences in presentation and behavior, including physical findings of thickening and a tendency to metastasize to unique locations.

While ILC is frequently associated with a good initial prognosis, recent analysis suggests that long-term outcomes of ILC may be worse than those stage-matched to ductal breast cancer.

Current imaging tools are less reliable for early detection of lobular disease and detection of distant recurrence.

Standard of care chemotherapy and endocrine therapies may have different effectiveness applied to ILC and IDC.

Challenges

Growing interest in ILC research requires improved methods to identify, communicate with and link patients with ILC to clinical trials and research. Advocates with advanced science training are needed as partners for research proposals and grant reviews.

Lobular breast cancer is under-represented in key meetings and literature. Encouraging opportunities to share ILC research as agenda topics and fostering collaborations between researchers, clinicians and advocates can accelerate progress and refine clinical practices for screening, treatment and follow-up.

Patients living with ILC lack a central on-line source of lobular breast cancer information and resources. This information gap is a barrier to help patients recognize signs of lobular breast cancer's unique presentation and metastatic behaviors.

Results

The Lobular Breast Cancer Alliance (LBCA) was formed by patient advocates who attended the First International ILC Symposium in response to advocate-identified opportunities to advance research, refine treatments and enhance patient education.

LBCA's mission is to bridge patients, clinicians and researchers to increase our knowledge of lobular breast disease and promote research that leads to advancements in prevention, diagnosis, treatment and patient follow-up care.

Conclusions

LBCA is driving an increased awareness of lobular breast cancer with specific goals:

Build a clinically accurate, patient centered website devoted to lobular breast cancer at www.LobularBreastCancer.org.

Elevate lobular research and foster opportunities for researcher, advocate and clinician collaborations at prominent conferences and meetings.

Identify barriers to conduct research on ILC and metastasis and link patients and advocates to ILC tumor research and clinical trials.

Initiate peer-to-peer clinician outreach strategy through targeted literature, meetings and education services to share information on ILC presentation, metastatic patterns and screening and treatment challenges of patients with ILC.

Build partnerships with existing breast cancer organizations to integrate ILC into existing information resources and work on common goals.

Citation Format: Petitti L, Axelrod J, Campbell-Kotler M, Frank E, Jaremek J, Levine J, McWilliams M, Migyanka F, Ryan N, Viggiano E, Metzger-Filho O, Oesterreich S, Pate L. Lobular breast cancer alliance - Advocates advancing research, screening, treatment and follow-up care for lobular breast disease [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 P5-17-01.

Abstract P5-06-03: Generation and characterization of a novel invasive lobular breast carcinoma cell line WCRC-25

Background: Invasive Lobular Breast Carcinoma (ILC) is the second most common histologic subtype of breast cancer, comprising 10-15% of all cases. ILC is clinically and molecularly distinguished from the major subtype–Invasive Ductal Carcinoma (IDC)–by loss of E-cadherin (CDH1). Studies on ILC remain sparse, in part due to limited cell culture models. The Women's Cancer Research Center (WCRC) has therefore set up a combined effort of breast surgical oncologists, medical oncologists, pathologists, and cancer biologists to collect fresh tissues and establish additional ILC cell lines.

Methods: Tumor cells were grown using irradiated fibroblast conditioned media (CM) in hypoxic (5% O2) conditions. Sanger sequencing and Droplet Digital PCR (ddPCR) were utilized to test for mutation in CDH1 in tumor and circulating DNA (cfDNA), using germline DNA as control. DNA copy number status in the tumor was detected using nanoString approach. Expression of E-cadherin and a series of lineage markers was elucidated using Immunoblotting (IB) and Immunofluorescence (IF). A panel of ILC (MDA-MB-134, Sum44PE, IPH-926) and IDC (MCF-7, MDA-MB-231) cell lines was included for comparison. After establishment, WCRC-25 population doubling was compared between growth in CM or Dulbecco's Modified Eagle's Medium (DMEM), and hypoxic (5% O2) or normoxic (21% O2) conditions. Growth phenotypes were characterized in 2D, Ultra Low Attachment (ULA), and soft agar.

Results: WCRC-25 was successfully established from the pleural effusion of a 77-year old patient with metastatic ILC. The patient had stage IV (T3N3M1) ER+/PR-/HER2- ILC; was treated with bilateral mastectomy, radiation therapy, and multiple lines of chemotherapy (FOLFOX due to initial misdiagnosis; 2 cycles carboplatin/paclitaxel; anastrazole, fulvestrant, pegylated liposomal doxorubicin, gemcitabine, exemastane, and eribulin (with denosumab for bone lesions); had metastatic lesions in stomach, bone, pleura, and pericardium; and ultimately passed away from progressive pleural effusions roughly 3 years after diagnosis. A novel nonsense mutation of CDH1 was observed in exon 13 (Q705*) in cell line DNA, resulting in a premature stop codon. The same mutation was confirmed in cfDNA obtained from longitudinal blood samples from the patient. Copy number analysis revealed deletion of the second CDH1 copy in tumor, and E-cadherin protein loss was confirmed by IB and IF. WCRC-25 cells expressed epithelial cell markers CK8/18 and EpCAM, and as expected did not express stromal marker αSMA. ERα expression was very low, and not sufficient for measurable hormone response. Population doubling was significantly faster in hypoxic compared to normoxic conditions, regardless of media type, but minimal in 3D.

Conclusions: WCRC-25 is a novel ILC cell line, defined by CDH1 nonsense truncating mutation and LOH, resulting in loss of E-cadherin protein expression. Cells show favorable growth characteristics in hypoxic conditions and maintain epithelial-dominated protein expression. We are currently performing RNA seq analysis of the matched primary tumor and metastatic samples from the stomach, peritoneum/falciform ligament, pleural effusion and skin, which we will compare and contrast with that of the established WCRC-25 cell line.

Citation Format: Kota K, Bossart E, Basudan A, Minteer T, Meier C, Brown D, Gurda GT, Miller L, Dabbs DJ, Lee A, Puhalla S, Jankowitz R, McAuliffe P, Lucas P, Oesterreich S. Generation and characterization of a novel invasive lobular breast carcinoma cell line WCRC-25 [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 P5-06-03.

CYP2D6 genotype is not associated with survival in breast cancer patients treated with tamoxifen: results from a population-based study

PURPOSE

A number of studies have tested the hypothesis that breast cancer patients with low-activity CYP2D6 genotypes achieve inferior benefit from tamoxifen treatment, putatively due to lack of metabolic activation to endoxifen. Studies have provided conflicting data, and meta-analyses suggest a small but significant increase in cancer recurrence, necessitating additional studies to allow for accurate effect assessment. We conducted a retrospective pharmacogenomic analysis of a prospectively collected community-based cohort of patients with estrogen receptor-positive breast cancer to test for associations between low-activity CYP2D6 genotype and disease outcome in 500 patients treated with adjuvant tamoxifen monotherapy and 500 who did not receive any systemic adjuvant therapy.

METHODS

Tumor-derived DNA was genotyped for common, functionally consequential CYP2D6 polymorphisms (*2, *3, *4, *6, *10, *41, and copy number variants) and assigned a CYP2D6 activity score (AS) ranging from none (0) to full (2). Patients with poor metabolizer (AS = 0) phenotype were compared to patients with AS > 0 and in secondary analyses AS was analyzed quantitatively. Clinical outcome of interest was recurrence free survival (RFS) and analyses using long-rank test were adjusted for relevant clinical covariates (nodal status, tumor size, etc.).

RESULTS

CYP2D6 AS was not associated with RFS in tamoxifen treated patients in univariate analyses (p > 0.2). In adjusted analyses, increasing AS was associated with inferior RFS (Hazard ratio 1.43, 95% confidence interval 1.00-2.04, p = 0.05). In patients that did not receive tamoxifen treatment, increasing CYP2D6 AS, and AS > 0, were associated with superior RFS (each p = 0.0015).

CONCLUSIONS

This population-based study does not support the hypothesis that patients with diminished CYP2D6 activity achieve inferior tamoxifen benefit. These contradictory findings suggest that the association between CYP2D6 genotype and tamoxifen treatment efficacy is null or near null, and unlikely to be useful in clinical practice.

Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen

Steroid receptor coactivator-1 (SRC-1), a well-studied coactivator of estrogen receptor (ER), is known to play an important and functional role in the development and maintenance of bone tissue. Previous reports suggest SRC-1 maintains bone mineral density primarily through its interaction with ER. Here we demonstrate that SRC-1 can also affect bone development independent of estrogen signaling as ovariectomized SRC-1 knockout (SRC-1 KO) mouse had decreased bone mineral density. To identify estrogen-independent SRC-1 target genes in osteoblastogenesis, we undertook an integrated analysis utilizing ChIP-Seq and mRNA microarray in transformed osteoblast-like U2OS-ERα cells. We identified critical osteoblast differentiation genes regulated by SRC-1, but not by estrogen including alkaline phosphatase and osteocalcin. Ex vivo primary culture of osteoblasts from SRC-1 wild-type and KO mice confirmed the role of SRC-1 in osteoblastogenesis, associated with altered ALPL levels. Together, these data indicate that SRC-1 can impact osteoblast function in an ER-independent manner.

Abstract P6-07-07: ESR1 amplification and 5'-3' exon imbalance in metastatic breast cancer

BACKGROUND: Growing evidence indicates that base pair mutations in ESR1 are relatively uncommon in newly diagnosed, treatment-naive breast cancer, but frequently acquired in hormone-resistant metastatic breast cancer (MBC). We and others have recently identified ESR1 gene fusion and amplification in MBC, with the ESR1 fusions generally encompassing AF1 and the DNA binding domain. The genomic break required for gene fusions often results in an imbalance in the DNA copy number of exons around the break. We examined ESR1 amplification and 5' and 3' exon copy number imbalance in MBC.

MATERIALS and METHODS: We designed NanoString DNA hybridization probes against coding and non-coding exons (n=9) in ESR1 and 15 reference probes. We analyzed 128 samples consisting of 61 ER-positive and 44 ER-negative metastases, and 23 primary breast cancers. DNA copy number (CN) was determined using nSolver, with &gt;2.7CN as copy number gain, and &gt;10 as CN amplification. ESR1 CN was calculated by averaging the DNA copy number obtained from all coding exons. The 5'-3' copy number ratio was the average copy number of the 5' exons (3-6) divided by the 3' exons (7-10).

RESULTS: 8 (13%) ER positive metastatic breast cancers showed ESR1 amplification with 5 (8%) having &gt;2.7CN, and 3 (5%) with &gt;10CN. In contrast, in ER-negative metastases, we did not detect any samples with amplification &gt;10CN, and a gain (&gt;2.7 CN) in one case. Similarly, in ER+ primary cancers we did not detect any samples with &gt;10 CN amplifications and 2 samples with CN gain (&gt;2.7 CN). ESR1 showed 5'-3' CN imbalance in 1 primary (5%) and in 5 metastatic (5%) breast cancers. We are currently confirming and expanding these data in a larger dataset.

CONCLUSIONS: In addition to ESR1 mutations, ESR1 CN amplifications and 5'-3' imbalance are represent frequent occurrences in endocrine resistant breast cancer. Future studies are aimed at understanding whether the observed exon imbalances are associated with generation of fusion proteins, and whether and how ESR1 amplifications cause changes in endocrine treatment response.

Citation Format: Oesterreich S, Basudan A, Preideigkeit N, Hartmaier RJ, Bahreini A, Gyanchandani R, Leone JP, Lucas PC, Hamilton RL, Brufsky AM, Lee AV. ESR1 amplification and 5'-3' exon imbalance in metastatic 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 P6-07-07.

Abstract P3-04-02: Differential turnover of estrogen receptor alpha in invasive lobular carcinoma

Background: Invasive lobular carcinoma (ILC) accounts for 10-15% of invasive breast cancers diagnosed annually. There is increasing evidence that endocrine treatment response might differ between Invasive Ductal Carcinoma (IDC) and ILC, and that patients with ILC have worse long-term survival when other prognostic factors are taken into account. One such factor is ER status, which is more likely to be positive in ILC (90-95%) compared to IDC (60-70%). There are few studies that have directly compared mRNA and protein levels between ER+ ILC and ER+ IDC.

Hypothesis: Differences in ER protein steady state levels, and/or turn-over rates contribute to differences in endocrine treatment response between patients with ILC vs IDC.

Methods: We utilized publicly available TCGA data to compare ER mRNA and protein levels between ER+ ILC (n=184) and IDC (n=534). Correlation analysis with Spearman's rank order coefficient (ρ) was used to study the relationship between mRNA and protein levels. METABRIC data were analyzed to compare ER mRNA levels between ER+ ILC (n=130) and IDC (n=1152). ER H-scores and mRNA levels were also analyzed from patients with ER+ ILC (n=180) and IDC (n=1183) seen at our local UPMC Magee Womens Hospital. Finally, ER mRNA and total protein levels, and RNA and protein turn-over rates were determined in 2 IDC and 2 ILC breast cancer cell lines, using qRT-PCR and immunoblots analysis.

Results: Analysis of ESR1 gene expression in the TCGA database revealed significantly lower levels of ER mRNA (Mann-Whitney, p&lt;.0005) in ER+ ILC compared to IDC, whereas ER protein levels were similar in the two histological subtypes. The correlation between ER mRNA and protein levels is weaker in ER+ ILC (ρ=0.60) compared to ER+ IDC (ρ=0.69) tumors, though not statistically significant. The weaker correlation between mRNA and protein expression in ILC is more clear when analyzing all 130 RNA and protein pairs with available RRPA data, (ILC median ρ=0.28; IDC median ρ=0.34, p&lt;.0005). In the METABRIC dataset, ESR1 mRNA levels were also found to be lower in ER+ ILC tumor samples compared to IDCs (Mann-Whitney, p&lt;0.005). In concordance with these observations, the study of patients seen at our local hospital showed similar ER IHC H-scores for ER+ ILCs (H-score = 244) and IDCs (H Score = 248), despite there being significantly lower ESR1 mRNA in ILC (p&lt;0.005). Finally, our in vitro data showed that rate of estrogen-mediated turn-over of ER protein was significantly lower in the ILC cell lines compared to the IDC cell lines, which might explain the lack of lower ER protein levels despite lower ER mRNA levels. We are currently confirming these findings in additional cell lines, and deciphering the mechanisms through the study of ER ubiquitin-modification and proteasome machinery comparing ILC and IDC.

Conclusion: We have provided functional and in silico data that collectively suggest altered ER protein turn-over in ILC compared to IDC. We are currently testing if and how this affects sensitivity of ILC cells to SERDs, and underlying mechanisms.

Citation Format: Sreekumar S, Levine K, Sikora MJ, Boone D, Dabbs DJ, Lee AV, Jankowitz RC, Oesterreich S. Differential turnover of estrogen receptor alpha in invasive lobular carcinoma [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 P3-04-02.

Abstract P3-07-04: WNT4 mediates endocrine response and resistance in invasive lobular carcinoma cells

Invasive lobular carcinoma (ILC) is a breast cancer subtype affecting ~30,000 U.S. women annually. Over 90% of ILC are estrogen receptor (ER)-positive; however, endocrine therapy may have poorer efficacy in a subset of ILC patients versus invasive ductal carcinoma (IDC) patients. This prompted us to assess global ER activity in ILC cell lines MDA MB 134VI (MM134) and SUM44PE (44PE) to identify novel mediators of ER signaling. These analyses identified the Wnt ligand WNT4 as an ILC-specific ER target gene, with an ILC-specific ER binding site (ERBS) at the WNT4 locus. Considering the critical role of WNT4 in normal mammary gland expansion, we hypothesize that ILC cells utilize WNT4 signaling to drive endocrine response and resistance.

We assessed whether WNT4 is necessary for ILC cell growth using siRNA. WNT4 knockdown completely blocked estrogen-induced growth in ILC cells but not IDC cells. In parallel, the WNT4 ERBS was only occupied in ILC cells in response to estrogen, but progesterone-induced WNT4 in IDC was not associated with this ERBS. This suggests that, via the ILC-specific WNT4 ERBS, ILC cells drive estrogen-regulated proliferation by hijacking a developmental Wnt pathway. Wnt pathways typically activate β-catenin; however, we observed β-catenin dysfunction in ILC cells and that WNT4 cannot activate β-catenin. Thus, WNT4 signals in ILC cells via a novel non-canonical pathway.

Using long-term estrogen-deprived (LTED) variants of MM134 and 44PE (4 and 2 lines, respectively), we assessed WNT4 in ILC endocrine resistance. WNT4 is over-expressed, but uncoupled from ER, in all MM134-LTED. Conversely, WNT4 is reduced in 44PE-LTED but remains ER-regulated; ER occupies the WNT4 ERBS only in 44PE-LTED cells and not MM134-LTED. Using siRNA, MM134-LTED (high WNT4) are growth-inhibited by WNT4 knockdown, while 44PE-LTED (low WNT4) are insensitive. However, WNT4 knockdown sensitizes 44PE-LTED to endocrine therapy. Taken together, uncoupling and upregulating WNT4 or WNT4/ER cross-talk may represent convergent endocrine resistance mechanisms in ILC. Further characterization of ILC-LTED cells demonstrated WNT4 expression is driven by activated NFκB signaling in MM134-LTED, and implicated the pluripotency factor Oct4 in regulating WNT4 in 44PE-LTED cells. In both parental ILC cells and ILC-LTED cells, WNT4 leads to suppression of CDKN1A/p21, which is critical for ILC cell proliferation; CDKN1A knockdown partially reverses the effects of WNT4 knockdown.

Clinical observations suggest that ER regulates unique pathways in ILC. We identified WNT4 as a downstream effector of endocrine signaling in ILC, with critical roles in both estrogen-induced growth and endocrine resistance. WNT4 signaling may represent a novel target to modulate endocrine response specifically for ILC patients.

Citation Format: Sikora MJ, Oesterreich S. WNT4 mediates endocrine response and resistance in invasive lobular carcinoma cells [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 P3-07-04.

Abstract PD1-05: Breast cancer brain metastases show limited intrinsic subtype switching, yet exhibit acquired ERBB2 amplifications and activating mutations

BACKGROUND: Metastasis is the major cause of mortality in breast cancer (BrCa) patients. Our understanding of brain metastasis (BrM) is limited, reflected by a lack of effective treatments. We aimed to (1) determine BrCa gene signature differences between primary tumors and matched BrM and (2) uncover BrM-specific alterations that may be clinically actionable.

MATERIALS and METHODS: NanoString expression profiling of 127 genes from 5 major prognostic tests (MammaPrint, EndoPredict, PAM50, OncotypeDX, MGI) was performed on 20 patient-matched primary (10 ER-neg, 10 ER-pos) and metastatic brain tumors. Subtype classification was performed using genefu. Protein changes in ER and HER2 (ERBB2) were confirmed by IHC. BrM-specific ERBB2 gains were corroborated in a publicly available dataset of 18 additional patient-matched cases (dbGAP phs000730.v1.p1). To test whether ERBB2 amplification and base pair mutation is metastasis-site specific, we further analyzed an expanded cohort of 7,884 breast tumors enriched for metastatic samples (52%) including liver (16.7%), lung (4.3%), bone (3.6%), and brain (2.0%) using comprehensive hybrid-capture sequencing of ERBB2.

RESULTS: 17/20 BrM retained the PAM50 subtype of the primary BrCa. Despite this concordance, 17/20 BrM harbored expression changes (&lt; or &gt; 2-fold) in clinically actionable genes including gains of FGFR4 (30%), FLT1 (20%), AURKA (10%) and loss of ESR1 expression (45%). The most recurrently upregulated gene was ERBB2, showing a &gt;2-fold expression increase in 35% of BrM. 3 of 13 (23.3%) cases originally HER2-negative, and thus HER2-therapy naive, in the primary BrCa were IHC-positive (3+) in the paired BrM with an observed metastasis-specific amplification of the ERBB2 locus. In an independent dataset, 2 of 9 (22.2%) HER2-negative BrCa switched to HER2-positive with one BrM acquiring ERBB2 amplification and the other showing metastastic enrichment of the activating V777L ERBB2 mutation. Analysis of a large cohort of breast tumors (n=7,884) showed that across all organs ERBB2 amplification and/or base pair mutation was similar (p=0.18) between primary (13%) and metastatic disease (12%), however, a strong and significant enrichment was seen for BrM (primary 13% vs BrM 24%, p&lt;0.0005).

CONCLUSIONS: Taken together, these results demonstrate that the majority (85%) of patient-matched BrM retain the intrinsic subtype of the primary cancer. However, despite this transcriptional similarity, alterations in clinically actionable genes are common, with BrM acquiring ERBB2 amplifications and/or base pair mutations at a frequency of ∼20%, even in HER2-therapy naive tumors. In a large cohort of primary and metastatic breast cancers, there is also a unique enrichment for ERBB2 alterations in BrM. This study provides a strong rationale to molecularly profile metastatic lesions to both better understand biological mechanisms of metastases and to perhaps refine therapeutic decision-making in advanced cancers.

Citation Format: Priedigkeit N, Hartmaier RJ, Chen Y, Vareslija D, Basudan A, Thomas R, Leone JP, Lucas PC, Bhargava R, Hamilton RL, Chmielecki J, Davidson NE, Oesterreich S, Brufsky AM, Young L, Lee AV. Breast cancer brain metastases show limited intrinsic subtype switching, yet exhibit acquired ERBB2 amplifications and activating mutations [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 PD1-05.

Abstract P6-11-07: Methylation of BRCA1 and response to the PARP inhibitor veliparib

This abstract was not presented at the symposium.

Abstract P6-08-02: Developing in vitro models of ductal carcinoma in situ from primary tissue

BACKGROUND: Because there are currently no reliable predictors for progression of ductal carcinoma in situ (DCIS) to invasive disease, nearly all patients receive aggressive therapy, leading to over-treatment in many cases. Few in vitro models for studying DCIS progression have been developed. We report here the successful culture and expansion of primary DCIS from surgical specimens using a conditional reprogramming protocol.

MATERIALS AND METHODS: From 2/2014 to 4/2015, patients with percutaneous core needle biopsy demonstrating DCIS were enrolled in a tissue banking protocol after informed consent was received. Under supervision of the surgical pathologist, fresh tissue measuring between 5-15 mm in length was taken from lumpectomy or mastectomy specimens. Tissue was divided such that half was mechanically and enzymatically dissociated and then cultured in medium conditioned by irradiated mouse fibroblasts and supplemented with rho-associated protein kinase (ROCK) inhibitor, and the second half, known as the "mirror image" remained as part of the clinical specimen.

RESULTS: Of 49 consented patients, mean age was 59 ± 10 years. 7 were excluded due to final pathology not consistent with DCIS: 4 upstaged to invasive ductal cancer, 2 had microinvasion and 1 showed pleomorphic lobular carcinoma in situ. Of the remaining 42, 9 were failures: 5 tissues were not received in lab and 4 cases were received, but no cells grew in culture. Of the remaining 33 cases of DCIS, 70% (n=23) and 27% (n=9) were nuclear grade 2 and 3 respectively. 91% (n=30) were ER-positive, with H-score ranging between 4 and 300. 19 (58%) were expanded in cell culture for up to two months in culture, and 14 were frozen immediately after mechanical dissociation for future growth. The 19 cell cultures could be cryopreserved and expanded. The cultures are almost exclusively composed of cytokeratin 8- and EpCAM-positive luminal cells and cytokeratin 14-, cytokeratin 5-, and p63-positive basal mammary epithelial cells, suggesting maintenance of heterogeneity in vitro. Furthermore, as assessed by luminal and basal marker expression, these cells retain their cellular identities both in the "conditionally reprogrammed" proliferative state and when conditioned media and ROCK inhibitor were withdrawn. When grown to 100% confluency, the cultures appear to organize into luminal and basal layers as well as luminal compartments surrounded by basal cells.

CONCLUSION: Primary cultures of DCIS derived directly from patient tissues may serve as in vitro models for the study of DCIS.

Citation Format: McAuliffe PF, Brown DD, Oesterreich S, Lee AV, Johnson RR, McGuire KP, Davidson NE, Brufsky AM, Dabbs DJ. Developing in vitro models of ductal carcinoma in situ from primary tissue. [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 P6-08-02.

Abstract P3-05-14: A neoadjuvant window trial of endocrine response in women with invasive lobular carcinoma

Background:

Patients with invasive lobular carcinoma (ILC) would be expected to have favorable outcomes compared to patients with invasive ductal carcinoma (IDC) given that ILC is more often hormone receptor-positive (HR+), human epidermal growth factor receptor 2 (HER2)-negative, of lower grade, and displays decreased proliferation markers. Based on our preclinical studies showing differential hormone response in HR+ ILC vs. IDC and on recent studies suggesting differences in endocrine treatment response between patients with ILC vs. IDC, we designed a biomarker-driven, neoadjuvant window trial for newly diagnosed women with HR+, HER2-negative ILC. We hypothesize that Ki67 will be reduced by 85% in the fulvestrant arm compared with 60% and 75% reduction in the tamoxifen and anastrozole arms, respectively, and that Ki67 reduction will correlate with alterations in expression of ER and ER-regulated genes. Differential Ki67 effect will serve as a surrogate for outcome of patients with ILC on endocrine therapy.

Trial Design: This multicenter study (NCT02206984) will enroll 150 women with HR+ and HER2-negative ILC. A mandatory research breast tumor biopsy will be performed at baseline. Fifty patients will be randomized to each of three open-label treatment arms for 21 days: fulvestrant (two 250 mg IM injections on both day 1 and day 14), anastrozole (1mg orally daily), or tamoxifen (20 mg orally daily). Biomarkers of response will be assessed on baseline and post-treatment tumor tissue. Patients will proceed to definitive surgery on day 21 after study drug exposure, or they will undergo a second research breast core biopsy if further neoadjuvant treatment is planned.

Eligibility Criteria: Eligible patients include postmenopausal women with newly diagnosed, HR+, HER2-negative ILC (excluding pleomorphic subtype) measuring ≥ 1cm, with adequate organ function, ECOG PS ≥ 2, and agreeable to baseline research breast tumor biopsy.

Specific Aims: The primary endpoint is percent change from baseline to post-treatment Ki67 values in ILC tissue after 21 days of endocrine treatment. Comparisons across study arms will be made using a general linear model adjusting for institutional effect, with 80% power estimated for pairwise comparisons of log2(% staining) between treatment arms, allowing for 10% attrition. Secondary endpoints include post-therapy Ki67, and change in ER and PR protein expression by IHC. Finally, planned correlative studies include evaluation of gene expression, epigenetic markers, and DNA sequence variants in ILC tissues in an effort to identify biomarkers of endocrine response and putative drivers of endocrine resistance in ILC.

Target Accrual: This study will be open to enrollment by August 2015 at the University of Pittsburgh. Additional sites will be opened through the Translational Breast Cancer Research Consortium (TBCRC). We anticipate an accrual rate of 8 patients per month.

(Funding from Susan G. Komen® and AstraZeneca).

Citation Format: Jankowitz RC, McAuliffe PF, Sikora MJ, Butler L, Ahrendt G, Johnson R, Diego E, Bonaventura M, Puhalla S, Lembersky B, Clark B, Brufsky A, Kurland BF, Davidson NE, Dabbs DJ, Oesterreich S. A neoadjuvant window trial of endocrine response in women with invasive lobular carcinoma. [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 P3-05-14.

Abstract PD2-08: Potential role of prolactin signaling in development and growth of the lobular subtype of breast cancer

Invasive lobular carcinoma (ILC) is the eighth most frequently diagnosed cancer in any organ, and accounts for 8-11% of breast cancer. This histological subtype is characterized by loss of E-cadherin, and favorable prognostic factors, such as low Ki67 and high rates of ER/PR-positive tumors. Only recently is the lobular subtype gaining recognition as a distinct disease, displaying a unique growth pattern, unique molecular changes in addition to loss of E-cadherin, and evidence for late recurrences and reduced response to targeted endocrine therapy. It is widely accepted that a late age at first full term birth (FFTB) increases a women's risk for breast cancer. Interestingly, several published epidemiological studies have shown that the increased risk after a late age at FFTB is preferential for the lobular subtype of breast cancer compared to the ductal subtype. We therefore hypothesized that pregnancy hormones like prolactin play an integral role in the development and progression of ILC. Interrogation of the Cancer Genome Atlas (TCGA) data revealed a high expression of milk protein genes as well as prolactin signaling molecules, specifically Stat5a and Stat5b in lobular carcinomas compared to ductal carcinomas. We developed a lactation score including 7 milk protein genes and found that in the TCGA data set ILC tumors have a significantly higher lactation score than IDC tumors. Additionally, we found that ILC cell lines express increased prolactin receptor mRNA and protein levels compared to IDC cell lines. Prolactin treatment in ILC and IDC cells reveals divergent signaling pathways - prolactin stimulates ERK activation in IDC but not ILC cells. We are currently further delineating the prolactin signaling pathways, and resulting phenotypes, comparing ILC and IDC cells. We expect these experiments to move the field forward by establishing a relationship between prolactin and lobular carcinoma.

Citation Format: Oesterreich S, Katz TA, Logan G, Levine K, Nagle A, Huo Z, Tseng GC, Rui H, Lee AV, Butler LM. Potential role of prolactin signaling in development and growth of the lobular subtype of 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 PD2-08.

Abstract P1-08-11: Association of variants in candidate genes on lipid profiles in women with early breast cancer on adjuvant aromatase inhibitor therapy

Background

Aromatase inhibitors (AI) can exert unfavorable effects on lipid profiles, but previous studies have reported inconsistent results. Given the intricate biological relationship between estrogen and lipid profiles, these mixed results may be explained in part by variation in genes encoding proteins involved in the drug's target and in estrogen metabolism and signaling. The purpose of this study was to investigate associations of single-nucleotide polymorphisms (SNP) in candidate genes with AI-mediated changes in lipid profiles.

Methods

We completed a prospective multicenter randomized observational open-label study to test the association of SNPs in candidate genes on biomarkers of estrogenic and anti-estrogenic activity in post-menopausal women with early breast cancer who were recommended adjuvant AI therapy. Eligible women were randomly assigned to exemestane or letrozole, and were followed for 2 years. We genotyped 137 SNPs from germ line DNA in the following candidate genes: ARVCF, COMT, CYP19A1, ESR1, ESR2, PGR, EP300, EZH2, NCOA1-3, NCOR1-2, NRIP, and PELP1. Lipid profiles including total cholesterol (TC), low-density lipoprotein (LDL), high-density lipoprotein (HDL), and triglycerides (TG) were measured at baseline and 3 months after initiating AI. We conducted genetic association data analysis and multivariate linear regressions to analyze the genetic effects using dominant, recessive, and additive models. Multivariate analysis included age, body mass index, prior hormone replacement therapy, and prior tamoxifen. To adjust for multiple comparisons, only SNPs with a p&lt;0.0003 were considered significant.

Results

We enrolled 502 women in to the study, but for this analysis we excluded women who did not have genetic data (n = 33), had incomplete data (n = 23), discontinued or crossed over AI therapy (n = 48), women not fasting at both time points (n = 89), or those on lipid-lowering medications (n = 162). A total of 200 women were evaluable (letrozole 107, exemestane 93). Lipid profiles in all patients (n = 200) at baseline and 3 months after initiating AI, respectively, were as follows: TC 204.9 and 203.3 (unchanged, p = 0.43); HDL 61.3 and 56.8 (decreased, p = 6.3E-10); LDL 122.2 and 124.6 (unchanged, p = 0.22); and TG 107.1 and 103.6 (unchanged, p = 0.26). Genetic association and multivariate analysis revealed that SNPs in ESR1 and NCOR1 are significantly associated with additional changes in lipid parameters as summarized in Table 1.

Table 1.Significant findings of multivariate linear regressions analyzing genetic associations between candidate gene SNPs and lipid profiles of AI-treated women.CohortNumberSNP (gene)Minor Allele FrequencyLipid ParameterModel UsedMean Absolute Change (mg/dL)P-valueAll patients184rs9340958 (ESR1)0.07TCRecessive-2.250.0003Letrozole96rs9340958 (ESR1)0.07TCRecessive5.280.00009 101rs3020368 (ESR1)0.09TCRecessive6.350.00007Exemestane93rs3798758 (ESR1)0.03HDLDominant, additive-7.970.00001 88rs926848 (ESR1)0.03HDLDominant, additive-7.970.00002 93rs61753150 (NCOR1)0.01TGDominant, additive-11.630.00003

Conclusions

Variants in genes involved in estrogen metabolism and signaling are associated with changes in lipid profiles in AI-treated women and should be validated in other studies.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-11.

Abstract P5-09-03: Endocrine response in invasive lobular carcinoma is characterized by unique estrogen-mediated gene expression and de novo tamoxifen resistance

Invasive lobular carcinoma (ILC) represents ∼10% of newly diagnosed breast tumors, or ∼30,000 cases annually in the US. However, ILC-specific signaling and endocrine responsiveness are not well characterized. Retrospective analyses suggest that ILC patients treated with endocrine therapy have poorer outcomes than invasive ductal carcinoma (IDC) patients with similar biomarkers, and that ILC patients may not benefit from adjuvant tamoxifen. We hypothesize that estrogen receptor-alpha (ER) regulated gene expression is unique in ILC cells and drives endocrine resistance.

The ER-positive ILC cell lines MDA MB 134VI and SUM44PE were used as in vitro models of cell growth and ER-regulated gene expression in response to estradiol (E2). To examine the ER-regulated transcriptome, we performed gene expression microarray analyses and ER ChIP-Seq following E2 treatment. In parallel, E2 response was assessed in vivo in the primary ILC xenograft HCI-013. Response to endocrine therapies, tamoxifen (Tam), 4-hydroxytamoxifen (4OHT), endoxifen (Bx), and fulvestrant (ICI), were also examined in ILC cell lines.

We observed that E2 induced growth and ER target gene expression in MDA MB 134VI and SUM44PE. We compared our ILC microarray data to published data from ER-positive IDC cell lines (MCF-7, T47D, BT474), and identified 254 genes that were E2-regulated in all 5 cell lines (e.g. GREB1, MYC). 915 genes were E2-regulated only in both ILC cell lines. Consistent with this, roughly half of ER binding sites identified in MDA MB 134VI ChIP-Seq were unique versus published MCF-7 data. We chose a subset of ILC-specific and common E2-regulated genes (n = 107) to assess in vivo using Nanostring gene expression analyses of HCI-013. E2-regulation was observed for 32/107 target genes (30%), suggesting that these genes may be E2-regulated in vivo in ILC patient tumors.

Consistent with clinical data, both ILC cell lines presented de novo tamoxifen resistance. SUM44PE were growth-inhibited by ICI, but unaffected by Tam, 4OHT, or Bx. Similarly, ICI blocked E2-induced growth in MDA MB 134VI, but Tam, 4OHT, and Bx acted as partial agonists, inducing ∼25% growth. Partial agonism was not limited to tamoxifen, as other SERMs (e.g. raloxifene) also induced growth. We then measured ER-regulated gene expression in MDA MB 134VI following tamoxifen treatment. Tam, 4OHT, and Bx acted as agonists for 38/107 genes, whereas ICI acted as an antagonist. All 38 genes were E2-repressed targets (e.g. CCNG2), suggesting that ER-mediated gene repression may be critical to tamoxifen-resistance in ILC. Finally, we observed that FGFR1, frequently amplified in ILC, may be critical for ILC cell survival in the presence of tamoxifen.

These data support the hypothesis that unique ER-mediated gene expression in ILC cells drives endocrine resistance. The de novo tamoxifen resistance observed in ILC cells may correlate with the worse outcomes in ILC patients recently reported. We hypothesize that genes regulated by tamoxifen as an agonist may play a role in tamoxifen-induced growth or serve as biomarkers of resistance. Targeting growth factor signaling using FGFR1 inhibitors may block survival pathways required by ILC cells and reverse tamoxifen resistance.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-09-03.

Abstract P4-05-03: Unique genetic, epigenetic, and transcriptomic changes in premenopausal breast cancer suggest novel strategies for therapy

Breast cancer in premenopausal women (preM) is frequently associated with worse prognosis compared to that in postmenopausal women (postM) even when controlling for prognostic variables. In particular, preM ER+ tumors have a poor prognosis on endocrine therapy. There is, however, a paucity of studies characterizing molecular alterations in premenopausal tumors, a potential avenue for finding personalized therapies for this group of women.

We analyzed gene expression, CNV, methylation, and somatic mutations in tumors from preM (≤45; ER+ n = 110, and ER- n = 39) and postM (≥55, ER+ n = 392, and ER- n = 102) women in The Cancer Genome Atlas (TCGA). Unbiased hierarchical clustering of 2,900 most variably expressed genes (using both RNA-seq and Agilent expression array data) in the whole dataset (n = 643) identified four major subtypes which correlated highly with the PAM50 defined subtypes LumA, LumB, Basal and HER2; however, there wasn't any separation between preM and postM samples. Similarly, principal component analysis using 10,000 genes with the highest inter-quartile range (IQR) demonstrated high similarity across preM and postM samples. Direct examination of gene expression differences between PreM and PostM ER+ tumors using unpaired t-test (5% FDR) identified 3,044 differentially expressed genes. The genes most upregulated in premenopausal tumors included AREG, TFPI2, MSMB, TCN1, and GLRA3. Ingenuity Pathway Analysis revealed a highly significant enrichment for TGFb (p&lt;1.9E-16) pathway activity in preM tumors. Intriguingly, no significant gene expression differences between preM and postM ER- tumors were identified. We thus then focused on genetic and epigenetic alterations that may underlie these transcriptomic changes in ER+ preM tumors.

Comparison of methylation (450K Illumina array) between preM and postM ER+ tumors showed a difference in 1% (n = 1,738) of the probes. Genes with the largest difference included ESR1, SIM2, and KLF6. Significant differences in DNA copy number variation (Affymetrix SNP 6.0 array) were also identified in ER+ preM tumors. A number of somatic mutations were significantly enriched in preM ER+ tumors including DSPP and GATA3. Integrated analysis also showed that approximately half of the observed differences in gene expression are driven by CNVs.

Conclusion: Our in silico study has identified a number of genes and pathways which are significantly altered between preM and postM ER+ breast cancer. Distinct genetic and epigenetic differences suggest unique etiology for some preM tumors. Currently ongoing Paradigm analysis, and confirmatory studies using METABRIC data are expected to further identify pathways that could specifically be targeted in premenopausal breast cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-03.

Abstract P6-05-12: Lack of Frequent Estrogen Receptor Mutation in Primary Breast Tumors

The estrogen receptor alpha (ESR1) is a critical driver of breast tumorigenesis, and as such has been a target for therapy for many years. Early reports using Sanger sequencing and conformational assays reported that there were little if any mutations in ER-positive tumors, although a few somatic mutations have recently been described in tumors and cell lines. We set out to validate the authenticity of these reported somatic mutations by performing analysis of ER DNA sequence variants (DSVs) in 66 ER+ breast tumors, and 39 breast cancer cell lines. We utilized a combined approach of target capture sequencing of ESR1, and subsequent testing for novel and previously identified DSVs using an orthogonal mass spectrometry based sequencing approach. A DNA capture approach was designed to capture all exons, flanking splice sites, and the 3′ UTR of ESR1. DNA was captured and sequenced using SOLiD.

Using stringency with a cut-off with at least 2 variant reads, variants in at least 20% of the reads, and requiring evidence for the variants in both strands, we identified 4 previously reported SNPs (rs2077647; rs46432; rs1801132; rs2228480), and two previously reported somatic mutations H6Y and N532Y. We developed mass-spectrometry assays, including controls, for these DSVs, and in addition, we included 10 DSVs which had previously been reported as somatic mutations in breast (and other) cancer. Applying mass-spec based analysis to breast tumors and cell lines, we were able to confirm previously reported SNPs, and one previously reported mutations (H6Y). This mutation was found in one breast tumor and one cell line. None of the other reported somatic mutations could be confirmed in tumors or cell lines. Functional assays on the ESR1H6Y DSV failed to identify differences to wildtype receptor. The lack of a phenotype, and the infrequent occurrence of this DSV do not support a major driver role for ESR1H6Y.

This analysis suggests that ESR1 mutations are a rare event in ER+ primary breast cancer.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-05-12.

Abstract P2-09-02: Epigenetic Regulation of histone variants - a role in hormone therapy resistant breast cancer?

OBJECTIVE To utilize a genome wide approach to characterize epigenetic changes associated with resistance to estrogen deprivation, thus mimicking resistant to AIs.

BACKGROUND Mechanisms of endocrine resistance include the activation of growth factor receptor pathways, overexpression of ER co-activators, and metabolic resistance due to polymorphisms in metabolizing enzymes. Recently, epigenetic mechanisms have been investigated to explain endocrine resistance. The majority of mechanisms for acquired resistance have been described following tamoxifen therapy, but the mechanisms for resistance to aromatase inhibitors (AI) remain less well known.

HYPOTHESIS Estrogen deprivation results in altered methylation and altered expression of critical target genes in breast cancer cells, which helps the cell to survive in the absence of estrogen, contributing to acquired AI resistance in breast cancer patients.

MATERIALS AND METHODS We utilized derivatives of the ER_ MCF-7 cell line which were isolated after being cultured in estrogen-free media for 9 months (C4-12 cell line) and 18–24 months (LTED, Long term estrogen deprivation cell line). A genome-wide methylation screen was performed using Methyl CpG binding Domain (MBD) pull down assay followed by hybridization into Affymetrix Human Promoter 1.0R Array. Altered DNA methylation was validated by bisulfite genomic sequencing assays while gene expression of candidate genes was studied by qRT-PCR and Western blotting.

RESULTS There were a significant amount of differentially methylated genes in C4-12 and LTED when compared to MCF7. Intriguingly, among the genes which were significantly hypomethylated in both endocrine resistant cell lines were a number of histone genes, with the homomorphic variant HIST1H2BE showing the strongest hypomethylation. Canonical histones have both homomorphic and heteromorphic variants, which differ in their timing of expression and similarity to the canonical histone protein's amino acid sequence. Overexpression of various heteromorphic histone variants have been implicated in carcinogenesis, but to date, there have been no studies on homomorphic variants, and specifically H2B variants, in regards to their role in tumorigenesis. We show that hypomethylation of HIST1H2BE was associated with its upregulation in C4-12 and LTED cells. Furthermore, knockdown of of HIST2BE resulted in decreased growth in the endocrine resistant cells, but not in the parental MCF-7 cell lines.

CONCLUSION & FUTURE DIRECTIONS The study is novel in two ways; first, this is the first study to show a potential role for histone variants in endocrine resistance. Second, this is one of very few examples where hypomethylation (instead of hypermethylation) results in altered expression of genes critical in tumorigenesis. Current studies include the detailed characterization of the phenotype following over-expression and knockdown of HIST1H2BE, the examination of the timing of expression of this variant in the S phase, and finally we are measuring methylation and expression of HIST2BE in a large collection of tumors from AI-treated breast cancer patients.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-09-02.

Abstract P6-04-20: Endocrine resistance in invasive lobular carcinoma cells parallels unique estrogen-mediated gene expression

Invasive lobular carcinoma (ILC) represents ∼10% of newly diagnosed breast tumors, accounting for ∼30,000 cases annually in the US. However, ILC has been understudied as a breast cancer subtype. ILC-specific signaling pathways and responses to endocrine therapies are not well characterized. Recent retrospective analyses of luminal-type breast cancers suggest that ILC patients treated with endocrine therapy have poorer disease-free survival and overall survival than invasive ductal carcinoma (IDC) patients with similar biomarkers. We hypothesize that unique transcriptional control of estrogen receptor-alpha (ERα) by estrogens and anti-estrogens in ILC cells drive a differential response of ILC tumors to endocrine therapies.

The ILC cell lines MDA MB 134VI and SUM44PE were used as in vitro models of ILC tumors to examine responses to estradiol (E2) and the anti-estrogens tamoxifen (Tam), 4-hydroxytamoxifen (4OHT), endoxifen (Bx), and fulvestrant (ICI). We examined cell growth and expression of canonical ERα-regulated genes in response to E2. Cells were also treated with anti-estrogens +/− E2 to examine their ability to inhibit E2-induced growth. To establish a genome-wide profile of ERα-mediated gene regulation in ILC cells, ILC cells were subjected to gene expression microarray analysis following 0–24hrs treatment with 1nM E2. In parallel to these in vitro studies, in vivo models of ILC are being assessed for endocrine responsiveness, including MDA MB 134VI xenografts and the primary human tumor xenograft HCI-013.

We observed that both MDA MB 134VI and SUM44PE are growth-induced by E2 treatment. However, both cell lines also present de novo resistance to Tam, 4OHT, and Bx. While ICI treatment completely blocked E2-induced growth in MDA MB 134VI, Tam, 4OHT, and Bx acted as partial agonists. Treatment with these compounds alone induced ∼25% growth relative to E2, and E2-induced growth could only be inhibited ∼75%. Similarly, SUM44PE cells are strongly growth-inhibited by ICI treatment, whereas growth is not reduced by Tam, 4OHT, or Bx treatment. Consistent with these observations, novel patterns of gene expression are induced by E2 treatment in ILC cells. E2-treatment induced canonical targets (e.g. GREB1, IGFBP4) in both ILC cell lines. However, in MDA MB 134VI cells only ∼35% of genes regulated by E2 at 24hrs overlap with those regulated in the IDC cell line MCF-7. Further, a subset of the overlapping genes is differentially regulated between cell types, including ESR1 (1.25-fold and 0.67-fold versus control in MDA MB 134VI and MCF-7, respectively), HOXC6, PMP22, and L1CAM. Examination of these observations in in vivo models is currently ongoing.

These data are consistent with the hypothesis that E2 and anti-estrogens differentially regulate ERα-mediated gene expression in ILC cells versus IDC cells. The de novo resistance to tamoxifen observed in ILC cells may correlate with the worse outcomes in ILC patients observed in retrospective analyses. We hypothesize that elucidation of the mechanisms responsible for differential ERα regulation may reveal novel therapeutic targets for treating ILC patients and overcoming endocrine resistance.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-04-20.

A SNP in steroid receptor coactivator-1 disrupts a GSK3β phosphorylation site and is associated with altered tamoxifen response in bone

The coregulator steroid receptor coactivator (SRC)-1 increases transcriptional activity of the estrogen receptor (ER) in a number of tissues including bone. Mice deficient in SRC-1 are osteopenic and display skeletal resistance to estrogen treatment. SRC-1 is also known to modulate effects of selective ER modulators like tamoxifen. We hypothesized that single nucleotide polymorphisms (SNP) in SRC-1 may impact estrogen and/or tamoxifen action. Because the only nonsynonymous SNP in SRC-1 (rs1804645; P1272S) is located in an activation domain, it was examined for effects on estrogen and tamoxifen action. SRC-1 P1272S showed a decreased ability to coactivate ER compared with wild-type SRC-1 in multiple cell lines. Paradoxically, SRC-1 P1272S had an increased protein half-life. The Pro to Ser change disrupts a putative glycogen synthase 3 (GSK3)β phosphorylation site that was confirmed by in vitro kinase assays. Finally, knockdown of GSK3β increased SRC-1 protein levels, mimicking the loss of phosphorylation at P1272S. These findings are similar to the GSK3β-mediated phospho-ubiquitin clock previously described for the related coregulator SRC-3. To assess the potential clinical significance of this SNP, we examined whether there was an association between SRC-1 P1272S and selective ER modulators response in bone. SRC-1 P1272S was associated with a decrease in hip and lumbar bone mineral density in women receiving tamoxifen treatment, supporting our in vitro findings for decreased ER coactivation. In summary, we have identified a functional genetic variant of SRC-1 with decreased activity, resulting, at least in part, from the loss of a GSK3β phosphorylation site, which was also associated with decreased bone mineral density in tamoxifen-treated women.

Abstract P4-02-01: Correlations between Genetic Variants in CYP2D6 and UGT2B7 and Survival in Breast Cancer Patients Treated with or without Tamoxifen: Results from a Large Cohort Study

Background. A large number of studies testing the hypothesis that genetic variants in drug metabolizing enzymes can influence breast cancer patient response to the selective estrogen receptor modulator tamoxifen have provided equivocal and conflicting data. Possible confounding factors in all studies to date include the relatively small number of patients, lack of comprehensive genotyping analysis (in particular regarding the cytochrome P450 2D6 (CYP2D6) enzyme), use of selective serotonin reuptake inhibitors (SSRIs) (antidepressant medication), and lack of untreated (i.e. no tamoxifen treatment) control groups. Currently, it is not clear whether genotype determinations can predict which patients will likely benefit from tamoxifen therapy.

Methods: We conducted a large community-based cohort study to test for associations between clinical outcomes and variants in CYP2D6, one of the key enzymes responsible for the conversion of tamoxifen to its potent anti-estrogenic metabolite endoxifen, as well as variants in UDP-glucuronosyltransferase 2B7 (UGT2B7), an enzyme responsible for the elimination of endoxifen. The majority of patients in this cohort began their tamoxifen treatment more than twenty ago, at a time when SSRIs (a possible confounding factor in CYP2D6 studies) were not widely used. Five hundred patients with ER+ early breast cancer treated adjuvantly with tamoxifen monotherapy and 500 who did not receive any adjuvant therapy were genotyped and assigned a CYP2D6 “score” based on known specific allele activities from 0 (no activity) to 2 (high activity) and also grouped as either low, intermediate and high UGT2B7 activity based on the *2 allele.

Results: Univariately, Kaplan-Meier estimates in conjunction with the log-rank test did not reveal any significant associations between either CYP2D6 or UGT2B7 score and time to relapse (TTR). In tamoxifen treated cases, after adjustment for tumor size, nodal status and PgR, Cox regression found increased CYP2D6 score, reflecting increased conversion of tamoxifen to endoxifen, was significantly associated with worse time to relapse (HR=1.53, p=0.02). This was not seen in the patients without endocrine treatment (HR=0.73, p=0.10). Patients with high UGT2B7 activity, reflecting increased elimination of endoxifen had better survival rates (HR= 0.75, p = 0.04) in the tamoxifen treated group, while again no effect of UGT2B7 was seen in the untreated group (HR=1.0, p=0.78). Finally, CYP2D6 and UGT2B7 genotypes were not associated with any special tumor characteristics in either patient group. Conclusion: In our study, CYP2D6 and UGT2B7 genotypes associated with increased endoxifen levels were associated with worse outcome in tamoxifen treated (but not untreated) breast cancer patients. Thus, the data from this cohort study do not support the hypothesis that breast cancer patients with low CYP2D6 are resistant to tamoxifen.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-02-01.

A Single Nucleotide Polymorphism in Steroid Receptor Coactivator-1 Diminishes the Coactivation of ERα

Estrogen signaling is critical in the progression of a large fraction of breast cancers as well as in the maintenance of bone mineral density. Generally speaking, Tamoxifen, a selective estrogen receptor modulator (SERM), blocks estrogen signaling in the breast by acting as an antagonist at the same time as promoting estrogen signaling in the bone by acting as an agonist. This tissue specific action characteristic of SERMs is thought to be maintained by the balance of levels and/or activities of estrogen receptor (ER) coregulators. Because of this critical role, single nucleotide polymorphisms (SNPs) in ER coregulators could have a dramatic effect on tamoxifen action.Previous studies have implicated steroid receptor coactivator-1 (SRC-1) as a critical coregulator for the mixed antagonist-agonist specificity of tamoxifen. By using an ERE-Tk-Luciferase transient transfection assay, we have shown that a SNP causing the amino acid change P1272S in SRC-1 dramatically reduces its ability to coactivate ERα.To assess the impact of this SNP on tamoxifen action in breast cancer we decided to genotype the SRC-1 P1272S SNP in a breast tumor DNA bank. This bank was generated from archived tumors from individuals either exclusively receiving adjuvant tamoxifen or not receiving any adjuvant therapy following surgical resection. Currently, the bank is composed of 1000 samples divided equally among the two groups. Genotyping for the SRC-1 P1272S SNP is currently underway.Since SRC-1 has also been shown to be important in proper maintenance of bone mineral density (BMD) and in the agonist action of tamoxifen in certain tissues, we also assessed the impact of the P1272S SNP in bone following tamoxifen therapy. We genotyped breast cancer patients exclusively receiving tamoxifen therapy (i.e. no chemotherapy, no radiation) who had lumbar (n=113) and/or hip (n=108) BMD scans before and after 12 months of tamoxifen therapy. We observed a significant association between the SNP and bone loss; women harboring the P1272S SNP lost 6.4% of their lumbar BMD, while women with the WT version lost only 1.3% of their lumbar BMD.These findings illustrate the critical role of SRC-1 in tamoxifen action in bone, and potentially other hormone responsive tissues. Studies are ongoing to decipher the mechanism for decreased coactivation activity of the SNP, and also to extend the clinical association studies.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 66.

Estrogen Deprivation Results in Altered DNA Methylation Profile in Breast Cancer Cells – Role in Endocrine Resistance?

Postmenopausal breast cancer patients benefit from aromatase inhibitors (AIs) that reduce the levels of estrogens which are critical for tumor growth. To date, epigenetic contributions to hormonal therapy resistance have not been well characterized, with only a limited understanding of antiestrogen mediated epigenetic modification of chromatin and altered gene expression. Furthermore, no genome-wide studies have been undertaken to identify altered DNA methylation patterns due to estrogen deprivation, which mimic AI therapy. We hypothesized that estrogen deprivation results in altered methylation, and therefore altered expression of critical target genes in breast cancer cells, which ultimately helps the cell to survive in the absence of estrogen and thus would contribute to acquire AI resistance in breast cancer patients.We used previously established MCF-7 cell clones, termed C4-12 and LTED (Long Term Estrogen Deprivation) that were isolated after being cultured in estrogen-free media for 9 months and 18-24 months, respectively. A genome-wide methylation screen was done using Methyl CpG binding Domain (MBD) pull down assay followed by hybridization into Affymetrix Human Promoter 1.0R Array. Altered DNA methylations were validated by bisulfite genomic sequencing assays and gene expression of some selected genes were studied by qRT PCR.From the array, we found that long term estrogen deprivation results in widespread genomic hyper- and hypomethylation events. 267 and 301 genes were hypermethylated in C4-12 and LTED respectively. In both resistant cell lines, the number of hypermethyled genes was more prominent than hypomethylated genes since only 82 and 97 genes were hypomethylated in C4-12 and LTED respectively. While hypomethylation of genes generally correlated with increased gene expression, hypermethylation did not in many cases. A gene which was heavily methylated in both cell line system, possibly reflecting a more general and important pathway in estrogen-deprivation, was HOXC10. Transient and stable silencing of HOXC10 in MCF-7 cells resulted in increased cell proliferation in estrogen deprived medium, suggesting a potential role of HOXC10 in developing resistance to endocrine therapy.This is the first genome-wide approach to identify gene-specific epigenetic alterations, and the functional consequences of these changes in developing resistance to estrogen deprivation therapy. This approach allows the development of epigenetic signatures of therapeutic resistance to be used concurrently with genomic signatures to better understand the molecular mechanism of endocrine resistance. This study might provide the basis for future clinical trials such as combination therapy of DNA demethylating agents and aromatase inhibitors.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5127.

Estrogen and IGF-I Independently Down-Regulate Critical Repressors of Breast Cancer Growth

Background: Estrogen receptor and insulin-like growth factor (IGF) signaling pathways are important for both normal mammary gland development and breast cancer pathogenesis. Despite this evidence, cross-talk between these two critical mitogenic and survival pathways remains poorly understood, particularly at the level of downstream gene transcriptional networks.Methods: We performed microarray analysis on ER-positive MCF-7 breast cancer cells following stimulation with either estradiol (10nM) or IGF-I (10nM) for 3hr or 24hr. We defined an E2-IGF gene expression signature and examined the effect of the gene signature on time to recurrence in ER+ tumors in the publicly available NKI dataset. Q-RT-PCR was used to validate the effects of IGF-I and E2 on mRNA of repressed genes. To examine gene regulation further, MCF-7 cells were incubated with various signaling inhibitors and gene expression measured.Results: We found 183 probesets to be co-regulated by E2 and IGF-I after 3hr of stimulation and 454 probesets to be co-regulated at the 24hr time point. Patients with tumors that had the same set of genes up- and down-regulated had a poor outcome (p=7.04E-07). E2-IGF co-regulated genes showed a significant enrichment for down-regulated genes (p&lt;0.001). The top 10% of down-regulated genes contained four (BLNK, SOCS2, CCNG2, and ING4) that have previously been shown to have tumor suppressor function and/or show loss in human breast tumors. We confirmed that E2 and IGF-I indeed repressed levels of these candidate genes. Blockade of ER by ICI 182780 (ICI) completely reversed E2-mediated repression but had little or no effect on IGF-mediated repression of these genes. Similarly, blockade of IGF-IR was able to completely reverse IGF-I-mediated repression of all four genes, but had essentially no effect upon E2-mediated repression. Inhibition of the PI3K pathway with LY294002 (20μM) affected short-term (3hr) down-regulation of BLNK and SOCS2 by both E2 and IGF-I, and CCNG2 by IGF-I. By 24 hours, LY completely reversed both E2 and IGF-I mediated repression of CCNG2, and significantly reversed both E2 and IGF-I repression of BLNK and SOCS2. Blockade of MEK1/2 with U0126 (10μM) had no effect on short-term repression by E2 or IGF-I, though after 24hr it affected both E2 and IGF-I repression of BLNK and SOCS2.Conclusions: E2 and IGF-I co-regulate a set of genes that affect breast cancer outcome. E2 and IGF-I down-regulate several critical tumor suppressor genes. While the down-regulation is independent of each other at the level of ER and IGF-IR, for some genes, there is convergence on the PI3K pathway for repression.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1126.

What Is the Histone Code, and Why Is It Important?

The field of epigenetics is rapidly expanding, and has changed and revised traditional paradigms of inheritance. Epigenetics, literally “beyond genetics” or “in addition to genetics”, is defined as the study of heritable changes in gene expression that occur without a change in DNA sequence. Within this presentation, I will focus on modifications of histones, an important mechanism to convey epigenetic information. Histones, small proteins which serve as spools for DNA wrapped in nucleosomes, are critical regulators of the dynamic state of chromatin. They are subject to numerous posttranslational modifications, including acetylation, methylation, ubiquitylation, and phosphorylation. The best characterized modifications are acetylations and methylations. Increased acetylation of histones by histone acetyltransferases is associated with gene activation due to weakened charge attraction between DNA and histone; histone deacetylases in contrast remove acetyl groups leading to gene inactivation. Histone methylation mediated by histone methyltransferases has either positive effects or negative effects on gene expression depending on location and association of other protein complexes. In general, it is difficult to predict gene regulation based on the study of a single histone modification, since it is the combination of these modifications, also called the histone code, which ultimately controls gene expression. I will discuss details of the histone modification, how they regulate gene expression, and also their relevance in disease, especially breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr ES4-2.

Progesterone Receptor (PR) Promoter Methylation – Role as a Predictive and Prognostic Marker in Breast Cancer

Estrogen receptor α expression is a well known and clinically utilized predictor of endocrine treatment response. In addition, loss of expression of the progesterone receptor (PR), an estrogen induced gene, has been shown to be associated with resistance to endocrine therapy. PR is known to be epigenetically regulated by DNA methylation, but only a few studies have correlated PR DNA methylation with its expression in breast cancer. Previous studies are contradictory and have been limited by small sample size. There is also evidence that differential expression of the two PR isoforms, PRA and PRB, might contribute to breast tumorigenesis, and altered hormone response. Whether PRA and/or PRB DNA methylation could predict response to endocrine therapy remains an open question. Further, there are no published studies so far testing whether PRA and/or PRB methylation have prognostic significance.Our objective was 1) to determine whether there was an association between PRA and/or PRB methylation levels with total PR expression in breast tumors, and 2) to determine if PRA and/or PRB methylation would have predictive and/or prognostic value. For this study, we utilized tumor DNA from patients with ER-positive breast tumors which were treated with adjuvant tamoxifen after surgery (n=500), and from patients treated with surgery only (n=500). PR expression was determined by ligand binding assay, and PRA and PRB promoter methylation was measured by bisulfite pyrosequencing.Both PRA and PRB methylation were significantly (p&lt;0.0001) associated with PR expression, in an inverse relationship. Low PR expression was significantly (p=0.02) associated with worse overall survival (OS), and there was a trend towards shorter disease free survival (DFS) in the tamoxifen treated group. There was no association between PR expression and survival in the untreated group. PRA methylation was significantly (p&lt;0.0001) associated with PRB methylation. Intriguingly, increased PRA methylation was significantly associated with shorter DFS (p=0.047) and OS (p=0.0067) in tamoxifen treated patients, and with shorter OS (p=0.008) in the untreated patients. In contrast, there was no significant association between PRB methylation and survival in either tamoxifen treated or untreated patients.Our results show that PR expression is significantly associated with PR methylation. The data suggest that PRA methylation is a predictive marker for tamoxifen response and also a prognostic marker for breast cancer progression. This is the largest study so far to elucidate the association of PRA and PRB methylation with PR status, response to tamoxifen, and tumor prognosis, and we believe that it provides useful insights into the role of PR methylation in breast tumorigenesis.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2002.

Sumoylation of Corepressor SAFB1 – Mechanism of Action and Biological Relevance in Breast Cancer

Scaffold attachment factor B1 (SAFB1) was originally isolated due to its ability to bind Scaffold/Matrix attachment regions of genomic DNA. Subsequently, SAFB1 has also been shown to be involved in RNA processing, chromatin organization and stress response. Work from our laboratory has shown that SAFB1 can bind and modulate transcription of the HSP-27 promoter and repress activity of ERα. Repression of ERα occurs through an independent and transferable c-terminal repression domain. Further work has indicated that SAFB1 can interact with and repress transactivation of a host of nuclear receptors including PPARg and FXR, suggesting a general role for SAFB1 in transcriptional repression.Many proteins associated with transcriptional regulation are post translationally modified by small ubiquitin like modifier (SUMO). SUMO is a 98 amino acid mature polypeptide that is added post translationally to target proteins usually within a consensus sumoylation motif, ΨKXE (where Ψ is a large hydrophobic residue, K-lysine of modification and X any residue). The process of sumoylation is analogous to ubiquitination. SUMO modification of proteins associated with transcription has generally been associated with transcriptional repression. The mechanism by which this modification leads to transcriptional repression has yet to be defined.Work by our laboratory has indicated that SAFB1 is modified by sumoylation. In silico analysis indicated two consensus sumoylation motifs within SAFB1. Immunoprecipitation studies revealed SUMO modified forms of SAFB1. Mutating the lysine's within the sumoylation motifs to arginine (K231,294R) lead to a loss of sumo modified SAFB1 indicating these as the sites of modification. Transient ERE-Tk-Luciferase assays showed a loss of transcriptional repression with over expression of SAFB1 K231,294R compared to SAFB1 wildtype. Loss of transcriptional repression was also seen utilizing transient Gal4DBD reporter assays indicating an effect of sumoylation on SAFB1's intrinsic repressive function. Co-immunopreciptation studies have indicated interaction between SAFB1 and SUMO E3 ligases suggesting these may be important for modifying SAFB1. Additionally, over expression of members of the sumoylation machinery can enhance SAFB1 repressive activity indicating this modification is important for SAFB1 transcriptional repression. Loss of SAFB1 sumoylation does not alter protein half life indicating the loss of transcriptional repression is not through this mechanism.Our studied have indicated that sumoylation of SAFB1 is important for its repressive activity. Additional studies within the lab are aimed at addressing the mechanism and the complete extent of functional consequences of sumoylation of SAFB1. A better understanding of post translational modification of SAFB1 may provide additional insights into the diverse functions of SAFB1 and its role in breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4142.

Estrogen Receptor-Mediated Repression of Target Genes: Mechanism of Action, and Biological Significance

Estrogen-bound estrogen receptor (ER) can regulate the transcription of a large number of genes. Although estrogen represses as many genes as it induces, induction has been studied in detail while the repression mechanisms remain largely unknown. In this study we characterized several estrogen-repressed ERα target genes that are directly repressed by estrogen in breast cancer cells. Interestingly, many repressed genes are tumor suppressor genes, playing critical roles in cell cycle inhibition and/or apoptosis. One gene that particularly piqued our interest is Reprimo (RPRM) because of its robust repression in a number of cell lines, and its role as a cell cycle inhibitor. Additionally, it is highly methylated in a variety of cancers including breast cancer and maps to a locus that displays loss of heterozygosity, suggesting that it may be a tumor suppressor gene. As a result, E2-mediated repression of this gene may be a crucial step in the progression of breast cancer. We did show that RPRM decrease (by siRNA) enhances estrogen-mediated S-phase entry, strongly suggesting a biological role of its repression. RPRM was actively and strongly repressed by estrogen and this repression was not due to a quicker turnover of the RPRM mRNA by estrogen. E2-mediated repression of RPRM levels did not require new protein synthesis since it is also repressed in the presence of the translation inhibitor, cycloheximide. We find that estrogen repression of RPRM requires a tripartite interplay between ERα, FoxA1, and HDAC7 as knockdown of these proteins abrogates its repression. Remarkably, silencing of HDAC7 significantly relieved repression of the majority of eleven estrogen-repressed genes tested. Further examination of the interplay between HDAC7 and ERα revealed that HDAC7 can interact with ERα and repress its transcriptional activity in a deacetylase-independent manner. Chromatin immunoprecipitation assays demonstrate that ERα, FoxA1, and HDAC7 are all recruited to a cis-regulatory enhancer (-4.8 kb) in the RPRM gene in the presence of estrogen, which was associated with a release of RNA Pol II from the proximal promoter. Repression requires FoxA1 to be recruited to an epigenetic signature characterized by H3K4 mono- and di-methylation. In summary, we have uncovered a unique requirement for a deacetylase-independent function of HDAC7 in estrogen repression of genes such as RPRM.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4136.