Estrogen regulation and functional role of FGFR4 in estrogen receptor positive breast cancer

Background

Resistance to endocrine therapy is a major challenge of managing estrogen receptor positive (ER+) breast cancer. We previously reported frequent overexpression of FGFR4 in endocrine resistant cell lines and breast cancers that recurred and metastasized following endocrine therapy, suggesting FGFR4 as a potential driver of endocrine resistance. In this study, we investigated the role of FGFR4 in mediating endocrine resistance and explored the therapeutic potential of targeting FGFR4 in advanced breast cancer.

Methods

A gene expression signature of FGFR4 activity was examined in ER+ breast cancer pre- and post-neoadjuvant endocrine therapy and the association between FGFR4 expression and patient survival was examined. A correlation analysis was used to uncover potential regulators of FGFR4 overexpression. To investigate if FGFR4 is necessary to drive endocrine resistance, we tested response to FGFR4 inhibition in long term estrogen deprived (LTED) cells and their paired parental cells. Doxycycline inducible FGFR4 overexpression and knockdown cell models were generated to examine if FGFR4 was sufficient to confer endocrine resistance. Finally, we examined response to FGFR4 monotherapy or combination therapy with fulvestrant in breast cancer cell lines to explore the potential of FGFR4 targeted therapy for advanced breast cancer and assessed the importance of PAM50 subtype in response to FGFR4 inhibition.

Results

A FGFR4 activity gene signature was significantly upregulated post neoadjuvant aromatase inhibitor treatment, and high FGFR4 expression predicted poorer survival in patients with ER+ breast cancer. Gene expression association analysis using TCGA, METABRIC and SCAN-B datasets uncovered ER as the most significant gene negatively correlated with FGFR4 expression. ER negatively regulates FGFR4 expression at both the mRNA and protein level across multiple ER+ breast cancer cell lines. Despite robust overexpression of FGFR4, LTED cells did not show enhanced responses to FGFR4 inhibition compared to parental cells. Similarly, FGFR4 overexpression, knockdown or hotspot mutations did not significantly alter response to endocrine treatment in ER+ cell lines, nor did FGFR4 and fulvestrant combination treatment show synergistic effects. The HER2-like subtype of breast cancer showed elevated expression of FGFR4 and an increased response to FGFR4 inhibition relative to other breast cancer subtypes.

Conclusions

Despite ER-mediated upregulation of FGFR4 post endocrine therapy, our study does not support a general role of FGFR4 in mediating endocrine resistance in ER+ breast cancer. Our data suggests that specific genomic backgrounds such as HER2 expression may be required for FGFR4 function in breast cancer and should be further explored.

Systems approach for congruence and selection of cancer models towards precision medicine

Cancer models are instrumental as a substitute for human studies and to expedite basic, translational, and clinical cancer research. For a given cancer type, a wide selection of models, such as cell lines, patient-derived xenografts, organoids and genetically modified murine models, are often available to researchers. However, how to quantify their congruence to human tumors and to select the most appropriate cancer model is a largely unsolved issue. Here, we present Congruence Analysis and Selection of CAncer Models (CASCAM), a statistical and machine learning framework for authenticating and selecting the most representative cancer models in a pathway-specific manner using transcriptomic data. CASCAM provides harmonization between human tumor and cancer model omics data, systematic congruence quantification, and pathway-based topological visualization to determine the most appropriate cancer model selection. The systems approach is presented using invasive lobular breast carcinoma (ILC) subtype and suggesting CAMA1 followed by UACC3133 as the most representative cell lines for ILC research. Two additional case studies for triple negative breast cancer (TNBC) and patient-derived xenograft/organoid (PDX/PDO) are further investigated. CASCAM is generalizable to any cancer subtype and will authenticate cancer models for faithful non-human preclinical research towards precision medicine.

ESR1 fusion proteins invoke breast cancer subtype-dependent enrichment of ligand independent pro-oncogenic signatures and phenotypes

Breast cancer is a leading cause of female mortality and despite advancements in diagnostics and personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. Fortunately, identification of mechanisms of therapeutic resistance have rapidly transformed our understanding of cancer evasion and is enabling targeted treatment regimens. When the druggable estrogen receptor (ER, ESR1 ), expressed in two-thirds of all breast cancer, is exposed to endocrine therapy, there is risk of somatic mutation development in approximately 30% of cases and subsequent treatment resistance. A more recently discovered mechanism of ER mediated endocrine resistance is the expression of ER fusion proteins. ER fusions, which retain the protein's DNA binding domain, harbor ESR1 exons 1-6 fused to an in-frame gene partner resulting in loss of the 3' ER ligand binding domain (LBD). In this report we demonstrate that in no-special type (NST) and invasive lobular carcinoma (ILC) cell line models, ER fusion proteins exhibit robust hyperactivation of canonical ER signaling pathways independent of the ligand estradiol or anti-endocrine therapies such as Fulvestrant and Tamoxifen. We employ cell line models stably overexpressing ER fusion proteins with concurrent endogenous ER knockdown to minimize the influence of endogenous wildtype ER. Cell lines exhibited shared transcriptomic enrichment in pathways known to be drivers of metastatic disease, notably the MYC pathway. The heterogeneous 3' fusion partners, particularly transcription factors SOX9 and YAP1 , evoked varying degrees of transcriptomic and cistromic activity that translated into unique phenotypic readouts. Herein we report that cell line activity is subtype-, fusion-, and assay-specific suggesting that the loss of the LBD, the 3' fusion partner, and the cellular landscape all influence fusion activity. Therefore, it will be critical to generate additional data on frequency of the ER fusions, in the context of the clinicopathological features of the tumor.

Significance

ER fusion proteins exhibit diverse mechanisms of endocrine resistance in breast cancer cell lines representing the no special type (NST) and invasive lobular cancer (ILC) subtypes. Our emphasize upon both the shared and unique cellular adaptations imparted by ER fusions offers the foundation for further translational research and clinical decision making.

WCRC-25: A novel luminal Invasive Lobular Carcinoma cell line model

Breast cancer is categorized by the molecular and histologic presentation of the tumor, with the major histologic subtypes being No Special Type (NST) and Invasive Lobular Carcinoma (ILC). ILC are characterized by growth in a single file discohesive manner with stromal infiltration attributed to their hallmark pathognomonic loss of E-cadherin ( CDH1 ). Few ILC cell line models are available to researchers. Here we report the successful establishment and characterization of a novel ILC cell line, WCRC-25, from a metastatic pleural effusion from a postmenopausal Caucasian woman with metastatic ILC. WCRC-25 is an ER-negative luminal epithelial ILC cell line with both luminal and Her2-like features. It exhibits anchorage independent growth and haptotactic migration towards Collagen I. Sequencing revealed a CDH1 Q706* truncating mutation, together with mutations in FOXA1, CTCF, BRCA2 and TP53 , which were also seen in a series of metastatic lesions from the patient. Copy number analyses revealed amplification and deletion of genes frequently altered in ILC while optical genome mapping revealed novel structural rearrangements. RNA-seq analysis comparing the primary tumor, metastases and the cell line revealed signatures for cell cycle progression and receptor tyrosine kinase signaling. To assess targetability, we treated WCRC-25 with AZD5363 and Alpelisib confirming WCRC-25 as susceptible to PI3K/AKT signaling inhibition as predicted by our RNA sequencing analysis. In conclusion, we report WCRC-25 as a novel ILC cell line with promise as a valuable research tool to advance our understanding of ILC and its therapeutic vulnerabilities.

Financial support

The work was in part supported by a Susan G Komen Leadership Grant to SO (SAC160073) and NCI R01 CA252378 (SO/AVL). AVL and SO are Komen Scholars, Hillman Foundation Fellows and supported by BCRF. This project used the UPMC Hillman Cancer Center and Tissue and Research Pathology/Pitt Biospecimen Core shared resource which is supported in part by award P30CA047904. This research was also supported in part by the University of Pittsburgh Center for Research Computing, RRID:SCR_022735, through the resources provided. Specifically, this work used the HTC cluster, which is supported by NIH award number S10OD028483. Finally, partial support was provided by the Magee-Womens Research Institute and Foundation, The Shear Family Foundation, and The Metastatic Breast Cancer Network.

FOXA1 Reprogramming Dictates Retinoid X Receptor Response in ESR1-Mutant Breast Cancer

Estrogen receptor alpha (ER/ESR1) mutations occur in 30% to 40% of endocrine resistant ER-positive (ER+) breast cancer. Forkhead box A1 (FOXA1) is a key pioneer factor mediating ER-chromatin interactions and endocrine response in ER+ breast cancer, but its role in ESR1-mutant breast cancer remains unclear. Our previous FOXA1 chromatin immunoprecipitation sequencing (ChIP-seq) identified a large portion of redistributed binding sites in T47D genome-edited Y537S and D538G ESR1-mutant cells. Here, we further integrated FOXA1 genomic binding profile with the isogenic ER cistrome, accessible genome, and transcriptome data of T47D cell model. FOXA1 redistribution was significantly associated with transcriptomic alterations caused by ESR1 mutations. Furthermore, in ESR1-mutant cells, FOXA1-binding sites less frequently overlapped with ER, and differential gene expression was less associated with the canonical FOXA1-ER axis. Motif analysis revealed a unique enrichment of retinoid X receptor (RXR) motifs in FOXA1-binding sites of ESR1-mutant cells. Consistently, ESR1-mutant cells were more sensitive to growth stimulation with the RXR agonist LG268. The mutant-specific response was dependent on two RXR isoforms, RXR-α and RXR-β, with a stronger dependency on the latter. In addition, T3, the agonist of thyroid receptor (TR) also showed a similar growth-promoting effect in ESR1-mutant cells. Importantly, RXR antagonist HX531 blocked growth of ESR1-mutant cells and a patient-derived xenograft (PDX)-derived organoid with an ESR1 D538G mutation. Collectively, our data support the evidence for a stronger RXR response associated with FOXA1 reprograming in ESR1-mutant cells, suggesting development of therapeutic strategies targeting RXR pathways in breast tumors with ESR1 mutation.

IMPLICATIONS

It provides comprehensive characterization of the role of FOXA1 in ESR1-mutant breast cancer and potential therapeutic strategy through blocking RXR activation.

Mixed invasive ductal lobular carcinoma is clinically and pathologically more similar to invasive lobular than ductal carcinoma

BACKGROUND

Mixed invasive ductal lobular carcinoma (mDLC) remains a poorly understood subtype of breast cancer composed of coexisting ductal and lobular components.

METHODS

We sought to describe clinicopathologic characteristics and determine whether mDLC is clinically more similar to invasive ductal carcinoma (IDC) or invasive lobular carcinoma (ILC), using data from patients seen at the University of Pittsburgh Medical Center.

RESULTS

We observed a higher concordance in clinicopathologic characteristics between mDLC and ILC, compared to IDC. There is a trend for higher rates of successful breast-conserving surgery after neoadjuvant chemotherapy in patients with mDLC compared to patients with ILC, in which it is known to be lower than in those with IDC. Metastatic patterns of mDLC demonstrate a propensity to develop in sites characteristic of both IDC and ILC. A meta-analysis evaluating mDLC showed shared features with both ILC and IDC with significantly more ER-positive and fewer high grades in mDLC compared to IDC, although mDLCs were significantly smaller and included fewer late-stage tumours compared to ILC.

CONCLUSIONS

These findings support clinicopathologic characteristics of mDLC driven by individual ductal vs lobular components and given the dominance of lobular pathology, mDLC features are often more similar to ILC than IDC. This study exemplifies the complexity of mixed disease.

RET signaling in breast cancer therapeutic resistance and metastasis

RET, a single-pass receptor tyrosine kinase encoded on human chromosome 10, is well known to the field of developmental biology for its role in the ontogenesis of the central and enteric nervous systems and the kidney. In adults, RET alterations have been characterized as drivers of non-small cell lung cancer and multiple neuroendocrine neoplasms. In breast cancer, RET signaling networks have been shown to influence diverse functions including tumor development, metastasis, and therapeutic resistance. While RET is known to drive the development and progression of multiple solid tumors, therapeutic agents selectively targeting RET are relatively new, though multiple multi-kinase inhibitors have shown promise as RET inhibitors in the past; further, RET has been historically neglected as a potential therapeutic co-target in endocrine-refractory breast cancers despite mounting evidence for a key pathologic role and repeated description of a bi-directional relationship with the estrogen receptor, the principal driver of most breast tumors. Additionally, the recent discovery of RET enrichment in breast cancer brain metastases suggests a role for RET inhibition specific to advanced disease. This review assesses the status of research on RET in breast cancer and evaluates the therapeutic potential of RET-selective kinase inhibitors across major breast cancer subtypes.

Abstract P3-08-10: Combining multiomics and histological assessment to identify patient derived xenograft models of invasive lobular carcinoma

Background Most breast cancers (~85%) are of no special histologic subtype (NST), and the most common special subtype is invasive lobular cancer (ILC). ILC accounts for 10-15% of all breast cancers, and there will be ~40,000 new cases in 2022 in the US alone. If considered an “independent” cancer type, ILC is the 6th most common cancer in women. The pathognomonic feature of ILC is loss of E-cadherin (CDH1). The resulting lack of adherens junctions causes the unique single-file growth pattern of discohesive ILC cells, which decreases the ability for detection by mammography, in turn resulting in late detection and hence larger tumors. Although ILCs show better prognostic factors than NST, patients with ILC have worse long-term outcome, which is not well understood. Additionally, ILC has historically been understudied, which is in part due to lack of appropriate research models. For example, the Cancer Cell Line Encyclopedia (CCLE) contains 54 NST cell lines but only 2 ILC cell lines, and only a limited number of patient-derived xenograft (PDX) models are evident in the published literature. There is a critical need for additional in vitro and in vivo models to study ILC biology, as well as to test targeted therapies. ILC PDX and patient derived xenograft organoids (PDXO) are particularly valuable tools to enable target validation and assess drug treatment response. Methods To identify and validate new ILC PDX models, we used Champions Oncology’s Lumin Bioinformatics to screen Champions’ collection of breast cancer models (n=126) for PDX harboring CDH1 mutation and/or low E-cadherin expression. We performed histological analysis on selected PDX models including H&E staining, and immunohistochemical assessment of E-cadherin, P120, estrogen receptor, progesterone receptor, HER2 and Ki67. Models with 2+ HER2 staining were assessed by FISH. All staining was interpreted by a certified breast pathologist. PDX tumor tissue was further used to develop PDXO models. Results Using Champions Oncology’s Lumin tool, we identified 10 putative ILC PDX models based upon CDH1 mutation, low E-cadherin mRNA expression, or clinical annotation of ILC (Table 1). Of the 10 PDX models analyzed, two cases were clinically annotated as ILC, while the remainder were classified as ‘carcinoma’ (n=5) or as NST (n=3). Histologic analysis revealed loss of E-cadherin and cytoplasmic P120 (lobular pattern) in 8/10 models assessed, and pathologic assessment confirmed these as having a lobular histology. IHC analysis classified these PDXs as 5 TNBC and 5 ER+ tumors, with none showing amplification of HER2 by FISH. All tumors demonstrated high (35%, n=1) or very high (>55%, n=9) Ki67 proliferation marker levels. We further developed PDXOs from one PDX model as proof of concept, and the resulting organoid demonstrated classic ‘grape-like’ ILC morphology. Conclusion Our study demonstrates how existing PDX banks with in-depth multi-omic and pathology analyses can be interrogated to identify models of unique histological and molecular subtypes of breast cancer. Of the PDX models selected from Champions Oncology’s breast cancer cohort, 7 models were classified as ILC either through re-classification from NST/carcinoma to ILC or confirmation of ILC histology. In addition, 1 PDX was re-classified as mixed type. Some of these models are ER+/HER- and thus have the classic molecular features of ILC. Our collaborative omics guided approach allows for reclassification of PDX models to increase available research models for unique breast cancer subtypes such as ILC which in turn will enhance translational research in unique histological subtypes of breast cancer.

Citation Format: Jennifer M. Atkinson, Megan Yates, Daniel D. Brown, Jagmohan Hooda, Rohit Bhargava, Paolo Schiavini, Marianna Zipeto, Steffi Oesterreich, ADRIAN V. LEE. Combining multiomics and histological assessment to identify patient derived xenograft models of invasive lobular carcinoma [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-08-10.

Abstract PD10-02: PD10-02 Novel ER fusion detection method to gain insight in fusion prevalence and endocrine resistant mechanisms

Breast cancer is a leading cause of female mortality and despite advancements in diagnostics and personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. The druggable estrogen receptor (ER, ESR1), overexpressed in two-thirds of all breast cancer, evolves in 30% of tumors exposed to endocrine therapy consequently resulting in treatment resistance. A more recently discovered mechanism of ER mediated endocrine resistance is ER fusion proteins. ER fusions, found predominately in metastatic endocrine resistant disease, harbor ESR1 exons 1-6 fused to an in-frame gene partner due to an ESR1 intron 6 translocation break. Our lab has demonstrated that ER fusion proteins, which lack the C-terminal ligand-binding domain (LBD), recapitulate phenotypes of ER proteins harboring endocrine-resistant point mutations occurring in the LBD. Our research goals aim to 1) determine fusion prevalence and emergence, 2) understand fusion mechanisms of resistance and 3) explore alternative treatment options for our patients. The promiscuous nature of fusion partners hinders fusion detection by traditional sequencing and thus our research team has developed a novel ER fusion detection method, EnRich. The EnRich probe set (4,324 probes in total) is composed of two separate probe pools targeting at 2x tiling intronic and exonic ESR1, the upstream promoter region and select oncogenic genes. To optimize the EnRich pipeline, DNA was extracted from a frozen tumor sample and a PDX model harboring ESR1-DAB2 and ESR1-LPP fusions, respectively. ESR1-DAB2 and ESR1-LPP were accurately detected by quantifying discordant paired-end or split reads mapped to chromosome 6. In addition, liquid biopsies from 15 patients with ER positive advanced breast cancer were also assessed through EnRich to uncover unidentified ESR1 structural variants. Two patient samples were detected to harbor ESR1 fusions (ESR1-CCDC170, ESR1-AKAP12 and ESR1-YAP1) and were further validated in corresponding mRNA. These recurrent and novel fusions were supported with more than 10 reads each, indicating that the EnRich pipeline is an effective and accurate sequencing approach to understanding ER fusion prevalence. Our lab, furthermore, has studied ER fusion proteins mechanistically. We have stably overexpressed ER fusions in transgenic breast cancer cell lines engineered with shRNA targeting the endogenous wildtype ER (ESR1-WT). In this ESR1-WT depleted cellular context, we found that ER fusions (notably ESR1-SOX9 and ESR1-YAP1) demonstrate ER hyperactivation through an estrogen response element (ERE) assay compared to ESR1-WT and a truncated exon 1-6 ESR1 (ESR1∆CTD). Importantly, fusion ERE activity was robust in the absence of the ER ligand, estradiol, as well as in the presence of endocrine therapies, implying ER fusion proteins function in a ligand independent, endocrine resistant mechanism. ER fusion positive cell lines were also enriched in oncogenic phenotypes such as enhanced 3D growth, cell survival via colony formation, and migration in a wound scratch assay. These enhanced metastatic potentials of the ER fusions were observed in both invasive ductal and lobular carcinoma cell lines, albeit at varying magnitudes depending on the 3’ fusion partner and phenotype being assessed. Although the ER fusions harbored unique characteristics due to the C-terminal partner, transcriptomic profiling revealed that enhanced EMT and KRAS signaling signatures were shared among all fusions when compared to the ESR1-WT and ESR1∆CTD cell lines, which may serve as future exploitable drug targets. Comprehensive detection and functional evaluation of ER fusion proteins will provide clinicians and patients with better understanding of tumor endocrine-resistant prevalence and discovery of more effective treatment options.

Citation Format: Megan E. Yates, Tiantong Liu, Jagmohan Hooda, Sichun Yang, Riyue Bao, Jennifer M. Atkinson, ADRIAN V. LEE, Steffi Oesterreich. PD10-02 Novel ER fusion detection method to gain insight in fusion prevalence and endocrine resistant mechanisms [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD10-02.

Abstract P6-14-02: Hope for OTHERS – An organ donation program for metastatic breast cancer research

Background: Previous studies have shown that rapid autopsies (RA) provide a unique opportunity for tissue collection from patients who succumb to the disease. Because cancer patients are unable to donate their organs to other people, this program provides the patient an opportunity to leave a legacy by donating their body to research. These donations are vital for advancing breast cancer research. The UPMC/Pitt RA group revamped an existing program in 2018 through the formation of a larger multidisciplinary team that includes breast cancer laboratory and clinical researchers, pathologists, nurses, bioinformaticians, and tissue bankers. Because recruitment to the RA program was a challenge, we recently added patient advocates to the team to provide their essential perspective, and a dedicated research coordinator who serves as an ambassador for the program. Methods: Autopsy is performed by the Autopsy and Forensic Pathology Center of Excellence/Decedent Affairs Service of UPMC. Samples are banked in the Pitt Biospecimen Core (PBC), in addition to immediate processing including preparing of samples for sequencing and growing of organoids in the laboratory. Immunohistochemical (IHC) analysis is performed by UPMC/Magee Pathology. Results: The research coordinator quickly became an integral part of the program and closely interacts with care providers, patients and their families, pathologists on call, and manages interactions with transport services. Five breast cancer advocates have been instrumental in advising on additional changes to the program. The advocates attend regular team meetings and have formulated patient considerations for the the RA program, including appropriate and sensitive recruitment of patients, the role of physicians in decision making by the patient, registration for more than one RA program, potential issues with transporting a body across state lines and more. The advocates also developed the name for the program - “Hope for OTHERS” with Others standing for “Our Tissue Helping Enhance Research & Science”. As of June 2022, the team has completed 26 autopsies, and an additional 20 patients have consented to the program. The completed autopsies include patients with breast tumors representing different molecular and histological classes, ethnicities, and genders. The average disease-free survival and overall survival of patients that underwent autopsy was 81.6 and 127.8 months, respectively. Most patients passed outside the hospital (86%), with 62% in home hospice and 24% in inpatient hospice. Average time between death and start and end of autopsy was 4.56 hrs and 7.09 hours, respectively. The most common metastatic sites from which specimens are collected are liver, lung and lymph nodes. Per patient we collect on average specimens from 4 different organs. In addition to the metastatic lesions, we have access to primary tumor tissue and liquid biopsies obtained during the breast cancer disease progression for 44% and 73% of the patients, respectively. For a subset of the patients, tissue has been grown as patient-derived organoids or xenograft models. Preliminary IHC and sequencing analysis has provided insight into inter- and intra-patient and intra-tumor heterogeneity. Further molecular studies are ongoing. Conclusion In summary, over the last 5+ years, we have established a successful post-mortem tissue collection program, by addressing a series of barriers through the formation and work of a multi-disciplinary well-coordinated team. We are currently expanding our omics studies using state-of-the-art technologies to improve understanding how intra- and inter-tumor heterogeneity play a role in the clinical course of advanced breast cancer, to increase diversity of the patients enrolled in the RA program, and to support the successful implementation of other RA programs nationwide and worldwide.

Citation Format: Steffi Oesterreich, Lori Miller, Margaret Q. Rosenzweig, Tanner L. Bartholow, Megan Yates, Ashuvinee Elangovan, Laura Savariau, Allison N. Casey, Nolan Priedigkeit, Kai Ding, Abdalla Wedn, Jie Bin Liu, Daniel D. Brown, Tara Hyder, Geoffrey Pecar, Neil Carleton, Humberto Trejo Bittar, Daniel Geisler, Oscar Lopez-Nunez, Amanda M. Clark, Alan Wells, Partha Roy, Shannon Puhalla, Naomi Howard, Christine Needles, Susan Trent, Stephanie Walker, Christine Hodgdon, Rohit Bhargava, Jennifer M. Atkinson, Adrian V. Lee. Hope for OTHERS – An organ donation program for metastatic breast cancer research [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-14-02.

Abstract PD4-07: PD4-07 Uncovering molecular heterogeneity of mixed ductal and lobular carcinoma using digital spatial profiling

Background Mixed invasive ductal and lobular carcinoma (mDLC) is a rare special subtype (3-6%, ~10,000 cases/annually in US) of invasive breast cancer with elusive pathophysiology. This entity exhibits a mix of ductal-like and lobular-like tumor sub-components within the same tumor. With few seminal studies, mDLC remains poorly understood with little molecular understanding of its sub-components including their origin and implications on disease evolution, prognosis, and treatment response. With increasing recognition of no special type (NST) and invasive lobular carcinoma (ILC) as distinct diseases with unique biology, it is important to understand whether this mixed entity, and its sub-components are like NST and ILC subtypes or a distinct disease. Methods We identified mDLC cases from the UPMC cancer registry. These underwent comprehensive evaluation by a panel of expert pathologists. Three cases (each with a ductal and lobular sub-component on the same FFPE block) were shortlisted. These cases underwent digital spatial profiling (DSP) using Nanostring GeoMX Human Whole Transcriptome Atlas. Briefly, 5um slides were stained using RNAscope morphology marker probes (E-cadherin and PanCK) and GeoMX DSP oligo-conjugated RNA detection probes. Between 3-6 ductal and lobular regions of interest (ROI) per tumor were selected by pathologists. DSP barcodes were cleaved off using UV light and collected into 96-well plate. These underwent library preparation and sequencing. Raw reads were aligned to reference probes to quantify RNA counts. Q3 normalized counts were used in downstream analyses using R version 4.1. Linear modeling was used to assess differentially expressed genes (DEGs). Hypergeometric enrichment tests were used for geneset enrichment. T-tests was used to compare gene expression between two groups. Results In total 26 ROIs (14 ductal and 15 lobular) were profiled across the three mDLC FFPE slides. Overall data quality was excellent with > 90% sequencing saturation across profiled ROIs. Principle component analysis and consensus clustering showed that lobular and ductal ROIs clustered separately indicating distinct molecular profiles. Similarly, PAM50 analysis showed that ductal and lobular ROIs within each patient tumor had distinct PAM50 subtypes. To further investigate the molecular differences between ductal vs lobular ROIs, we performed differential gene expression analysis. We identified 38 up-regulated and 78 down-regulated genes in lobular compared to ductal ROIs. To assess whether mDLC sub-components share any molecular similarities to pure counterparts i.e., ILC and NST, we compared mDLC lobular vs ductal DEGs with those from TCGA ILC vs NST comparison. SHROOM1, KLK10 and KLK11 were up-regulated while CDH1, DCD, and CPB1 were down-regulated in both mDLC lobular ROIs and ILC vs mDLC ductal ROIs and NST, respectively. Pathway analysis revealed estrogen response, adhesion, and metabolism related differences between mDLC lobular vs ductal ROIs. Furthermore, key transcription factor signatures enriched in the up-regulated genes in lobular vs ductal ROIs included ESR1, FOXA2, GATA1/2 and AR signatures while those enriched in the down-regulated genes in lobular vs ductal ROIs included RCOR1, MYC, ZBTB7A, NELFE, and SPI1 signatures. Conclusion and Future Work Using DSP, we uncovered the molecular heterogeneity of mDLC. We revealed that lobular and ductal sub-components have distinct biology with differences in transcriptional signatures and hormone signaling, adhesion and metabolism related pathways. Our pilot study is the first to shed light on this elusive mixed entity using spatial profiling. Our future work will focus on DNA sequencing of mDLC sub-components to identify sub-component specific driver mutations. Our findings will need further investigation in larger mDLC cohorts to better understand their clinical implications in terms of evolution of this disease and its prognosis.

Citation Format: Osama Shiraz Shah, Azadeh Nasrazadani, Jennifer M. Atkinson, Celina Kleer, Priscilla F. McAuliffe, Rohit Bhargava, Jorge Reis-Filho, Peter C. Lucas, ADRIAN V. LEE, Steffi Oesterreich. PD4-07 Uncovering molecular heterogeneity of mixed ductal and lobular carcinoma using digital spatial profiling [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD4-07.

Loss of E-cadherin Induces IGF1R Activation and Reveals a Targetable Pathway in Invasive Lobular Breast Carcinoma

No special-type breast cancer [NST; commonly known as invasive ductal carcinoma (IDC)] and invasive lobular carcinoma (ILC) are the two major histological subtypes of breast cancer with significant differences in clinicopathological and molecular characteristics. The defining pathognomonic feature of ILC is loss of cellular adhesion protein, E-cadherin (CDH1). We have previously shown that E-cadherin functions as a negative regulator of the IGF1R and propose that E-cadherin loss in ILC sensitizes cells to growth factor signaling that thus alters their sensitivity to growth factor-signaling inhibitors and their downstream activators. To investigate this potential therapeutic vulnerability, we generated CRISPR-mediated CDH1 knockout (CDH1 KO) IDC cell lines (MCF7, T47D, and ZR75.1) to uncover the mechanism by which loss of E-cadherin results in IGF pathway activation. CDH1 KO cells demonstrated enhanced invasion and migration that was further elevated in response to IGF1, serum and collagen I. CDH1 KO cells exhibited increased sensitivity to IGF resulting in elevated downstream signaling. Despite minimal differences in membranous IGF1R levels between wild-type (WT) and CDH1 KO cells, significantly higher ligand-receptor interaction was observed in the CDH1 KO cells, potentially conferring enhanced downstream signaling activation. Critically, increased sensitivity to IGF1R, PI3K, Akt, and MEK inhibitors was observed in CDH1 KO cells and ILC patient-derived organoids.

IMPLICATIONS

Overall, this suggests that these targets require further exploration in ILC treatment and that CDH1 loss may be exploited as a biomarker of response for patient stratification.

Abstract 881: Functional characterization and clinical prevalence of ESR1 fusions in advanced endocrine resistant breast cancer

Breast cancer is the most frequently diagnosed women’s cancer with one in eight women being diagnosed during her lifetime. Even within the era of novel therapeutics and improved diagnostic screening, mortality rates remain stable, with an estimated 43,600 deaths occurring in 2021 alone. Malignant transformation of breast cancer to advanced disease is the mainstay driver of mortality and is largely attributed to treatment resistance. Fortunately, identification of therapeutic resistance mechanisms has rapidly transformed our understanding of cancer evasion and is enabling personalized treatment guidance and regimens. Notably, mutations and amplifications of the estrogen receptor (ER, ESR1) remain a prominent source of endocrine therapy resistance. Two-thirds of all breast cancer are positive for ER, making it an attractive druggable target that has revolutionized patient care. Unfortunately, however, 30% of tumors exposed to endocrine therapy subsequently develop resistance. Recently identified ER fusion proteins, discovered in metastatic endocrine resistant disease, result in substitution of the C-terminal ER ligand binding domain with a variety of fused in-frame gene partners due to genomic translocations occurring at ESR1 intron 6. Our lab has demonstrated that ER fusion proteins drive robust ER hyperactivation and metastatic potential independent of ER ligand estradiol and in the presence of endocrine therapies such as Fulvestrant. Overexpression of ER fusion proteins, particularly ESR1-SOX9 and ESR1-YAP1, in invasive ductal and invasive lobular carcinoma models with endogenous ER knockdown, resulted in enhanced 3D growth, increased migration by wound scratch assay, enhanced colony formation as a proxy of survival and ER pathway hyperactivation. Targeted endogenous ER knockdown utilizing short hairpin RNA enhances fusion driven phenotypes that are unique to fusion partner proteins and cellular context. ER fusion prevalence in advanced breast cancer remains a challenge due to the promiscuous fusion partners disrupting traditional sequencing techniques. Our group has developed a novel method of ESR1 fusion detection, EnRich, which exploits the ESR1 fusion breakpoints. Importantly, we have assessed EnRich fusion discovery with the use of circulating tumor DNA (ctDNA) from non-invasive liquid biopsies. Our pilot study of 15 blood ctDNA samples detected three different ESR1 fusion gene products which have been further validated by PCR. EnRich will help us identify and monitor treatment resistance of known and novel ESR1 fusions in patient samples irrespective of treatment regime as well as in longitudinal samples collected from patients undergoing endocrine therapy. The in vitro resistant properties of fusion proteins emphasize the necessity to better detect these mutations in patients with advanced disease and determine more appropriate treatment measures.

Citation Format: Megan E. Yates, Tiantong Liu, Jagmohan Hooda, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich. Functional characterization and clinical prevalence of ESR1 fusions in advanced endocrine resistant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 881.

Abstract 81: In depth single cell profiling of a case of breast cancer bone metastases with associated organoid models reveal a precision medicine approach to treatment

Occurring in 65-80% of metastatic breast cancer (BC), bone metastasis (BoM) is the major cause of BC related mortality. Lack of understanding of BoM evolution and heterogeneity at patient specific levels and precise application of targeted therapies are major challenges of managing BoM. In this study, we described in depth histologic and molecular characterization of a case of invasive lobular breast cancer (ILC) bilateral metastasis to bone, and identified and tested potential targets for treating BoM. H&E/IHC staining, whole exome sequencing (WES), and RNAseq were performed on FFPE primary tumor and pelvis and tibia BoMs collected from our study case. Organoids were derived from the two BoMs and single cell RNA sequencing (scRNAseq) undertaken on the organoids and their originating tumors. H&E/IHC demonstrated evolution of the disease from an ER+ primary ILC to ER- BoM with mixed lobular and ductal carcinoma features. WES revealed two druggable mutations including PIK3CA (E545K) and BRCA1 (D1813H/H399P). RNAseq revealed upregulation of TGF-β, Wnt/beta-catenin and PI3K pathways, epithelial to mesenchymal transition (EMT) and angiogenesis in BoM compared to primary tumor, representing promising targets for BoM. scRNAseq revealed 5 major cell types including epithelial, fibroblasts, immune, osteoclasts and endothelial cells, and pronounced intracellular heterogeneity. Six epithelial clusters were identified, featuring high TNF-α signaling, high partial EMT signatures regulated by PRRX1/2, TWIST1/2, and FOXS1, high proliferation, and endocrine resistance signatures. In fibroblasts, 9 clusters were identified representing ECM remodeling, angiogenesis, osteoclast-like, MSC, IFN response and myofibroblasts. Immune cells majorly composed of monocytes/macrophages, CD4+, CD8+ and Treg T cells, and NK cell. WES and scRNAseq analysis demonstrated that organoids preserved mutational landscape and cellular heterogeneity of matched BoMs. Consistent with the BRCA1 and PIK3CA mutations, organoids were responsive to a PARP (Talazoparib: IC50 1.3uM) and PI3K (Alpelisib: IC50 4-9uM) inhibitors. In summary, we have identified potential therapeutic targets from understanding evolution and heterogeneity of BC BoM, and evaluated these in patient-specific organoids, thereby providing insights for the design of a precision medicine based clinical treatment strategy.

Citation Format: Kai Ding, Fangyuan Chen, Nolan Priedigkeit, Daniel D. Brown, Tanya Heim, Rebecca Watters, Kurt Weiss, Peter C. Lucas, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee. In depth single cell profiling of a case of breast cancer bone metastases with associated organoid models reveal a precision medicine approach to treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 81.

Abstract 2690: Loss of E-cadherin induces IGF1R activation revealing a targetable pathway in invasive lobular breast carcinoma

Invasive Ductal Carcinoma (IDC) and Invasive Lobular Carcinoma (ILC) are two major subtypes of breast cancer with significant differences in their histological and molecular underpinnings. ILC has a unique loss of E-cadherin (CDH1) which we have previously demonstrated as a negative regulator of the Insulin-like Growth Factor 1 receptor (IGF1R) through a comprehensive analysis of cell line models and tumor samples. We propose that loss of E-cadherin in ILC sensitizes cells to growth factor signaling and thus alters their sensitivity to growth factor signaling inhibitors. To investigate this, we used CRISPR to generate CDH1 knockout (KO) IDC cell lines (MCF7, T47D, ZR75.1) to uncover the mechanism by which E-cadherin loss activates the IGF pathway while also assessing its targetability. CDH1 KO cells exhibited anchorage independent growth in suspension culture and altered p120 catenin localization as observed in ILC tumors. Through in vitro studies, we show increased signaling sensitivity to IGF/insulin ligands and enhanced signaling duration in CDH1 KO cells. In addition, we observed a higher migratory potential of CDH1 KO cells compared to wild type (WT) cells, which was further enhanced as a chemotactic response to IGF1 or serum. Further, this phenotype could be reversed with an IGF1R inhibitor, BMS-754807. We additionally identified an increase in Collagen I haptotaxis in the CDH1 KO cells, which was also translated into a novel invasive phenotype towards serum in the T47D CDH1 KO cells. Despite no significant differences in membranous IGF1R levels between WT and CDH1 KO cells, higher ligand-receptor interaction was observed with CDH1 KO cells, demonstrating an increased ligand-receptor complex formation upon stimulation. Our results suggest that loss of CDH1 results in an increase in IGF1 receptor availability for ligand binding which in turn allows for an enhanced downstream signaling activation. Interestingly, a physical repression of E-cadherin on IGF1R could not be demonstrated, suggesting spatial changes on the membrane following E-cadherin loss may control ligand binding. Critically, increased sensitivity to IGF1R, PI3K, AKT and MEK inhibitors was observed in CDH1 KO cells suggesting that these targets should be further explored in ILC and that CDH1 loss may be exploited as a biomarker of response, or for patient stratification to inhibitors targeting these pathways.

Citation Format: Ashuvinee Elangovan, Laura Savariau, Megan E. Yates, Jagmohan Hooda, Alison M. Nagle, Steffi Oesterreich, Jennifer M. Atkinson, Adrian V. Lee. Loss of E-cadherin induces IGF1R activation revealing a targetable pathway in invasive lobular breast carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2690.

Abstract 956: Role of E-cadherin in progression of invasive breast lobular carcinoma

Invasive lobular carcinoma (ILC) is the second most frequently diagnosed histologic subtype of invasive breast cancer following invasive ductal carcinoma (IDC) and accounts for 15% of all cases. The hallmark of ILC is the genetic loss of E-cadherin (CDH1) causing the disruption of adherens junctions and resulting in discohesive, linear growth of ILC cells in tissues. Beyond its effects on this unique histology, there is limited data on the role of E-cadherin loss in ILC metastasis. Therefore, we generated three ILC cell lines (MDA-MB-134, SUM44PE and BCK4) with inducible E-cadherin overexpression. Using immunoblotting and immunofluorescence microscopy we confirmed E-cadherin expression, re-expression of other adherens junction proteins including α and β-catenin, and re-localization of cytoplasmic p120-catenin to the membrane. Successful cell adhesion to E-cadherin coated plates suggested formation of functional junctions. E-cadherin expression had no effect on 2D growth but did diminish cell growth in ultra-low attachment (ULA) conditions consistent with its previously described role in anoikis. We confirmed increased cell death of MM134 with E-cadherin overexpression compared to control cells when grown in ULA. Overexpression of E-cadherin failed to rescue poor migratory and invasive ability of ILC cell lines as measured by transwell assays. However, E-cadherin expression in SUM44PE lead to decreased haptotaxis to collagen I, and altered morphology from loose grape-like structure to tight sphere-like formation when embedded in collagen I.In vivo analyses revealed reduced primary tumor formation in E-cadherin-overexpression SUM44PE cells after mammary fat pad injection. Additional studies aimed at understanding E-cadherin’s effect on in vivo metastasis are ongoing.Collectively, our studies using novel cell line models will lead to an improved understanding of the hallmark loss of E-cadherin and disease mechanisms in ILC, which we hope will ultimately enable the development of more effective therapies and improve the outcome of patients with this understudied histological subtype of breast cancer.

Citation Format: Laura Savariau, Nilgun Tasdemir, Ashuvinee Elangovan, Kai Ding, Pooja Sree Tallapaneni, Jagmohan Hooda, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich. Role of E-cadherin in progression of invasive breast lobular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 956.

ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation

Estrogen receptor alpha (ER/ESR1) is frequently mutated in endocrine resistant ER-positive (ER+) breast cancer and linked to ligand-independent growth and metastasis. Despite the distinct clinical features of ESR1 mutations, their role in intrinsic subtype switching remains largely unknown. Here we find that ESR1 mutant cells and clinical samples show a significant enrichment of basal subtype markers, and six basal cytokeratins (BCKs) are the most enriched genes. Induction of BCKs is independent of ER binding and instead associated with chromatin reprogramming centered around a progesterone receptor-orchestrated insulated neighborhood. BCK-high ER+ primary breast tumors exhibit a number of enriched immune pathways, shared with ESR1 mutant tumors. S100A8 and S100A9 are among the most induced immune mediators and involve in tumor-stroma paracrine crosstalk inferred by single-cell RNA-seq from metastatic tumors. Collectively, these observations demonstrate that ESR1 mutant tumors gain basal features associated with increased immune activation, encouraging additional studies of immune therapeutic vulnerabilities.

Hotspot ESR1 Mutations Are Multimodal and Contextual Modulators of Breast Cancer Metastasis

Constitutively active estrogen receptor α (ER/ESR1) mutations have been identified in approximately one-third of ER+ metastatic breast cancers. Although these mutations are known as mediators of endocrine resistance, their potential role in promoting metastatic disease has not yet been mechanistically addressed. In this study, we show the presence of ESR1 mutations exclusively in distant but not local recurrences in five independent breast cancer cohorts. In concordance with transcriptomic profiling of ESR1-mutant tumors, genome-edited ESR1 Y537S and D538G-mutant cell models exhibited a reprogrammed cell adhesive gene network via alterations in desmosome/gap junction genes and the TIMP3/MMP axis, which functionally conferred enhanced cell-cell contacts while decreasing cell-extracellular matrix adhesion. In vivo studies showed ESR1-mutant cells were associated with larger multicellular circulating tumor cell (CTC) clusters with increased compactness compared with ESR1 wild-type CTCs. These preclinical findings translated to clinical observations, where CTC clusters were enriched in patients with ESR1-mutated metastatic breast cancer. Conversely, context-dependent migratory phenotypes revealed cotargeting of Wnt and ER as a vulnerability in a D538G cell model. Mechanistically, mutant ESR1 exhibited noncanonical regulation of several metastatic pathways, including secondary transcriptional regulation and de novo FOXA1-driven chromatin remodeling. Collectively, these data provide evidence for ESR1 mutation-modulated metastasis and suggest future therapeutic strategies for targeting ESR1-mutant breast cancer.

SIGNIFICANCE

Context- and allele-dependent transcriptome and cistrome reprogramming in mutant ESR1 cell models elicit diverse metastatic phenotypes related to cell adhesion and migration, which can be pharmacologically targeted in metastatic breast cancer.

Abstract PD1-08: Esr1 mutant breast cancers show elevated basal cytokeratins and immune activation

Estrogen receptor alpha (ER/ESR1) is mutated in 30-40% of endocrine resistant ER-positive (ER+) breast cancer. ESR1 mutations cause ligand-independent growth and increased metastasis in vivo and in vitro. Despite the distinct clinical features and changes in therapeutic response associated with ESR1 mutations, there are no data about their potential role in intrinsic subtype switching.Applying five different luminal and basal gene set pairs derived from cell lines and tumors, ESR1 mutant cell models and clinical samples showed a significant enrichment of basal subtype markers. Among them, the six basal cytokeratins (BCKs) were the most enriched genes (KRT5/6A/6B/14/16/17) uniquely in ESR1 mutant cells but not other endocrine resistant cell models. BCKs were observed to heterogeneously express in a minor cell subpopulation in ESR1 mutant cell models and clinical specimens. ER ChIP-seq showed the mutant-specific induction of BCKs was independent of ER binding and instead selectively expressed in clones with low ER expression. In contrast, BCKs are associated with chromatin reprogramming centered around a progesterone receptor-orchestrated 154 kb insulated neighborhood at the KRT14/16/17 genomic region. Stronger CTCF binding was detected at the bases of chromatin loop in ESR1 mutant cells. Knockdown of progesterone receptor but not glucocorticoid receptor drastically blocked the induction of KRT14/16/17 in ESR1 mutant cells. Unexpectedly, high BCK expression in ER+ primary breast cancer is associated with good prognosis, and these tumors show enriched activation of a number of immune pathways, a distinctive feature shared with ESR1 mutant tumors. While the BCK-associated immune activation is not related to tumor mutation burdens, S100A8 and S100A9 were identified as the most highly induced immune mediators shared between high-BCKs ER+ and ESR1 mutant tumors, which was further validated in the plasma samples of a cohort of 18 patients with ER+ metastases (11 WT vs 7 mutant). Finally, single-cell RNA-seq analysis in an ER+ bone metastasis case inferred the involvement of S100A8 and S100A9 in paracrine crosstalk between epithelial and stromal cells, particularly macrophages and fibroblasts through TLR4 signaling. Collectively, these observations demonstrate that ESR1 mutant tumors gain basal features with induction of basal cytokeratins via epigenetic mechanisms in rare subpopulation of cells. This is associated with increased immune activation, encouraging additional studies of immune therapeutic vulnerabilities in ESR1 mutant tumors.

Citation Format: Zheqi Li, Yang Wu, Olivia Mcginn, Amir Bahreini, Nolan M. Priedigkeit, Kai Ding, Sayali Onkar, Carol A. Sartorius, Lori Miller, Margaret Rosenzweig, Nikhil Wagle, Jennifer K. Richer, William J. Muller, Laki Buluwela, Simak Ali, Dario A.A. Vignali, Yusi Fang, Li Zhu, George C. Tseng, Jason Gertz, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich. Esr1 mutant breast cancers show elevated basal cytokeratins and immune activation [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD1-08.

Abstract P5-12-03: Wcrc-25: A novel luminal invasive lobular carcinoma cell line model

Breast cancer is categorized by the molecular and histologic presentation of the tumor; with the major histologic subtypes observed in patients being Invasive Ductal Carcinoma (IDC) and Invasive Lobular Carcinoma (ILC). ILC are characterized by growth in a single file discohesive manner with stromal infiltration attributed to their hallmark loss of E-cadherin. The lower incidence of ILC, relative to IDC, resulted in this subtype being understudied in the field. The Cancer Cell Line Encyclopedia (CCLE) currently only lists 2 ILC cell lines; emphasizing the need to expand the inventory of models available to researchers. To that end, here we report the successful establishment and characterization of a novel ILC cell line from a metastatic pleural aspirate from a postmenopausal Caucasian woman with ER+ metastatic ILC. The patient underwent a bilateral mastectomy, several pleural fluid aspirations and multiple treatment changes as her disease progressed until she succumbed to the disease. Various cell culture methods were attempted with the pleural aspirate and a standard practice of DMEM supplemented with 10% FBS in normoxic conditions was deemed effective. A cell line was developed, WCRC-25 which is ER-. WCRC-25 appears to be E2 unresponsive in vitro and is morphologically larger than other ILC cells currently in use, namely, MDA-MB-134, BCK4 and IPH-926, while exhibiting better adherence to 2D plates and a less rounded morphology. Sequencing revealed a CDH1 Q706 truncating mutation in the cells, which was also observed in the patient’s cfDNA with its enrichment increasing over time, supporting elevated disease burden. RNA-seq analysis comparing the primary tumor to metastases and the cell line reveal a signature for cell cycle progression and Akt signaling. To assess targetability, we subjected WCRC-25 to AZD5363 and Alpelisib which confirmed WCRC-25 as susceptible to PI3K/Akt signaling inhibition. Finally, we generated mouse xenograft models of WCRC-25 through mammary fat pad injection and observed small, but palpable tumors and metastasis to several sites. In conclusion, we report WCRC-25 as a novel ILC cell line with much promise as an invaluable research tool to advance our understanding of ILC and its therapeutic vulnerabilities.

Citation Format: Ashuvinee Elangovan, Emily A Bossart, Ahmed Basudan, Nilgun Tasdemir, Osama Shiraz Shah, Kai Ding, Carolin Meier, Tanya Heim, Lori Miller, Tiantong Liu, Shannon L Puhalla, Grzegorz Gurda, Peter C Lucas, Priscilla F McAuliffe, Jennifer M Atkinson, Adrian V Lee, Steffi Oesterreich. Wcrc-25: A novel luminal invasive lobular carcinoma cell line model [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-12-03.

Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities

The molecular events and transcriptional plasticity driving brain metastasis in clinically relevant breast tumor subtypes has not been determined. Here we comprehensively dissect genomic, transcriptomic and clinical data in patient-matched longitudinal tumor samples, and unravel distinct transcriptional programs enriched in brain metastasis. We report on subtype specific hub genes and functional processes, central to disease-affected networks in brain metastasis. Importantly, in luminal brain metastases we identify homologous recombination deficiency operative in transcriptomic and genomic data with recurrent breast mutational signatures A, F and K, associated with mismatch repair defects, TP53 mutations and homologous recombination deficiency (HRD) respectively. Utilizing PARP inhibition in patient-derived brain metastatic tumor explants we functionally validate HRD as a key vulnerability. Here, we demonstrate a functionally relevant HRD evident at genomic and transcriptomic levels pointing to genomic instability in breast cancer brain metastasis which is of potential translational significance.

Getting to YES: The Evolution of the University of Pittsburgh Medical Center Hillman Cancer Center Youth Enjoy Science (YES) Academy

The University of Pittsburgh Medical Center Hillman Cancer Center Academy (Hillman Academy) has the primary goal of reaching high school students from underrepresented and disadvantaged backgrounds and guiding them through a cutting-edge research and professional development experience that positions them for success in STEM. With this focus, the Hillman Academy has provided nearly 300 authentic mentored research internship opportunities to 239 students from diverse backgrounds over the past 13 years most of whom matriculated into STEM majors in higher education. These efforts have helped shape a more diverse generation of future scientists and clinicians, who will enrich these fields with their unique perspectives and lived experiences. In this paper, we describe our program and the strategies that led to its growth into a National Institutes of Health Youth Enjoy Science-funded program including our unique multi-site structure, tiered mentoring platform, multifaceted recruitment approach, professional and academic development activities, and a special highlight of a set of projects with Deaf and Hard of Hearing students. We also share student survey data from the past six years that indicate satisfaction with the program, self-perceived gains in key areas of scientific development, awareness of careers in STEM, and an increased desire to pursue advanced degrees in STEM.

The Development and Implementation of an Autopsy/ Tissue Donation for Breast Cancer Research

There is growing interest in tissue procurement for cancer research through autopsy. Establishing an autopsy/tissue donation programme for breast cancer research within an academic medical centre in the United States requires consideration, planning, multi-departmental collaboration and labour-intensive maintenance. It is the purpose of this paper to outline the necessary considerations in implementing and maintaining a tissue donation and autopsy programme within a breast cancer centre at a comprehensive cancer centre. Considerations of programme planning include: patient engagement, the recruitment of patients and families into the programme, the role and scope of work of the clinical coordinator, regulatory issues and the coordination with both pathology and the research team at time of death and autopsy/tissue donation. All aspects of the tissue donation/rapid autopsy programme development and implementation are discussed and illustrated through case study. An Autopsy/ Tissue Donation for breast cancer research can be successfully developed and implemented.

Prognostic Utility of Breast Cancer Index to Stratify Distant Recurrence Risk in Invasive Lobular Carcinoma

PURPOSE

The prognostic utility of Breast Cancer Index (BCI) for risk assessment of overall (0-10 years), early (0-5 years), and late (5-10 years) distant recurrence (DR) in hormone receptor-positive (HR+) invasive lobular carcinoma (ILC) was evaluated.

EXPERIMENTAL DESIGN

BCI gene expression analysis was performed blinded to clinical outcome utilizing tumor specimens from patients with HR+ ILC from a multi-institutional cohort. The primary endpoint was time to DR. Kaplan-Meier analyses of overall, early, and late DR risk were performed, and statistical significance was evaluated by log-rank test and Cox proportional hazards regression. The prognostic contribution of BCI in addition to clinicopathologic factors was evaluated by likelihood ratio analysis.

RESULTS

Analysis of 307 patients (99% ER+, 53% T1, 42% N+, 70% grade II) showed significant differences in DR over 10 years based on BCI risk categories. BCI low- and intermediate-risk patients demonstrated similar DR rates of 7.6% and 8.0%, respectively, compared with 27.0% for BCI high-risk patients. BCI was a significant independent prognostic factor for overall 10-year DR [HR = 4.09; 95% confidence interval (CI), 2.00-8.34; P = 0.0001] as well as for both early (HR = 8.19; 95% CI, 1.85-36.30; P = 0.0042) and late (HR = 3.04; 95% CI, 1.32-7.00; P = 0.0224) DR. In multivariate analysis, BCI remained the only statistically significant prognostic factor for DR (HR = 3.49; 95% CI, 1.28-9.54; P = 0.0150).

CONCLUSIONS

BCI is an independent prognostic factor for ILC and significantly stratified patients for cumulative risk of 10-year, early, and late DR. BCI added prognostic value beyond clinicopathologic characteristics in this distinct subtype of breast cancer.

Abstract 2864: RET as a novel therapeutic target in breast cancer brain metastases

Brain metastases (BrM) are reported in approximately 10-30% of breast cancer patients with a poor median overall survival of 8.5 months. Current therapeutic strategies are mostly limited to surgery, chemotherapy and radiotherapy, making the study of novel druggable targets and brain-permeable small molecule inhibitors an urgent clinical need.

Our lab recently reported a hybrid-capture exome RNA-sequencing study on 21 patient-matched pairs of primary breast tumors and brain metastases and identified upregulation of several receptor tyrosine kinases including RET in BrM. The ligand for RET is Glial Cell Derived Neurotrophic Factor (GDNF), which is released by astrocytes and microglia in response to neuroinflammation and brain tissue damage. Clinical BrM cell growth in ex vivo cultures was reduced by the multikinase inhibitor Cabozantinib, indicating a potential role for RET in the growth of BrM lesions. We hypothesize that the high level of brain-derived GDNF provides a permissive microenvironment for RET overexpressing breast cancer cells to form brain metastases, and will evaluate the therapeutic potential of RET targeted therapies for breast cancer BrM patients.

Our preliminary data show that in RET-overexpressing (RET-OE) breast cancer cell models, 30-minute GDNF treatment induces RET phosphorylation at two distinct tyrosine residues, along with downstream signaling illustrated by ERK1/2, AKT, and STAT3 phosphorylation. This induction was effectively abrogated after shRNA-mediated RET knockdown. We employed a phospho-kinase array to identify novel downstream targets regulated by the GDNF-RET signaling axis, and found that GDNF induces phosphorylation of multiple targets (including p27 and RSK) in RET-OE cells. Interestingly, phosphorylation of multiple Src family kinases (Lck, Lyn, Fgr) was downregulated with GDNF treatment. We will further examine these downstream targets via reverse phase protein array (RPPA).

GDNF triggers migration of RET-OE cell lines in both 2D wound scratch and 3D transwell migration assays. Additionally, we present results obtained through an ex vivo organotypic coculture system, in which RET-OE cells are cultured on top of 300-micron thick murine brain, kidney, or liver slices. RET overexpression increases colony formation compared with empty vector control, suggesting a role for RET signaling in the initial establishment of metastatic brain lesions. Differences in colonization between empty vector transfected and RET-OE cells remain minimal in kidney and liver sections, suggesting a role for RET specific to the brain microenvironment.

We will examine RET-driven brain metastasis in vivo by employing RET-OE and RET-deficient cell lines in intracranial, intracardiac, and mammary fat pad injection. These models of BrM will be randomized to RET inhibitor or vehicle treatment to evaluate the efficacy of RET-targeted therapy in the setting of breast cancer brain metastasis.

Citation Format: Simeng Liu, Geoffrey Pecar, Jagmohan Hooda, Jennifer M. Atkinson, Fangyuan Chen, Adrian V. Lee, Steffi Oesterreich. RET as a novel therapeutic target in breast cancer brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2864.

Abstract 2848: Neomorphic cell-cell adhesion reprogramming facilitates metastasis of ESR1 mutant breast cancer

Background: Hotspot estrogen receptor-α (ER/ERα/ESR1) mutations occur in 30-40% endocrine resistant ER+ breast cancer and are associated with worse outcome. How these mutations facilitate metastasis remains ambiguous. It is necessary to identify a clear mechanism for therapeutic intervention.

Methods: ESR1 mutations were detected by ddPCR. Transcriptome data were derived from cell lines and clinical samples. Y537S and D538G genome-edited MCF7 and T47D cell lines were used for in vitro phenotypic characterization. Cell-cell adhesive properties were assessed using calcein-labelled adhesion, spontaneous cell aggregation and ibidi microfluidic assays. Altered cell-cell adhesion genes were validated using qRT-PCR, immunoblot and immunostaining. Desmosome blocking peptides and carbenoxolone were used for blockade of adhesion. ER cistromes were profiled by ChIP-seq. Tail vein injection was performed on athymic nude mice to evaluate metastasis in vivo. Circulating tumor cell (CTC) clustering propensity in vivo was assessed via intracardiac injection followed by CTC microfilter capture. CTC-cluster gene signatures were generated from ER+ breast cancer CTC RNA-seq data.

Results: ESR1 mutations were significantly enriched in distant metastases (12/48) vs local (0/27) recurrences, confirming their critical role in promoting metastasis. Transcriptomic analysis revealed altered cell-cell interaction pathways in ESR1 mutant tumors. ESR1 mutant cells formed more compact spheroids in suspension culture, and exhibited stronger cell-cell adhesion in static condition. Under microfluidic condition with physiological shear stress, mutant ESR1 cells derived more and larger clusters, which were prominently preserved from pre-existing clusters. This effect was correlated with increased expression of desmosome and gap junction genes in mutant cells and pharmacological blockade significantly reduced the enhanced cell-cell adhesion. ER ChIP-seq revealed no de novo mutant ER binding sites at the loci of the target genes, suggesting indirect regulation by mutant ER. This was exemplified by a secondary regulation from cFos/AP1 signaling of GJA1 expression, and an epigenetic regulation at DSC1/DSG1 loci through enhanced H3K4me2 and H3K27ac modification. In vivo studies showed ESR1 mutant cells derived more distant metastases, and MCF7 Y537S cells formed larger CTC clusters with increased compactness compared to WT cells. Finally, ER+ CTC-cluster signatures were enriched in ESR1 mutant tumors, suggesting their unique dependence on this pathway during metastasis.

Conclusion: Hotspot ESR1 mutations induce expression of multiple desmosome and gap junction genes and confer enhanced cell-cell adhesion, which facilitates breast cancer metastasis via increased CTCs clustering propensity. These findings provide insights to the development of drugs targeting gap junction in ER mutant tumors.

Citation Format: Yang Wu, Zheqi Li, Amir Bahreini, Jian Chen, Ye Qin, Kevin M. Levine, Nilgun Tasdemir, Nolan M. Priedigkeit, Li Zhu, George C. Tseng, Yu Jiang, Benjamin Troness, Laki Buluwela, Simak Ali, Spencer Arnesen, Jason Gertz, Ben Ho Park, Jennifer M. Atkinson, Dorraya El-Ashry, Adrian V. Lee, Steffi Oesterreich. Neomorphic cell-cell adhesion reprogramming facilitates metastasis of ESR1 mutant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2848.

Exosomes in Breast Cancer - Mechanisms of Action and Clinical Potential

Extracellular vesicles (EV) are a heterogeneous group of cell-derived membrane vesicles comprising apoptotic bodies, microvesicles, and small EVs also called as exosomes. Exosomes when initially identified were considered as a waste product but the advancement in research techniques have provided insight into the important roles of exosomes in cell-cell communication, various biological processes and diseases, including cancer. As an important component of EVs, exosomes contain various biomolecules such as miRNAs, lipids, and proteins that largely reflect the characteristics of their parent cells. Notably, cancer cells generate and secrete many more exosomes than normal cells. A growing body of evidence suggests that exosomes, as mediators of intercellular cross-talk, play a role in tumorigenesis, cancer cell invasion, angiogenesis, tumor microenvironment (TME) formation, and cancer metastasis. As we gain more insights into the association between exosomes and cancer, the potential of exosomes for clinical use is becoming more intriguing. This review is focused on the role of exosomes in breast cancer, in terms of breast cancer biology, mechanism of action, potential as biomarkers, and therapeutic opportunities.

Abstract PS19-06: Role of the calcium-sensing receptor (CaSR) in invasive lobular breast carcinoma metastasis to the ovary

Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer, after the more common invasive ductal carcinoma (IDC). ILC accounts for 10 to 15% of all invasive breast carcinomas, affecting approx. 26,000-40,000 women in 2020 in the US alone. Despite 95% of ILC being Luminal A conferring patients a favorable prognosis, patients with ILC have poorer long-term outcomes when compared to patients with Luminal A IDC. ILC spread to common sites of ER+ breast cancer metastasis such as the bones, but are also three times more likely to spread to the ovaries, peritoneum, and gastrointestinal tract compared to IDC, and these unique aspects of metastases remain poorly understood. To better understand metastasis to the ovary we performed DNA and RNA sequencing of 11 pairs of primary breast tumor and ovarian metastasis as well as 13 orphan breast cancer ovarian metastases. Our cohort was enriched for lobular histology, with 13 samples originating from ILC, 6 from IDC and 6 from mixed ILC/IDC. We found mutations in CDH1 (43%), PIK3CA (40%), and FOXA1 (29%) highlighting the enrichment in ILC cases present in our cohort. Gene expression analysis lead to identification of 874 differentially expressed between primary tumors and ovarian metastases. We identified the calcium-sensing receptor CaSR as one of the top upregulated in ovarian metastases compared to primary tumor in 10 out of the 11 paired samples. Other genes highly expressed in ovarian metastases included TAC3, GLRA2, ALLC, MUC19, CHRNA2, PIP, CST4, and TEX15. Pathways analyses showed an enrichment of signaling through glutamate receptor and glycine receptor families. To assess the contribution of CaSR to breast cancer cell proliferation and metastatic properties, and due to the absence of breast cancer cell lines expressing CaSR, we generated CaSR overexpression models using lentiviral infection in MDA-MB-134, MDA-MB-330, BCK4 and SUM44PE ILC cell lines. While overexpression of CaSR alone did not confer a cell growth advantage or migratory ability to the cell lines, stimulation with calcium or a calcium mimetic resulted in enhanced migration in transwell assays in 3 of the 4 cell lines. Scratch assays further confirmed the stimulation of cell migration in cells with CaSR overexpression in the presence of calcium. Cell migration in CaSR overexpression models could be stimulated with the calcimimetic R568, and inhibited by the calcilytics NPS2143, and F-actin staining confirmed the need to activate the receptor to enhance migratory properties. Our studies further revealed that the induced migratory properties of CaSR overexpressing cells required estradiol and ER signaling, and that migration could be blocked with ER inhibitors such as ICI 182,780 and tamoxifen. Western blotting data revealed that the enhanced cell migratory properties of CaSR overexpressing cells was via activation of the MEK/ERK pathway and migration could be inhibited using specific small molecule pathway inhibitors.Altogether, our study provides insight on the potential mechanism by which upregulation of the CaSR supports breast cancer ovarian metastasis. We hope that these studies will not only deepen our understanding of ILC ovarian metastasis but will eventually lead to the development of more effective therapies and improve the outcome of patients with this understudied type of breast cancer.

Citation Format: Ye Qin, Laura Savariau, Ahmed Mohammed Basudan, Osama Shah, Zheqi Li, Tiantong Liu, Nilgun Tasdemir, Lan Coffman, Esther Elishaev, Jennifer M Atkinson, Peter Lucas, Adrian V Lee, Steffi Oesterreich. Role of the calcium-sensing receptor (CaSR) in invasive lobular breast carcinoma metastasis to the ovary [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS19-06.

Abstract PS7-15: Mixed invasive ductal lobular carcinomas (mDLC) are clinically more similar to invasive lobular carcinoma (ILC) than to invasive ductal carcinoma (IDC)

Clinicopathologic differences between histological subtypes of invasive breast cancer are increasingly being appreciated. Mixed invasive ductal lobular carcinomas (mDLC) are thought to be composed of both ductal and lobular components, and we sought to determine whether mDLC clinically align more closely with invasive ductal (IDC) or invasive lobular (ILC) carcinoma subtypes or if they display intermediate or unique features dissimilar to either type. Key clinical and histologic parameters were compared between cohorts of patients with mDLC (N = 410), IDC (N = 12,979), and ILC (N = 1,569) identified from cancer registry data of a single large healthcare system.Patients with mDLC were older (59 years (49 - 68)) than those with IDC (57 years (48 - 67), p = 0.014)) and younger than those with ILC (61 years (51 - 70), p = 0.006). Tumor size in mDLC was larger (19mm (12 - 27)) than IDC (16mm (10 - 25), p < 0.001) and smaller than ILC (20mm (12 - 35), p = 0.036). Similar to ILC, mDLC were more likely than IDC to be ER+ (92% vs 78% in IDC, p < 0.001), and less likely to be HER2+ (8% vs 15% in IDC, p = 0.04). mDLC were also similar to ILC with regards to higher likelihood of diagnosis at higher stage (p < 0.001), yet with lower grade (p < 0.001), at diagnosis as compared to IDC. Heatmap visualization, as well as dimension reduction by multidimentional scaling (MDS), demonstrates significant overlap of the mDLC and ILC cohorts. Furthermore, an elastic net regression model based on clinicopathologic parameters predicts mDLC to align more closely with ILC than IDC. For patients for whom oncotype Dx scores were available, there was a trend for enrichment of low risk RS scores with rare high-risk RS tumors in mDLC, similar to ILC. With regards to response to neoadjuvant chemotherapy, a subset of the aforementioned cohorts who had received neoadjuvant chemotherapy, mDLC (N = 17), IDC (N = 180), and ILC (N = 57), were compared. Among patients in whom breast conserving surgery (BCS) was attempted, patients with IDC were more likely to have a successful BCS than those with ILC, with less margin positivity thereby avoiding re-excision and/or completion mastectomy (70% vs 32%, respectively; p = 0.003). Successful BCS was achieved with mDLC 56% of the time, although compared to IDC and ILC statistical significance was not reached. In a limited cohort receiving neoadjuvant endocrine therapy (mDLC (N = 7), IDC (N = 37), and ILC (N = 21)) no differences with regard to rates of successful BCS were identified. Pathologic complete response rates (pCR) were additionally evaluated, although small study numbers precluded our ability to perform statistical analysis.Collectively, the aforementioned findings support a higher concordance between mDLC and ILC as compared to IDC. It is feasible that the lobular component of mDLC tumors is predominant, leading to the observed histopathologic similarities noted between mDC and ILC cohorts. We are planning meta-analyses including data from other institutions, and molecular studies to further understand complexities of mDLC.The authors acknowledge grant support from ASCO Conquer Cancer (to NW and AN).

Citation Format: Azadeh Nasrazadani, Yujia Li, Yusi Fang, Osama Shah, Jennifer M Atkinson, Joanna S Lee, Priscilla F McAuliffe, Adrian V Lee, George Tseng, Peter Lucas, Steffi Oesterreich, Norman Wolmark. Mixed invasive ductal lobular carcinomas (mDLC) are clinically more similar to invasive lobular carcinoma (ILC) than to invasive ductal carcinoma (IDC) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS7-15.

Abstract PS17-23: Development of a breast cancer organoid resource faithfully representing epithelial heterogeneity and drug response

Organoid cultures are being explored as intermediate preclinical models in numerous cancer types including colon, liver and brain. Recently it has been demonstrated that organoids can be robustly isolated and cultured from breast cancer subtypes, that they maintain the histological, genomic and transcriptomic signatures of the primary tumor tissue, and that ER expression can be preserved (Sachs et al, 2018). The Institute for Precision Medicine (IPM), a collaboration between UPMC and the University of Pittsburgh initiated a program to develop breast cancer organoids in 2018. The IPM works closely with surgeons to consent patients with primary or metastatic breast cancer for tissue collection, and with an institutional biospecimen core for tissue procurement and deidentification. The IPM receives fresh, deidentified tissue typically within 60 minutes of the patient’s operation. Based on the protocol by Sachs et al, to date we have established 49 organoids from a total of 60 tumor samples received from patients undergoing resection of their primary or metastatic breast tumor, resulting in a success rate of 82%. Our current collection includes organoids from 17 treatment-naïve invasive ductal carcinomas, 12 treatment-naïve invasive lobular carcinomas, 10 primary tumors excised after neoadjuvant therapy and 5 from breast cancer metastasized to bone or ovary. Our organoids demonstrate a range of growth morphologies, consistent with those previously described. ER expression can be detected in a subset of our cultures as well as robust response to estradiol as indicated by the induction of GREB1 gene expression. We have further demonstrated that organoids are amenable to transient transfection of siRNA and lentiviral infection of reporter constructs which allows for RFP and luciferase-based detection of cells both in vitro and in vivo as well as expression of genes of interest. We additionally recognized that some of our organoid cultures can give rise to suspension cultures when maintained in organoid culture medium but without 3D matrix. This observation allows the opportunity for further phenotypic evaluation by increasing the number of assays amenable to these unique patient derived cultures. Single cell RNA sequencing (10X Genomics) of organoid cultures and paired tumor tissue confirms that organoid cultures faithfully maintain the heterogeneity of epithelial subpopulations found in the surgically resected tumors. Further, organoids show greater epithelial diversity and heterogeneity compared to single cell sequencing of breast cancer cell lines. We have further used sequencing data to identify targetable pathways in individual organoid cultures and demonstrate that drug sensitivity can be correlated with gene expression in these models. Collectively, these data indicate that breast cancer organoids represent a valuable model for preclinical breast cancer research.

Citation Format: Daniel D Brown, Kai Ding, Fangyuan Chen, Jian Chen, Brian Orr, Sarah Taylor, Kurt Weiss, Steffi Oesterreich, Peter C Lucas, Priscilla F McAuliffe, Jennifer M Atkinson, Adrian V Lee. Development of a breast cancer organoid resource faithfully representing epithelial heterogeneity and drug response [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS17-23.

Single-Cell Transcriptomic Heterogeneity in Invasive Ductal and Lobular Breast Cancer Cells

Invasive lobular breast carcinoma (ILC), one of the major breast cancer histologic subtypes, exhibits unique features compared with the well-studied ductal cancer subtype (IDC). The pathognomonic feature of ILC is loss of E-cadherin, mainly caused by inactivating mutations, but the contribution of this genetic alteration to ILC-specific molecular characteristics remains largely understudied. To profile these features transcriptionally, we conducted single-cell RNA sequencing on a panel of IDC and ILC cell lines, and an IDC cell line (T47D) with CRISPR-Cas9-mediated E-cadherin knockout (KO). Inspection of intracell line heterogeneity illustrated genetically and transcriptionally distinct subpopulations in multiple cell lines and highlighted rare populations of MCF7 cells highly expressing an apoptosis-related signature, positively correlated with a preadaptation signature to estrogen deprivation. Investigation of E-cadherin KO-induced alterations showed transcriptomic membranous systems remodeling, elevated resemblance to ILCs in regulon activation, and increased sensitivity to IFNγ-mediated growth inhibition via activation of IRF1. This study reveals single-cell transcriptional heterogeneity in breast cancer cell lines and provides a resource to identify drivers of cancer progression and drug resistance. SIGNIFICANCE: This study represents a key step towards understanding heterogeneity in cancer cell lines and the role of E-cadherin depletion in contributing to the molecular features of invasive lobular breast carcinoma.

Differential Regulation and Targeting of Estrogen Receptor α Turnover in Invasive Lobular Breast Carcinoma

Invasive lobular breast carcinoma (ILC) accounts for 10% to 15% of breast cancers diagnosed annually. Evidence suggests that some aspects of endocrine treatment response might differ between invasive ductal carcinoma (IDC) and ILC, and that patients with ILC have worse long-term survival. We analyzed The Cancer Genome Atlas dataset and observed lower levels of ESR1 mRNA (P = 0.002) and ERα protein (P = 0.038) in ER+ ILC (n = 137) compared to IDC (n = 554), and further confirmed the mRNA difference in a local UPMC cohort (ILC, n = 143; IDC, n = 877; P < 0.005). In both datasets, the correlation between ESR1 mRNA and ERα protein was weaker in ILC, suggesting differential post-transcriptional regulation of ERα. In vitro, 17β-estradiol (E2) decreased the rate of degradation and increased the half-life of ERα in ILC cell lines, whereas the opposite was observed in IDC cell lines. Further, E2 failed to induce robust ubiquitination of ERα in ILC cells. To determine the potential clinical relevance of these findings, we evaluated the effect of 2 selective estrogen receptor downregulators (SERDs), ICI 182,780 and AZD9496, on ERα turnover and cell growth. While ICI 182,780 and AZD9496 showed similar effects in IDC cells, in ILC cell lines, AZD9496 was not as effective as ICI 182,780 in decreasing ERα stability and E2-induced proliferation. Furthermore, AZD9496 exhibited partial agonist activity in growth assays in ILC cell lines. Our study provides evidence for a distinct ERα regulation by SERDs in ILC cell lines, and therefore it is important to include ILC models into preclinical and clinical testing of novel SERDs.

Abstract 4917: Estrogen receptor D538G mutation promotes cell migration via hyperactivation of Wnt signaling pathway

Background: Hotspot estrogen receptor-α (ERα/ESR1) mutations occur in 30-40% endocrine resistant ER+ breast cancer, with Y537S and D538G as the two most frequent hotspot mutations. A mostly unanswered question is and how these mutations facilitate metastatic processes.

Methods: Frequencies of different ESR1 hotspot mutations were compared within three publicly available cohorts. Y537S and D538G genome-edited MCF7 and T47D cell models were used for in vitro characterization. Wound scratching, spheroid collective migration, chemotaxis assays were applied to examine different metastatic properties. Tail vein injection in nude mice followed by human CK19 lung section immune staining was used to characterize in vivo metastasis. Canonical Wnt pathway activity was studied using top-flash reporter assays, immunoblotting, and overexpression of dominant negative TCF4. ChIP-seq and ATAC-seq were utilized to profile ER global binding patterns and chromatin accessibility in cell models, respectively. Porcupine inhibitor-LGK974 was used to evaluate the efficiency of Wnt-targeted therapy.

Results: D538G mutations were more frequent in ER+ metastatic lesions compared to Y537S among three metastatic breast cancer cohorts with unbiased SNV detection. In line with this, T47D-D538G ESR1 mutant cells showed strongly enhanced cell migration in vitro which was not observed in Y537S cells. We also observed increased lung micro-metastasis in vivo after tail vein injection of the D538G cells. Cell line transcriptomic analysis revealed uniquely hyperactivated Wnt pathway in D538G mutant cells, which was further confirmed in vitro by top-flash reporter and immunoblot. Suppression of canonical Wnt pathways blocked T47D-D538G specific cell migration. Combination treatment of fulvestrant and LGK974 synergistically inhibited D538G specific migration. Mechanistically, multiple Wnt regulator genes were found uniquely upregulated in D538G cells. Interestingly, none of these targets gained ER binding peaks at proximal regulatory regions, suggesting potential epigenetic regulation, which was confirmed in ATAC-seq results. Knockdown of FOXA1, a well-characterized pioneer factor, decreased canonical Wnt activity and abrogated the D538G-unique cell migration in short-term.

Conclusion: T47D-D538G cells showed uniquely enhanced cell migration via Wnt hyperactivation, potentially mediated via epigenetic remodeling. These findings suggest the further study of potential combinatorial targeting of Wnt and ER signaling in D538G ESR1 mutant tumors.

Citation Format: Zheqi Li, Kevin M. Levine, Spencer Arneson, Kristofer C. Berrett, Nolan M. Priedigkeit, Amir Bahreini, Jian Chen, Li Zhu, Jason S. Carroll, George C. Tseng, Peter C. Lucas, Jennifer M. Atkinson, Jason Gertz, Adrian V. Lee, Steffi Oesterreich. Estrogen receptor D538G mutation promotes cell migration via hyperactivation of Wnt signaling pathway [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4917.

Patient treatment and outcome after breast cancer orbital and periorbital metastases: a comprehensive case series including analysis of lobular versus ductal tumor histology

BACKGROUND

Breast cancer is the most common malignancy to spread to the orbit and periorbit, and the invasive lobular carcinoma (ILC) histologic subtype of breast cancer has been reported to form these ophthalmic metastases (OM) more frequently than invasive ductal carcinomas (IDC). We herein report our single academic institution experience with breast cancer OM with respect to anatomical presentation, histology (lobular vs. ductal), treatment, and survival.

METHODS

We employed the natural language processing platform, TIES (Text Information Extraction System), to search 2.3 million de-identified patient pathology and radiology records at our institution in order to identify patients with OM secondary to breast cancer. We then compared the resultant cohort, the "OM cohort," to two other representative metastatic breast cancer patient (MBC) databases from our institution. Histological analysis of selected patients was performed.

RESULTS

Our TIES search and manual refinement ultimately identified 28 patients who were diagnosed with breast cancer between 1995 and 2016 that subsequently developed OM. Median age at diagnosis was 54 (range 28-77) years of age. ER, PR, and HER2 status from the 28 patients with OM did not differ from other patients with MBC from our institution. The relative proportion of patients with ILC was significantly higher in the OM cohort (32.1%) than in other MBC patients in our institution (11.3%, p = 0.007). Median time to first OM in the OM cohort was 46.7 months, and OM were the second most frequent first metastases after bony metastases. After diagnosis of the first distant metastasis of any kind, median survival of patients with ILC (21.4 months) was significantly shorter than that of patients with IDC (55.3 months, p = 0.03). Nine patients developed bilateral OM. We observed a significant co-occurrence of OM and central nervous system metastases (p = 0.0053). The histological analysis revealed an interesting case in which the primary tumor was of a mixed ILC/IDC subtype, while only ILC was present in the OM.

CONCLUSIONS

OM from breast cancer are illustrative of the difference in metastatic behavior of ILC versus IDC and should be considered when treating patients with ILC, especially in those with complaints of visual acuity changes.

Abstract B58: Detection of ESR1 gene fusions in breast cancer cell-derived exosomal RNA

Background: Estrogen receptor-positive (ER+) breast cancer is often intractable due to endocrine therapy resistance. Although ER basepair hotspot mutations have been well characterized in ~20-30% of endocrine-resistant disease, accumulating evidence from our group and others suggests that other genetic alterations such as ER fusions (e.g., ESR1-DAB2) could also play a role. As an important component of liquid biopsies, exosomes have recently gained much attention in the field of clinical oncology. It is well established that some species of RNA, typically microRNA and mRNA, are packaged into these small membrane-enclosed structures, which could potentially serve as a noninvasive biomarker to constantly and comprehensively monitor tumor progression and tumor cell evolution. We tested whether ESR1 fusions could be detected in exosomal RNA (exoRNA) produced by breast cancer cell lines.

Methods: Multiple methods were used to characterize exosomes isolated from cell culture media: 1) Nanoparticle tracking analysis (NTA) confirmed concentration and size of exosomes, 2) immunoblotting identified protein markers that are enriched or lacking in exosomes, 3) transmission electron microscopy validated the size and shape of exosomes. During exoRNA extraction, DNA contamination was removed by DNase treatment. Fusion-specific regions in exoRNA were amplified by standard PCR.

Results: We used breast cancer cell lines stably infected with cDNA encoding ESR1 fusions ESR1-DAB2 and ESR1-SOX9. NTA shows that our isolated exosomes had a size ranging from 30-150 nm, with the peak at 80 nm. Immunoblotting showed TSG101 and CD81 as positive markers of our exosomes, while Grp94 was negative. By RT-PCR, we identified a fusion-specific region amplified for both ESR1-SOX9 and ESR1-LPP from exoRNA for the fusion cell lines.

Conclusions: Collectively, these data indicate that multiple ESR1 fusions are detectable in breast cancer cell line-derived exoRNA.

Citation Format: Tiantong Liu, Jagmohan Hooda, Nils Ludwig, Theresa Whiteside, Jennifer M. Atkinson, Steffi Oesterreich, Adrian Lee. Detection of ESR1 gene fusions in breast cancer cell-derived exosomal RNA [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B58.

IGF1R constitutive activation expands luminal progenitors and influences lineage differentiation during breast tumorigenesis

Breast tumors display tremendous heterogeneity in part due to varying molecular alterations, divergent cells of origin, and differentiation. Understanding where and how this heterogeneity develops is likely important for effective breast cancer eradication. Insulin-like growth factor (IGF) signaling is critical for normal mammary gland development and function, and has an established role in tumor development and resistance to therapy. Here we demonstrate that constitutive activation of the IGF1 receptor (IGF1R) influences lineage differentiation during mammary tumorigenesis. Transgenic IGF1R constitutive activation promotes tumors with mixed histologies, multiple cell lineages and an expanded bi-progenitor population. In these tumors, IGF1R expands the luminal-progenitor population while influencing myoepithelial differentiation. Mammary gland transplantation with IGF1R-infected mammary epithelial cells (MECs) resulted in hyperplastic, highly differentiated outgrowths and attenuated reconstitution. Restricting IGF1R constitutive activation to luminal versus myoepithelial lineage-sorted MECs resulted in ductal reconstitutions co-expressing high IGF1R levels in the opposite lineage of origin. Using in vitro models, IGF1R constitutively activated MCF10A cells showed increased mammosphere formation and CD44+/CD24-population, which was dependent upon Snail and NFκB signaling. These results suggest that IGF1R expands luminal progenitor populations while also stimulating myoepithelial cell differentiation. This ability to influence lineage differentiation may promote heterogeneous mammary tumors, and have implications for clinical treatment.

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.

Abstract P3-01-12: Breast cancer orbital and periorbital metastases can be bilateral, are associated with invasive lobular histology, and can co-occur with brain metastases

Breast cancer is responsible for most ophthalmic metastases (OM) to the orbit and periorbit. OM are associated with poor prognosis, as 95% of affected patients subsequently die of breast cancer. Previous studies have demonstrated an increased propensity for invasive lobular carcinoma (ILC) to spread to the eye compared to invasive ductal carcinoma (IDC). ILC is less common than IDC, and it can exhibit an unusual pattern of metastatic spread, including to sites such as the ovaries and GI tract. We herein report our single academic institution experience with OM from breast cancer with respect to anatomical presentation, histology (lobular vs. ductal), treatment and survival.

We used the natural language processing platform TIES (Text Information Extraction System) to identify OM caused by primary breast cancer in a database of over 2.3 million patients with electronically stored pathology and radiology reports at the University of Pittsburgh Medical Center. Search terms in TIES were translated into ontologies consisting of the NCI Metathesaurus’ synonyms and abbreviations. The search was thus not reliant on specific words. We then reviewed clinical notes, pathology reports, radiology reports, therapeutic regimens, and outcome data for the cases identified through TIES. Data from the patients identified through TIES was also compared to a large institutional database featuring 1,366 patients with metastatic breast cancer (MBC). Histological slides from 3 patients were analyzed.

We identified 28 patients diagnosed with primary breast cancer between 1995 and 2016 and subsequent OM. Median age at diagnosis was 54, with a range of 28 to 77. ER, PR, and HER2neu status from the 28 patients with OM did not differ from other patients with MBC in our institutional database. The relative proportion of patients with ILC was significantly higher in the patient cohort with OM (32.1%) than in the metastatic institutional database (11.3%, p=0.007). Median OS in the OM cohort was 78.4 months; distant metastasis free survival (DMFS) was 34.2 months. These survival times did not differ significantly from those patients in the large institutional metastatic database. DMFS tended to be longer (35.05 months) for patients with ILC compared to IDC (23.34 months), supporting a tendency for late relapse. Additionally, after a diagnosis of first metastasis, median survival of patients with ILC (21.4 months) was significantly shorter than that of patients with IDC (55.2 months) (p=0.03). OM were the second most frequent site of first metastasis in the OM cohort after bony metastases. Median time to first OM was 46.7 months. Of the 9 patients who developed bilateral OM, 4 had ILC, 1 had IDC, 2 had a mixed ILC/IDC, and 2 had an unknown histology. We observed a significant co-occurrence of OM and central nervous system (CNS) metastases (p=0.018). Of 14 patients that developed OM and CNS metastases, only 3 were diagnosed with ILC compared to 9 patients diagnosed with IDC. 57.1% of the patients with OM received radiation therapy to the eye, and 25 patients received at least one line of systemic therapy. The histological analysis revealed an interesting case in which the primary tumor was of a mixed ILC/IDC subtype, while only ILC was present in the OM.

To our knowledge, our report of 28 patients is the largest analysis of the histological subtype of breast cancer OM. Through our focus on anatomical presentation, histological subtype, treatment, and survival we provide a broad overview of this rare complication of breast cancer. Our data suggests that OM from breast cancer can often impact both eyes, can be associated with CNS metastases, and are more frequent in patients with ILC than IDC.

Citation Format: Martin Blohmer, Li Zhu, Jennifer M Atkinson, Sushil Beriwal, Joshua L. Rodriguez-Lopez, Margaret Rosenzweig, George C Tseng, Peter C Lucas, Adrian V Lee, Steffi Oesterreich, Rachel C Jankowitz. Breast cancer orbital and periorbital metastases can be bilateral, are associated with invasive lobular histology, and can co-occur with brain metastases [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-01-12.

Abstract P1-21-03: Unique estrogen receptor alpha turnover, regulation and targeting in invasive lobular breast carcinoma

Invasive lobular breast carcinoma (ILC) accounts for 10-15% of breast cancers diagnosed annually. Evidence suggests that endocrine treatment response might differ between invasive ductal carcinoma (IDC) and ILC, and that patients with ILC have worse long-term survival. ILCs are more likely to be estrogen receptor alpha (ER/ERα) positive (90-95%) compared to IDCs (60-70%). We investigated whether there are differences in ER protein steady state levels and/or turn-over rates in ILC that might explain differences in response to endocrine therapy. Analysis of the TCGA dataset revealed lower levels of ESR1 mRNA (P = 0.002) and ERα protein (P = 0.038) in ER+ ILC (n = 137) compared to ER+ IDC (n = 554). Supporting this observation, analysis of tumors from patients treated at UPMC Magee-Women’s Hospital (ILC, n = 143; IDC, n = 877), showed lower ESR1 mRNA (P &lt; 0.005) in ILC and similar ERα protein levels in both subtypes. In both datasets, the correlation between ESR1 mRNA and ERα protein was significantly weaker in ILC suggesting differential post-transcriptional regulation of ER. This was confirmed in in vitro studies showing 17β-estradiol (E2) decreased the rate of degradation and increased half-life of ERα in MDA-MB-134-VI and SUM44PE ILC cell lines, whereas the opposite was observed in IDC cell lines. Further analysis of MDA-MB-134-VI cells revealed that E2 downregulated ubiquitination pathway genes and failed to induce ubiquitination of ERα. To determine potential clinical relevance of our findings, we evaluated the effect of two selective estrogen receptor down-regulators (SERDs) on ERα turnover and E2-induced proliferation of IDC and ILC cell lines. While fulvestrant and AZD9496, a novel orally bioavailable SERD, showed similar effects in IDC cell lines, AZD9496 was less effective than fulvestrant in decreasing ERα protein stability and E2-induced proliferation in ILC cells. Furthermore, AZD9496 exhibited partial agonist activity in growth and gene expression assays in the absence of ligand. Collectively, our data provide evidence for distinct ligand-induced ERα turnover in ILC cell lines. In addition, the novel SERD AZD9496 displays partial agonist activity in ILC cells, and further studies should address whether these observations are causally linked. These results provide a strong rationale for inclusion of ILC subgroups into preclinical and clinical testing of SERDs.

Citation Format: Jennifer M Atkinson, Sreeja Sreekumar, Kevin M Levine, Matthew J Sikora, Jian Chen, David J Dabbs, Carolin Meier, Ahmed Basudan, Nilgun Tasdemir, David Boone, Priscilla F McAuliffe, Rachel C Jankowitz, Adrian V Lee, Steffi Oesterreich. Unique estrogen receptor alpha turnover, regulation and targeting in invasive lobular breast carcinoma [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-21-03.

Abstract P2-21-02: Implementation of a breast cancer post-mortem tissue donation program

BACKGROUND: Histologic and molecular differences between primary breast cancer and their subsequent metastases are well-established. Characterization of this heterogeneity may provide important information for both diagnosis and prognosis. Tissue donation via autopsy can aid in characterizing the microenvironment and understanding organ tropism. We describe the implementation, results, and challenges of a cohesive program of post-mortem tissue procurement in patients with breast cancer.

METHODS: Prior to formalization of the program, three autopsies were performed without specific operating procedures. In 2016, formal input from patients, their families, clinicians, and pathology technicians helped to operationalize a formal tissue donation program. Ten autopsies have been performed to date. Demographic and clinical data were collected for these patients through retrospective chart reviews. When available, primary tumor tissue and any prior metastasis which were biopsied or surgically resected were acquired from clinical archives at our institution, or requested from outside facilities for future analyses.

RESULTS: Between October 2011 and April 2019, autopsies were performed on 1 male and 9 female patients. Time from primary to metastatic disease was an average of 4 years. The median age at the time of death was 56 years (range 37-73). The average time from diagnosis of metastatic disease to consent to autopsy was 30 months. Although the majority of patients died outside the hospital (70%), the mean time between death and the start of autopsy was 4.7 hours. Samples of metastatic tissue were collected in all patients postmortem. There was an average of 16 samples collected from various sites that included both normal and metastatic tissue. The most common sites were the liver (80%), lung (70%), and lymph nodes (70%). Immunohistochemical analysis of metastatic tumors revealed intrapatient heterogeneity in ER, HER2 and Ki67 staining.

TABLE 1: CLINICAL COURSE OF PATIENTSN=10 patientsPatients (%)Age at Diagnosis, years (median)46.7 (24.9-57.8)GenderFemale9 (90)Male1 (10)AJCC stage at initial presentationStage 13 (30)Stage 23 (30)Stage 33 (30)Stage 41 (10)Molecular SubtypesHR+/HER 2-6 (60)HR+/HER 2+2 (20)HR-/HER 2-2 (20)HR-/HER 2+0 (0)Time from initial diagnosis to metastatic disease, years (median)4.3 (0-12.8)Tissue of Metastases Obtained While AliveYes4 (40)No6 (60)Median age at time of death, years56.5 (37-73)Total Survival (dx to death), years (median)7.7Metastatic Survival (mets to death), years (median)3.3

TABLE 2: POST MORTEM TISSUE DONATION PROGRAMTime from Metastatic Diagnosis to Consent for Autopsy, months (median)30.3Time from Consent for Autopsy to Death, months (median)10.25Location of DeathHome5 (50)Hospital3 (30)Inpatient Hospice Facility2 (20)Time from death to starting autopsy, hours (median)4.68Time to complete autopsy, hours (median) N=72.82Number of Samples Collected During Autopsy (median)16.2 (3-27)Sites for Metastatic Tissue Procurement Postmortem8 (80)Liver7 (70)Lung7 (70)Lymph Nodes4 (40)Brain4 (40)Ascitic Fluid3 (30)Bone2 (20)Adrenal2 (20)Pericardium2 (20)Pleural Effusion1 (10)Chest Wall1 (10)Gall Bladder1 (10)

CONCLUSION: Post-mortem tissue donation programs allow procurement of tissue that would otherwise be inaccessible in the living patient. Histological examination and immunohistochemical assessment of key biomarkers will be used to further characterize the tissue collected ante-mortem and post-mortem. This data combined with the clinical history and longitudinal specimens will help us better understand how intra- and inter-tumor heterogeneity play a role in the clinical course of breast cancer. Also, as we establish the program, we will identify barriers that need to be addressed in order to optimize the process.

Citation Format: Tara Hyder, Lori Miller, Jennifer M Atkinson, Zoe Wecht, Ashuvinee Elangovan, Kai Ding, Nolan Priedigkeit, Zheqi Li, Tiantong Liu, Laura Savariau, Fangyuan Chen, Oscar Lopez, Dayne Ashman, Daniel Geisler, Jacob A Smith, Rachel Jankowitz, Priscilla F McAuliffe, Shannon Puhalla, Humberto E Trejo Bittar, Jeffrey S Nine, Peter C Lucas, Adam Brufsky, Steffi Oesterreich, Adrian V Lee, Margaret Rosenzweig. Implementation of a breast cancer post-mortem tissue donation program [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-21-02.

Abstract P2-16-26: Mixed invasive ductal and lobular carcinoma (IDC/L) behaves similarly to invasive lobular carcinoma (ILC) with regard to neoadjuvant chemotherapy response and metastatic dissemination

Mixed invasive ductal and lobular carcinoma (Mixed IDC/L) is a rare subtype (3-5%) of invasive breast cancer with elusive pathophysiology. This entity is characterized by a mixed population of both ductal and lobular components within an individual tumor. Few studies have been published to date which compare Mixed IDC/L to invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) from a histopathologic perspective. Available literature on this topic is sparse and has been conflicting with regards to outcomes, and no studies to date describe the response of Mixed IDC/L to neoadjuvant chemotherapy. Patients with ILC have been shown to have lower response rates to neoadjuvant chemotherapy as compared to patients with IDC, which in turn leads to lower rates of successful breast conserving surgery and higher rates of re-excision due to positive margins. We aimed to compare Mixed IDC/L to pure ILC with regards to response to neoadjuvant chemotherapy and the need for repeat surgical intervention.

We identified 26 patients with Mixed IDC/L and 113 patients with ILC who received neoadjuvant chemotherapy at our institution between 1990 – 2017. At baseline, the groups had a similar median age, as well as ER H-score, PR H-score, and Ki-67 index. There was no statistical difference in rates of pathologic complete response (pCR) or percent tumor volume reduction post therapy between the two groups. Similarly, the percent of patients that required re-excision was not statistically different. Interestingly, the metastatic pattern was similar between the groups and included sites of dissemination such as the peritoneal cavity and omentum, which are not common sites of metastasis for IDC.

These findings suggest that Mixed IDC/L tumors behave similarly to ILC with regard to their response to neoadjuvant chemotherapy and patterns of metastatic spread. These findings support a prominent role for the lobular component in this mixed subtype in driving biology, including response to neoadjuvant therapy and metastatic dissemination. Ongoing efforts are directed towards incorporating data from the IDC cohort, as well as evaluation of changes in histology, ER/PR H-scores, and Ki-67 levels as a result of therapy. These data may imply that Mixed IDC/L tumors may behave clinically more like ILC than IDC, but larger studies are needed to study this rare breast cancer subtype.

Citation Format: Azadeh Nasrazadani, Jennifer M Atkinson, Yujia Li, Priscilla F McAuliffe, Rachel C Jankowitz, Leisha A Emens, George C Tseng, Adrian V Lee, Norman Wolmark, Steffi Oesterreich, Peter C Lucas. Mixed invasive ductal and lobular carcinoma (IDC/L) behaves similarly to invasive lobular carcinoma (ILC) with regard to neoadjuvant chemotherapy response and metastatic dissemination [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-16-26.

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.

Time-resolved FRET and NMR analyses reveal selective binding of peptides containing the LC3-interacting region to ATG8 family proteins

Selective autophagy sequesters cytoplasmic cargo for lysosomal degradation via the binding of autophagy receptors to Atg8 (autophagy-related 8) family proteins on the autophagic membrane. The sole yeast Atg8 gene has six mAtg8 (mammalian Atg8) homologs, including the MAP1LC3 (microtubule-associated protein-1 light chain 3) family and the GABA receptor-associated proteins. Selective autophagy receptors interact with two conserved hydrophobic pockets (termed the W-site and L-site) of mATG8 proteins through a linear motif called the LC3-interacting region (LIR) with the general composition (W/F/Y)XX(I/L/V). To address a lack in our knowledge regarding LIR peptide specificity toward each mATG8 homolog, here we used competitive time-resolved FRET to sensitively and quantitatively characterize the interactions between LIRs and mAtg8. We report that 14 representative LIR-containing peptides display differential binding affinities toward the mAtg8 proteins and identified the LIR domain peptide of TP53INP1 as exhibiting high affinity for all six mATG8 proteins. Using peptide truncation studies, we found that both N- and C-terminal acidic residues, as well as the C-terminal Cys residue of the TP53INP1 LIR peptide, are required for its high-affinity binding to LC3A and LC3B, whereas binding to the GABARAP subfamily proteins was facilitated by residues either N-terminal or C-terminal to the core motif. Finally, we used NMR chemical shift perturbation analysis to gain molecular insights into these findings. Collectively, our results may aid in the development of molecules that selectively disrupt specific mATG8-LIR interactions to dissect the biological roles of the six mATG8 homologs for potential therapeutic applications.

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 P3-06-03: 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.

Conductance Spectroscopy of Exfoliated Thin Flakes of Nb xBi2Se3

We study unconventional superconductivity in exfoliated single crystals of a promising three-dimensional (3D) topological superconductor candidate, Nb-doped Bi₂Se₃ through differential conductance spectroscopy and magneto-transport. The strong anisotropy of the critical field along the out-of-plane direction suggests that the thin exfoliated flakes are in the quasi-2D limit. Normal metal-superconductor (NS) contacts with either high or low transparencies made by depositing gold leads onto Nb-doped Bi₂Se₃ flakes both show significant enhancement in zero bias conductance and coherence dips at the superconducting energy gap. Such behavior is inconsistent with conventional Blonder-Tinkham-Klapwijk theory. Instead, we discuss how our results are consistent with p-wave pairing symmetry, supporting the possibility of topological superconductivity in Nb-doped Bi₂Se₃. Finally, we observe signatures of multiple superconducting energy gaps, which could originate from multiple Fermi surfaces reported earlier in bulk crystals.

An autophagy assay reveals the ESCRT-III component CHMP2A as a regulator of phagophore closure

The mechanism of phagophore closure remains unclear due to technical limitations in distinguishing unclosed and closed autophagosomal membranes. Here, we report the HaloTag-LC3 autophagosome completion assay that specifically detects phagophores, nascent autophagosomes, and mature autophagic structures. Using this assay, we identify the endosomal sorting complexes required for transport (ESCRT)-III component CHMP2A as a critical regulator of phagophore closure. During autophagy, CHMP2A translocates to the phagophore and regulates the separation of the inner and outer autophagosomal membranes to form double-membrane autophagosomes. Consistently, inhibition of the AAA-ATPase VPS4 activity impairs autophagosome completion. The ESCRT-mediated membrane abscission appears to be a critical step in forming functional autolysosomes by preventing mislocalization of lysosome-associated membrane glycoprotein 1 to the inner autophagosomal membrane. Collectively, our work reveals a function for the ESCRT machinery in the final step of autophagosome formation and provides a useful tool for quantitative analysis of autophagosome biogenesis and maturation.

Loss of E-cadherin Enhances IGF1-IGF1R Pathway Activation and Sensitizes Breast Cancers to Anti-IGF1R/InsR Inhibitors

Purpose: Insulin-like growth factor 1 (IGF1) signaling regulates breast cancer initiation and progression and associated cancer phenotypes. We previously identified E-cadherin (CDH1) as a repressor of IGF1 signaling and in this study examined how loss of E-cadherin affects IGF1R signaling and response to anti-IGF1R/insulin receptor (InsR) therapies in breast cancer.Experimental Design: Breast cancer cell lines were used to assess how altered E-cadherin levels regulate IGF1R signaling and response to two anti-IGF1R/InsR therapies. In situ proximity ligation assay (PLA) was used to define interaction between IGF1R and E-cadherin. TCGA RNA-seq and RPPA data were used to compare IGF1R/InsR activation in estrogen receptor-positive (ER+) invasive lobular carcinoma (ILC) and invasive ductal carcinoma (IDC) tumors. ER+ ILC cell lines and xenograft tumor explant cultures were used to evaluate efficacy to IGF1R pathway inhibition in combination with endocrine therapy.Results: Diminished functional E-cadherin increased both activation of IGF1R signaling and efficacy to anti-IGF1R/InsR therapies. PLA demonstrated a direct endogenous interaction between IGF1R and E-cadherin at points of cell-cell contact. Increased expression of IGF1 ligand and levels of IGF1R/InsR phosphorylation were observed in E-cadherin-deficient ER+ ILC compared with IDC tumors. IGF1R pathway inhibitors were effective in inhibiting growth in ER+ ILC cell lines and synergized with endocrine therapy and similarly IGF1R/InsR inhibition reduced proliferation in ILC tumor explant culture.Conclusions: We provide evidence that loss of E-cadherin hyperactivates the IGF1R pathway and increases sensitivity to IGF1R/InsR targeted therapy, thus identifying the IGF1R pathway as a potential novel target in E-cadherin-deficient breast cancers. Clin Cancer Res; 24(20); 5165-77. ©2018 AACR.

Endophilin B2 facilitates endosome maturation in response to growth factor stimulation, autophagy induction, and influenza A virus infection

Endocytosis, and the subsequent trafficking of endosomes, requires dynamic physical alterations in membrane shape that are mediated in part by endophilin proteins. The endophilin B family of proteins contains an N-terminal Bin/amphiphysin/Rvs (N-BAR) domain that induces membrane curvature to regulate intracellular membrane dynamics. Whereas endophilin B1 (SH3GLB1/Bif-1) is known to be involved in a number of cellular processes, including apoptosis, autophagy, and endocytosis, the cellular function of endophilin B2 (SH3GLB2) is not well understood. In this study, we used genetic approaches that revealed that endophilin B2 is not required for embryonic development in vivo but that endophilin B2 deficiency impairs endosomal trafficking in vitro, as evidenced by suppressed endosome acidification, EGFR degradation, autophagic flux, and influenza A viral RNA nuclear entry and replication. Mechanistically, although the loss of endophilin B2 did not affect endocytic internalization and lysosomal function, endophilin B2 appeared to regulate the trafficking of endocytic vesicles and autophagosomes to late endosomes or lysosomes. Moreover, we also found that despite having an intracellular localization and tissue distribution similar to endophilin B1, endophilin B2 is dispensable for mitochondrial apoptosis. Taken together, our findings suggest that endophilin B2 positively regulates the endocytic pathway in response to growth factor signaling, autophagy induction, and viral entry.