Basal-epithelial subpopulations underlie and predict chemotherapy resistance in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype, characterized by extensive intratumoral heterogeneity, high metastasis, and chemoresistance, leading to poor clinical outcomes. Despite progress, the mechanistic basis of these aggressive behaviors remains poorly understood. Using single-cell and spatial transcriptome analysis, here we discovered basal epithelial subpopulations located within the stroma that exhibit chemoresistance characteristics. The subpopulations are defined by distinct signature genes that show a frequent gain in copy number and exhibit an activated epithelial-to-mesenchymal transition program. A subset of these genes can accurately predict chemotherapy response and are associated with poor prognosis. Interestingly, among these genes, elevated ITGB1 participates in enhancing intercellular signaling while ACTN1 confers a survival advantage to foster chemoresistance. Furthermore, by subjecting the transcriptional signatures to drug repurposing analysis, we find that chemoresistant tumors may benefit from distinct inhibitors in treatment-naive versus post-NAC patients. These findings shed light on the mechanistic basis of chemoresistance while providing the best-in-class biomarker to predict chemotherapy response and alternate therapeutic avenues for improved management of TNBC patients resistant to chemotherapy.

The Role of Nodes and Nodal Assessment in Diagnosis, Treatment and Prediction in ER+, Node-Positive Breast Cancer

The majority of breast cancers are oestrogen receptor-positive (ER+). In ER+ cancers, oestrogen acts as a disease driver, so these tumours are likely to be susceptible to endocrine therapy (ET). ET works by blocking the hormone's synthesis or effect. A significant number of patients diagnosed with breast cancer will have the spread of tumour cells into regional lymph nodes either at the time of diagnosis, or as a recurrence some years later. Patients with node-positive disease have a poorer prognosis and can respond less well to ET. The nodal metastases may be genomically similar or, as is becoming more evident, may differ from the primary tumour. However, nodal metastatic disease is often not assessed, and treatment decisions are almost always based on biomarkers evaluated in the primary tumour. This review will summarise the evidence in the field on ER+, node-positive breast cancer, including diagnosis, treatment, prognosis and predictive tools.

Abstract PD10-09: PD10-09 Multiomics analysis of matched ER+ primary and recurrent breast cancers on or after adjuvant endocrine therapy

Background: 80% of all breast cancers (BCs) are ER-positive (ER+). Not all respond to adjuvant endocrine therapy (aET) and a significant number develop endocrine resistance and recur. The basis for primary and acquired endocrine resistance is poorly understood. A multiomics analysis of primary ER+ BCs matched with recurrences on or after completion of aET has been performed. Patients: A unique cohort of 520 women with matched primary and recurrent ER+, HER2-negative (HER2-) BC is being analysed. In the first subset of 75, all had surgery to clear margins, followed by aET. The endocrine therapy given was tamoxifen (66%), aromatase inhibitors (AI) (28%: 17% letrozole, 6% anastrozole, 2% exemestane, and 3% a succession of 2 different AIs), or a combination of tamoxifen and an AI (6%). aET duration was 5 years, unless the patient stopped treatment or developed a recurrence sooner. 16/75 patients (21%) had positive lymph nodes. All patients developed recurrences: local in 59/75, concurrent local and nodal in 13/75 and lymph node-only in 3/75. Median time to recurrence was 4.1 years (range: 0.7-29 years). 62% of patients were on aET at the time of recurrence. All patients have long-term follow-up. Methods: DNA and RNA were extracted from matched primary and recurrence BC tissue samples. Targeted DNA-exome and whole-genome expression analyses were performed. A custom targeted DNA panel was used to study genes implicated in endocrine therapy resistance (ETR): this included 73 different targets, selected based on our previous full-exome sequencing of sequential ET recurrences and those implicated in the literature and in curated somatic and cancer mutation databases. Somatic mutations and copy number alterations (CNA) were determined. Differential gene expression analysis was performed using two-class unpaired Significance Analysis of Microarrays (SAM). Validation of pathways implicated in ETR using NanoString GeoMx protein analysis is ongoing. Results: Targeted DNA-exome profiling identified 1 or 2 potential driver mutations in all but a few primary samples. Multiple aberrations and a highly diverse mutational landscape were observed in all the recurrences. Matched breast and lymph node samples from synchronous recurrences had very similar somatic profiles. Changes significantly enriched in recurrent samples included somatic aberrations in well-established drivers such as MAP3K1, PIK3CA, TP53 and CDH1, as well as ESR1. Aberrations were also common in PTEN and in ER-associated factors FOXA1 and GATA3. Transcriptomic analysis revealed a number of pathways implicated in resistance, including ER, HER2, GATA3, AKT, RAS and p63 signalling. A panel-based, targeted DNA sequencing approach for mutational profiling allowed capture of relevant mutational profiles linked to ETR in a cost-effective manner compared with traditional whole-exome sequencing. Ongoing analysis has linked mutational profiles to specific endocrine agents and has allowed us to demonstrate significant differences between recurrences on aET compared with those after completion of aET. Multiomics profiling of the remaining samples in the cohort is underway. Discussion: This multiomics study provides the largest cohort to-date of matched early and recurrent ER+/HER2- BCs. It has shed new light on how different adjuvant endocrine agents can affect primary drivers and lead to complex somatic and transcriptomic changes in recurrent disease. This work confirms that the mechanisms of endocrine resistance are diverse and has already identified mechanisms underlying ETR and clinically meaningful biomarkers of ETR, including potentially actionable mutations and targets.

Citation Format: Carlos Martinez-Perez, Charlene Kay, James Meehan, J Michael Dixon, Arran K Turnbull. PD10-09 Multiomics analysis of matched ER+ primary and recurrent breast cancers on or after adjuvant endocrine therapy [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 PD10-09.

Neoadjuvant endocrine therapy in postmenopausal women with HR+/HER2- breast cancer

INTRODUCTION

While endocrine therapy is the standard-of-care adjuvant treatment for hormone receptor-positive (HR+) breast cancers, there is also extensive evidence for the role of pre-operative (or neoadjuvant) endocrine therapy (NET) in HR+ postmenopausal women.

AREAS COVERED

We conducted a thorough review of the published literature, to summarize the evidence to date, including studies of how NET compares to neoadjuvant chemotherapy, which NET agents are preferable, and the optimal duration of NET. We describe the importance of on-treatment assessment of response, the different predictors available (including Ki67, PEPI score, and molecular signatures) and the research opportunities the pre-operative setting offers. We also summarize recent combination trials and discuss how the COVID-19 pandemic led to increases in NET use for safe management of cases with deferred surgery and adjuvant treatments.

EXPERT OPINION

NET represents a safe and effective tool for the management of postmenopausal women with HR+/HER2- breast cancer, enabling disease downstaging and a wider range of surgical options. Aromatase inhibitors are the preferred NET, with evidence suggesting that longer regimens might yield optimal results. However, NET remains currently underutilised in many territories and institutions. Further validation of predictors for treatment response and benefit is needed to help standardise and fully exploit the potential of NET in the clinic.

Mondor's disease of the breast: A cutaneous thromboembolic manifestation of Covid-19?

BACKGROUND

Mondor's disease is a rare disorder characterised by thrombosis of superficial veins within the subcutaneous tissue of the breast and other organs. While factors such as trauma, infection, physical exertion, breast cancer and breast surgery have been implicated, in the majority no cause is identified.

PATIENTS

Twenty patients presented with a clinical diagnosis of Mondor's disease to the Edinburgh Breast Services in 2020. We present the etiopathogenic data as well as clinical and imaging diagnostic findings.

RESULTS

During 2020, the annual incidence of Mondor's disease, in the UK's largest breast unit, increased five-fold compared to data from the previous year. This variation in the frequency of cases corresponded to trends in the frequency of Covid-19 infection during the pandemic. None of the patients had diagnosed COVID and few had any known etiopathogenic causes for their Mondor's.

CONCLUSION

Several recent studies have provided evidence for links between Covid-19 and thromboembolic events. Isolated reports have proposed a link between Covid-19 and Mondor's disease of the penis. Here we present data on a large series of Mondor's disease of the breast supporting a link between breast Mondor's and Covid-19.

Characterisation of the Stromal Microenvironment in Lobular Breast Cancer

Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer, and it exhibits a number of clinico-pathological characteristics distinct from the more common invasive ductal carcinoma (IDC). We set out to identify alterations in the tumor microenvironment (TME) of ILC. We used laser-capture microdissection to separate tumor epithelium from stroma in 23 ER + ILC primary tumors. Gene expression analysis identified 45 genes involved in regulation of the extracellular matrix (ECM) that were enriched in the non-immune stroma of ILC, but not in non-immune stroma from ER+ IDC or normal breast. Of these, 10 were expressed in cancer-associated fibroblasts (CAFs) and were increased in ILC compared to IDC in bulk gene expression datasets, with PAPPA and TIMP2 being associated with better survival in ILC but not IDC. PAPPA, a gene involved in IGF-1 signaling, was the most enriched in the stroma compared to the tumor epithelial compartment in ILC. Analysis of PAPPA- and IGF1-associated genes identified a paracrine signaling pathway, and active PAPP-A was shown to be secreted from primary CAFs. This is the first study to demonstrate molecular differences in the TME between ILC and IDC identifying differences in matrix organization and growth factor signaling pathways.

The IL6-like Cytokine Family: Role and Biomarker Potential in Breast Cancer

IL6-like cytokines are a family of regulators with a complex, pleiotropic role in both the healthy organism, where they regulate immunity and homeostasis, and in different diseases, including cancer. Here we summarise how these cytokines exert their effect through the shared signal transducer IL6ST (gp130) and we review the extensive evidence on the role that different members of this family play in breast cancer. Additionally, we discuss how the different cytokines, their related receptors and downstream effectors, as well as specific polymorphisms in these molecules, can serve as predictive or prognostic biomarkers with the potential for clinical application in breast cancer. Lastly, we also discuss how our increasing understanding of this complex signalling axis presents promising opportunities for the development or repurposing of therapeutic strategies against cancer and, specifically, breast neoplasms.

Tissue- and Liquid-Based Biomarkers in Prostate Cancer Precision Medicine

Worldwide, prostate cancer (PC) is the second-most-frequently diagnosed male cancer and the fifth-most-common cause of all cancer-related deaths. Suspicion of PC in a patient is largely based upon clinical signs and the use of prostate-specific antigen (PSA) levels. Although PSA levels have been criticised for a lack of specificity, leading to PC over-diagnosis, it is still the most commonly used biomarker in PC management. Unfortunately, PC is extremely heterogeneous, and it can be difficult to stratify patients whose tumours are unlikely to progress from those that are aggressive and require treatment intensification. Although PC-specific biomarker research has previously focused on disease diagnosis, there is an unmet clinical need for novel prognostic, predictive and treatment response biomarkers that can be used to provide a precision medicine approach to PC management. In particular, the identification of biomarkers at the time of screening/diagnosis that can provide an indication of disease aggressiveness is perhaps the greatest current unmet clinical need in PC management. Largely through advances in genomic and proteomic techniques, exciting pre-clinical and clinical research is continuing to identify potential tissue, blood and urine-based PC-specific biomarkers that may in the future supplement or replace current standard practices. In this review, we describe how PC-specific biomarker research is progressing, including the evolution of PSA-based tests and those novel assays that have gained clinical approval. We also describe alternative diagnostic biomarkers to PSA, in addition to biomarkers that can predict PC aggressiveness and biomarkers that can predict response to certain therapies. We believe that novel biomarker research has the potential to make significant improvements to the clinical management of this disease in the near future.

The Signal Transducer IL6ST (gp130) as a Predictive and Prognostic Biomarker in Breast Cancer

Novel biomarkers are needed to continue to improve breast cancer clinical management and outcome. IL6-like cytokines, whose pleiotropic functions include roles in many hallmarks of malignancy, rely on the signal transducer IL6ST (gp130) for all their signalling. To date, 10 separate independent studies based on the analysis of clinical breast cancer samples have identified IL6ST as a predictor. Consistent findings suggest that IL6ST is a positive prognostic factor and is associated with ER status. Interestingly, these studies include 4 multigene signatures (EndoPredict, EER4, IRSN-23 and 42GC) that incorporate IL6ST to predict risk of recurrence or outcome from endocrine or chemotherapy. Here we review the existing evidence on the promising predictive and prognostic value of IL6ST. We also discuss how this potential could be further translated into clinical practice beyond the EndoPredict tool, which is already available in the clinic. The most promising route to further exploit IL6ST's promising predicting power will likely be through additional hybrid multifactor signatures that allow for more robust stratification of ER+ breast tumours into discrete groups with distinct outcomes, thus enabling greater refinement of the treatment-selection process.

Current trends in the treatment of HR+/HER2+ breast cancer

Treatment for HR+/HER2+ patients has been debated, as some tumors within this luminal HER2+ subtype behave like luminal A cancers, whereas others behave like non-luminal HER2+ breast cancers. Recent research and clinical trials have revealed that a combination of hormone and targeted anti-HER2 approaches without chemotherapy provides long-term disease control for at least some HR+/HER2+ patients. Novel anti-HER2 therapies, including neratinib and trastuzumab emtansine, and new agents that are effective in HR+ cancers, including the next generation of oral selective estrogen receptor downregulators/degraders and CDK4/6 inhibitors such as palbociclib, are now being evaluated in combination. This review discusses current trials and results from previous studies that will provide the basis for current recommendations on how to treat newly diagnosed patients with HR+/HER2+ disease.

The Importance of the Tumor Microenvironment and Hypoxia in Delivering a Precision Medicine Approach to Veterinary Oncology

Treating individual patients on the basis of specific factors, such as biomarkers, molecular signatures, phenotypes, environment, and lifestyle is what differentiates the precision medicine initiative from standard treatment regimens. Although precision medicine can be applied to almost any branch of medicine, it is perhaps most easily applied to the field of oncology. Cancer is a heterogeneous disease, meaning that even though patients may be histologically diagnosed with the same cancer type, their tumors may have different molecular characteristics, genetic mutations or tumor microenvironments that can influence prognosis or treatment response. In this review, we describe what methods are currently available to clinicians that allow them to monitor key tumor microenvironmental parameters in a way that could be used to achieve precision medicine for cancer patients. We further describe exciting novel research involving the use of implantable medical devices for precision medicine, including those developed for mapping tumor microenvironment parameters (e.g., O₂, pH, and cancer biomarkers), delivering local drug treatments, assessing treatment responses, and monitoring for recurrence and metastasis. Although these research studies have predominantly focused on and were tailored to humans, the results and concepts are equally applicable to veterinary patients. While veterinary clinical studies that have adopted a precision medicine approach are still in their infancy, there have been some exciting success stories. These have included the development of a receptor tyrosine kinase inhibitor for canine mast cell tumors and the production of a PCR assay to monitor the chemotherapeutic response of canine high-grade B-cell lymphomas. Although precision medicine is an exciting area of research, it currently has failed to gain significant translation into human and veterinary healthcare practices. In order to begin to address this issue, there is increasing awareness that cross-disciplinary approaches involving human and veterinary clinicians, engineers and chemists may be needed to help advance precision medicine toward its full integration into human and veterinary clinical practices.

Comparative Analysis of the Development of Acquired Radioresistance in Canine and Human Mammary Cancer Cell Lines

Research using in vitro canine mammary cancer cell lines and naturally-occurring canine mammary tumors are not only fundamental models used to advance the understanding of cancer in veterinary patients, but are also regarded as excellent translational models of human breast cancer. Human breast cancer is commonly treated with radiotherapy; however, tumor response depends on both innate radiosensitivity and on tumor repopulation by cells that develop radioresistance. Comparative canine and human studies investigating the mechanisms of radioresistance may lead to novel cancer treatments that benefit both species. In this study, we developed a canine mammary cancer (REM-134) radioresistant (RR) cell line and investigated the cellular mechanisms related to the development of acquired radioresistance. We performed a comparative analysis of this resistant model with our previously developed human breast cancer radioresistant cell lines (MCF-7 RR, ZR-751 RR, and MDA-MB-231 RR), characterizing inherent differences through genetic, molecular, and cell biology approaches. RR cells demonstrated enhanced invasion/migration capabilities, with phenotypic evidence suggestive of epithelial-to-mesenchymal transition. Similarities were identified between the REM-134 RR, MCF-7 RR, and ZR-751 RR cell lines in relation to the pattern of expression of both epithelial and mesenchymal genes, in addition to WNT, PI3K, and MAPK pathway activation. Following the development of radioresistance, transcriptomic data indicated that parental MCF-7 and ZR-751 cell lines changed from a luminal A classification to basal/HER2-overexpressing (MCF-7 RR) and normal-like/HER2-overexpressing (ZR-751 RR). These radioresistant subtypes were similar to the REM-134 and REM-134 RR cell lines, which were classified as HER2-overexpressing. To our knowledge, our study is the first to generate a canine mammary cancer RR cell line model and provide a comparative genetic and phenotypic analysis of the mechanisms of acquired radioresistance between canine and human cancer cell lines. We demonstrate that the cellular processes that occur with the development of acquired radioresistance are similar between the human and canine cell lines; our results therefore suggest that the canine model is appropriate to study both human and canine radioresistant mammary cancers, and that treatment strategies used in human medicine may also be applicable to veterinary patients.

Evidence-based guidelines for managing patients with primary ER+ HER2- breast cancer deferred from surgery due to the COVID-19 pandemic

Many patients with ER+ HER2- primary breast cancer are being deferred from surgery to neoadjuvant endocrine therapy (NeoET) during the COVID-19 pandemic. We have collated data from multiple international trials of presurgical endocrine therapy in order to provide guidance on the identification of patients who may have insufficiently endocrine-sensitive tumors and should be prioritised for early surgery or neoadjuvant chemotherapy rather than NeoET during or in the aftermath of the COVID-19 pandemic for safety or when surgical activity needs to be prioritized. For postmenopausal patients, our data provide strong support for the use of ER and PgR status at diagnosis for triaging of patients into three groups in which (taking into account clinical factors): (i) NeoET is likely to be inappropriate (Allred ER <6 or ER 6 and PgR <6) (ii) a biopsy for Ki67 analysis (on-treatment Ki67) could be considered after 2-4 weeks of NeoET (a: ER 7 or 8 and PgR <6 or b: ER 6 or 7 and PgR ≥6) or (iii) NeoET is an acceptable course of action (ER 8 and PgR ≥6). Cut-offs for percentage of cells positive are also given. For group (ii), a high early on-treatment level of Ki67 (>10%) indicates a higher priority for early surgery. Too few data were available for premenopausal patients to provide a similar treatment algorithm. These guidelines should be helpful for managing patients with early ER+ HER2- breast cancer during and in the aftermath of the COVID-19 crisis.

Naturally-Occurring Canine Mammary Tumors as a Translational Model for Human Breast Cancer

Despite extensive research over many decades, human breast cancer remains a major worldwide health concern. Advances in pre-clinical and clinical research has led to significant improvements in recent years in how we manage breast cancer patients. Although survival rates of patients suffering from localized disease has improved significantly, the prognosis for patients diagnosed with metastatic disease remains poor with 5-year survival rates at only 25%. In vitro studies using immortalized cell lines and in vivo mouse models, typically using xenografted cell lines or patient derived material, are commonly used to study breast cancer. Although these techniques have undoubtedly increased our molecular understanding of breast cancer, these research models have significant limitations and have contributed to the high attrition rates seen in cancer drug discovery. It is estimated that only 3-6% of drugs that show promise in these pre-clinical models will reach clinical use. Models that can reproduce human breast cancer more accurately are needed if significant advances are to be achieved in improving cancer drug research, treatment outcomes, and prognosis. Canine mammary tumors are a naturally-occurring heterogenous group of cancers that have several features in common with human breast cancer. These similarities include etiology, signaling pathway activation and histological classification. In this review article we discuss the use of naturally-occurring canine mammary tumors as a translational animal model for human breast cancer research.

Precision Medicine and the Role of Biomarkers of Radiotherapy Response in Breast Cancer

Radiotherapy remains an important treatment modality in nearly two thirds of all cancers, including the primary curative or palliative treatment of breast cancer. Unfortunately, largely due to tumor heterogeneity, tumor radiotherapy response rates can vary significantly, even between patients diagnosed with the same tumor type. Although in recent years significant technological advances have been made in the way radiation can be precisely delivered to tumors, it is proving more difficult to personalize radiotherapy regimens based on cancer biology. Biomarkers that provide prognostic or predictive information regarding a tumor's intrinsic radiosensitivity or its response to treatment could prove valuable in helping to personalize radiation dosing, enabling clinicians to make decisions between different treatment options whilst avoiding radiation-induced toxicity in patients unlikely to gain therapeutic benefit. Studies have investigated numerous ways in which both patient and tumor radiosensitivities can be assessed. Tumor molecular profiling has been used to develop radiosensitivity gene signatures, while the assessment of specific intracellular or secreted proteins, including circulating tumor cells, exosomes and DNA, has been performed to identify prognostic or predictive biomarkers of radiation response. Finally, the investigation of biomarkers related to radiation-induced toxicity could provide another means by which radiotherapy could become personalized. In this review, we discuss studies that have used these methods to identify or develop prognostic/predictive signatures of radiosensitivity, and how such assays could be used in the future as a means of providing personalized radiotherapy.

Abstract P6-10-18: Development and validation of novel biomarkers of response to radiotherapy in breast cancer

Background: Radiotherapy (RT) plays an important role in the multimodal treatment of breast cancer (BC). Despite improvements in the accuracy of delivering radiation to specific biological target volumes, the clinical response of BC to RT is still affected by intrinsic/acquired radioresistance. These resistant cancer cells can contribute to the development of recurrent disease and poor patient outcomes. Clinical signs of RT response are often not apparent for several weeks post-treatment; patients who fail to respond will therefore initially go undetected. There are currently no clinically validated biomarkers that can predict which patients will respond to RT or assess response during treatment. Our study aims to address this major clinical need through the identification and validation of biomarkers of radiation responsiveness.

Methods: The effects of different radiation doses (2 - 10Gy) at a range of time points (1 - 24h) were investigated by analysing the protein secretion profiles from 3 BC cell lines: MCF-7 (ER+), ZR-751 (ER+) and MDA-MB-231 (ER-). Conditioned media was collected from each dose/time point and proteins isolated for mass spec analysis. For comparison, radioresistant models were derived from each of the 3 cell lines and were characterized by proliferation and colony formation assays, invasion and migration assays, whole-genome transcriptomic sequencing (WGTS) analysis and western blotting. To assess intrinsic response to RT a panel of 16 BC cell lines were evaluated by colony formation assays following a 2Gy dose of radiation. WGTS of a patient cohort of 230 (138 ER+ve, 92 ER-ve) post-menopausal women with BC, treated with breast conserving surgery and adjuvant RT but no systemic adjuvant therapy, with a median follow-up of 14 years, is currently underway.

Results: 9 biomarkers emerged whose secretion was significantly increased with radiation. These were evaluated by western blotting of conditioned media 24h after a 2Gy dose of RT in matched radio-sensitive and resistant cell lines; this confirmed significantly higher levels of radiation induced secretion from sensitive cells compared to resistant. Radioresistant cell lines were characterised by epithelial-to-mesenchymal-transition, enhanced invasion/migration, loss of ER and PgR and increased EGFR and PI3K signaling activity. Initial mechanistic investigations suggest that biomarker release in response to radiation occurs via microvesicles. A blood-based assay to test the level of these secreted biomarkers is currently under development. Pre-treatment levels of the 9 biomarkers were also found to be associated with prediction of intrinsic response to RT at both gene and protein level. A gene expression signature comprising the 9 candidates is strongly associated with the intrinsic response to RT across the 16 BC cell lines studied, with higher expression found in those more sensitive to RT compared with those less sensitive or resistant. Validation of the predictive power of these biomarkers in terms of recurrence-free and overall BC specific survival is currently being assessed at gene and protein level in the patient cohort.

Conclusions: We have identified 9 biomarkers which are released from BC cells sensitive to radiation 24h after a 2Gy dose (in line with current clinical standards) but not from radio-resistant derivatives.A blood based assay is currently under development which has the potential to monitor response to RT in the neoadjuvant and palliative settings.Intracellular levels of the 9 biomarkers are strongly associated with intrinsic response to RT and may hold predictive potential.These biomarkers may have the potential to improve patient care by identifying patients less likely to benefit from RT, paving the way for personalization of treatment, including altered dosing schedules and the future use of emerging radio-sensitizers.

Citation Format: James Meehan, Mark Gray, Carlos Martinez-Perez, Charlene Kay, J Michael Dixon, Jimi Wills, Carol Ward, Alex von Kriegsheim, Niall Quinn, Olga Oikonomidou, David Cameron, Simon P Langdon, David Argyle, Ian H Kunkler, Arran K Turnbull. Development and validation of novel biomarkers of response to radiotherapy in breast cancer [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 P6-10-18.

Abstract P6-16-04: IL6ST, a biomarker of endocrine therapy response, has potential in identifying a subgroup of women with ER+ DCIS who are more likely to benefit from adjuvant endocrine therapy

Background: Ductal carcinoma in situ (DCIS) lesions are non-obligate precursors to invasive breast cancer (IBC). With the ultimate goal of preventing the development of invasive disease, DCIS is typically treated by breast-conserving surgery (BCS). Adjuvant radiotherapy (RT) is given for high-grade disease to reduce the risk of in-breast tumour recurrence (IBTR). The use of endocrine therapy (ET) for DCIS varies, as studies show a modest benefit but no survival improvement; in the UK, guidelines recommend ET for DCIS in some scenarios but only instead of, rather than in addition to, RT. This project sought to characterise the biology of ER+ DCIS and identify a group of women who are likely to gain the most benefit from the addition of adjuvant ET.

Patients: Cohort A - 77 women with ER+ (Allred 7/8) high-grade DCIS treated with BCS plus RT, 20 of whom developed IBTR.Cohort B - 70 women with ER+ (Allred 7/8) low/intermediate-grade DCIS treated with BCS alone, 12 of whom developed IBTR.Cohort C - 68 women with ER+ (Allred 7/8) DCIS treated with BCS plus ET.

All patients were treated locally between 2000 and 2016 and the median follow-up is 6 years.

Methods: We performed whole-genome transcriptomic QuantSeq sequencing of samples from cohort A. Sequencing of cohort B and C is currently underway. IL6ST levels were validated using immunohistochemistry and RNAScope.

Results: In cohort A, only a subset (34/77) of tumours had gene expression profiles consistent with active ER signalling. Levels of IL6ST, a biomarker for ET response, could differentiate these two subgroups and this was validated at protein level using immunohistochemistry. The low ER signalling subgroup were associated with higher levels of EGFR, HER2 and MAPK signalling. 20/77 high-grade DCIS cases recurred within 10 years. 50% of these recurred as IBC (rather than DCIS) and these were associated with higher levels of IL6ST, had active ER signalling and higher levels of proliferation-associated and estrogen receptor target genes, known to be decreased by ET, in the primary DCIS lesion.

Discussion: Our findings suggest that some high-grade ER+ DCIS patients have active ER signalling while in others ER signalling remains low despite highly expressing the ER protein. IL6ST, a biomarker of endocrine therapy response can be used to differentiate these two groups of ER+ DCIS. DCIS lesions which recurred as IBC had active ER signalling and also higher levels of proliferation genes known to be decreased by ET compared with DCIS which recurred as further DCIS. These findings suggest that IL6ST may have a role in identifying a subset of ER+ DCIS which are at a higher risk of developing advanced disease and are also more likely to benefit from the addition of adjuvant ET, with a better risk-to-benefit ratio than observed in previous studies that considered a less targeted use of this treatment strategy, thus potentially reducing the risk of IBC recurrence. These findings will be validated in a cohort of low/intermediate-grade DCIS who received no adjuvant RT (cohort B) and a cohort of patients who received adjuvant ET as part of their treatment (cohort C).

Citation Format: Carlos Martinez-Perez, Charlene Kay, Rebecca Swan, Gregory E Ekatah, Laura M Arthur, James Meehan, Mark Gray, Andrew H Sims, Olga Oikonomidou, Arran K Turnbull, J Michael Dixon. IL6ST, a biomarker of endocrine therapy response, has potential in identifying a subgroup of women with ER+ DCIS who are more likely to benefit from adjuvant endocrine therapy [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 P6-16-04.

Abstract P1-18-07: Can some ER+/HER2+ patients be safely spared from treatment with chemotherapy plus herceptin?

Background: The ER+/HER2+ subtype accounts for up to 10% of all breast cancers (BCs) and most are treated with surgery followed by adjuvant chemotherapy with Herceptin +/- radiotherapy then adjuvant endocrine therapy (ET) to reduce the recurrence risk. Despite this it is clear that not all ER+/HER2+ patients gain benefit from the addition of chemotherapy and Herceptin. In particular, given the significant side effects associated with the chemotherapy, the risks may out way the benefit in some older patients and in those with co-morbidities. Currently there are no clinically validated tools to identify women with ER+/HER2+ BC whose risk of recurrence remains unchanged with the addition of chemotherapy plus Herceptin and who can be effectively managed with adjuvant ET alone. Using levels of IL6ST, a biomarker for ET response, ER+/HER2+ patients who gain benefit from ET can be differentiated from those for whom ET alone is not sufficient to reduce the risk of recurrence. The latter group were characterised by inactive ER signalling and active MAPK and PI3K signalling. The aim is to show that ER+/HER2+ patients predicted to respond less well to ET alone using IL6ST levels, gain additional benefit from chemotherapy plus Herceptin.

Patients:

• Cohort A - 32 post-menopausal women (PMW) with large ER+/HER2+ BC treated with neoadjuvant (3-6 months) then adjuvant letrozole. Neoadjuvant clinical response was assessed by changes in tumour volume. Tumour core biopsies were taken at 0, 14 days and 3 months. Gene expression analysis using Illumina HT12 whole-genome beadarrays was performed on a subset (n=17) where fresh tissue was available. Median follow-up was 7.5 years.

• Cohort B - 362 women with ER+/HER2+ BC treated with surgery +/- radiotherapy followed by adjuvant endocrine therapy between 2005 and 20010. 219 also received chemotherapy plus Herceptin. Median follow-up is 9.5 years.

Results: In cohort A, half (16/32) of the patients responded to ET with tumour volume reductions of &gt;70% with neoadjuvant treatment. Innate resistance was apparent in 3 patients with continued tumour growth on ET, whereas 13 patients acquired resistance after a period of response. Neoadjuvant clinical response was predicted with 92% accuracy using levels of IL6ST. Gene expression analysis in 17 patients showed increased MAPK and PI3K pathway activity in the 9 NR compared with the 8 R tumours. In the 16/32 patients who responded well to neoadjuvant ET the actuarial recurrence rate was 0% at 5 and 10 years. The rate of recurrence in the NR was 30% at both 5 and 10 years. Samples from cohort B are currently being profiled using IL6ST in tandem with custom gene expression assays for ER, MAPK and PI3K pathway activity.

Conclusions:

• IL6ST levels can differentiate ER+/HER2+ BCs who respond well to ET alone and those with a poor clinical response who have a higher risk of recurrence.

• NR to ET have increased expression of PI3K and MAPK pathways, consistent with active HER2 signalling.

• Analysis of cohort B is underway and will elucidate the benefit in terms of recurrence-free and overall breast cancer specific survival from the addition of chemotherapy plus Herceptin to the group predicted to respond less well to ET using IL6ST.

• There is potential role for IL6ST in selecting ER+/HER2+ patients that require and benefit from HER2-targeted therapies.

Citation Format: Arran K Turnbull, Victoria Webber, Daniel McStay, Laura M Arthur, Carlos Martinez-Perez, James Meehan, Mark Gray, Charlene Kay, Lorna Renshaw, Jane Keys, Robert Clarke, Andrew H Sims, Olga Oikonomidou, J Michael Dixon. Can some ER+/HER2+ patients be safely spared from treatment with chemotherapy plus herceptin? [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 P1-18-07.

Abstract P2-11-06: Assessment of ESR1 genomic aberrations and their role in endocrine therapy resistance in breast cancer

Background: Endocrine therapy (ET) is an effective treatment of estrogen receptor positive (ER+) breast cancer (BC). However, not all ER+ cancers respond to ET and many eventually acquire resistance. Genomic aberrations in ESR1 have been reported to play a role in resistance to treatment. ESR1 mutations (ESRMs), reported in 10-50% of metastatic or recurrent BCs treated with aromatase inhibitors (AIs), can lead to constitutive activation and reduced sensitivity to ET. The incidence and clinical implications of ESR1 amplification (ESRA) is not well-established. A variety of structural rearrangements involving ESR1 have been reported in primary BCs, with some more strongly associated with tamoxifen and AI resistance. This study aimed to establish a rapid, reliable and cost-effective method to screen and monitor ESR1 genomic aberrations in clinical BC tissue samples and relate these to the 1st line and subsequent ETs patients received.

Patients:

• Cohort A - 20 post-menopausal women (PMW) with ER+ BC who had acquired resistance to AIs and received subsequent lines of ET. Previous NGS data were available for these patients.

• Cohort (B) - 425 ER+ BC patients, with paired matched tissue samples from the primary and progressive/recurrent cancer on 1st line ET; sites included local recurrence (25%), nodal recurrence (29%), distant recurrence (3%) and primary progression on neoadjuvant ET (44%). Median follow-up 10 years. All patients received 2nd line ET, 14% developed a further recurrence on 2nd line ET.

Methods: ESRMs were assessed by allele-specific real-time quantitative (rt-qPCR) and digital droplet PCR (ddPCR) assays, a novel fluorometric in situ mutation detection (ISMD) approaches and AmpliSeq targeted sequencing. ESRA and ESR1 fusions were detected by targeted sequencing and validated using FISH and custom ligation assays for commonly-reported fusion proteins (currently ESR1-e6&gt;YAP1 and ESR1-e6&gt;PCDH11X), respectively.

Results: Results from ddPCR and ISMD were consistent with NGS findings in cohort A. There was expansion of D538G mutant clones with acquired resistance in 5/20 patients (25%). ESR1 copy number gain was seen in 11/20 patients (55%) in resistant samples. Gene amplification was confirmed by FISH in 6, corresponding to those with the highest gain from the NGS data. In cohort B, recurrent/resistant samples (including 2nd recurrences) with matched primaries are currently being screened for ESR1 genomic aberrations using all methods allowing for a comprehensive comparison. This will allow full characterisation of mutations, copy number changes and gene fusions in the largest cohort of ET resistant cancers to date. Results will be interpreted in the context of 1st line ET (51% Tamoxifen, 34% non-steroidal AI, 8% exemestane, 7% other ET) and 2nd line ET in the 14% of patients who developed a 2nd recurrence. ESR1 genomic aberrations have been identified in 38% of samples to date, with specific aberrations associated with particular ETs.

Discussion:

• A reliable, robust and cost-effective methodology for the detection and quantitation of ESR1 aberrations in clinical BC samples has been developed and compared with NGS and targeted sequencing approaches.

• This method would allow rapid screening for key aberrations with the potential to inform selection of 2nd line therapy.

• Multiplexing of fluorometric assays may enable in situ clonality analysis that allows visualisation of multiple genomic driver aberrations simultaneously.

• In the largest cohort of patients with resistance to ET to date, there is a high incidence of ESR1 genomic aberrations. These are associated with specific ETs. Analysis between these changes and response, disease-free and overall breast cancer-specific survival on 2nd line ET is currently ongoing.

Citation Format: Carlos Martinez-Perez, Charlene Kay, James Meehan, Mark Gray, Rebecca Swan, Lorna Renshaw, Jane Keys, Andrew H Sims, Olga Oikonomidou, J Michael Dixon, Arran K Turnbull. Assessment of ESR1 genomic aberrations and their role in endocrine therapy resistance in breast cancer [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 P2-11-06.

Abstract P4-02-09: Factors affecting the number of sentinel lymph nodes removed in the treatment and staging of breast cancer?

Background: A sentinel lymph node in breast cancer surgery is defined as a blue node or a “hot” radioactive node and includes nodes other than the hottest node providing that they contain at least 10% of the radioactivity of the hottest node. The false negative rate of SLNB in breast cancer surgery falls as the number of sentinel nodes removed increases. A recent large US study suggested that patients having 3 or more nodes removed had a better overall survival. Substantial variation remains in how many nodes surgeons remove and what constitutes an adequate SLNB. The aim of this study was to identify what factors influence the number of lymph nodes removed by SNLB.

Methods: Data were collected retrospectively from 426 patients with breast cancer who underwent sentinel lymph node biopsy at the Edinburgh Breast Unit by 10 different surgeons between March 2016 and September 2017. Patients with imaging and core biopsy-diagnosed invasive or in situ breast cancer who underwent SLNB as part of breast conserving surgery or mastectomy were eligible. Factors included were patient age, tumour size, tumour grade, type of surgery and surgeon, neoadjuvant chemotherapy (NACT), lympho-vascular invasion, hormone and HER2 receptor status and the number of positive nodes (defined by histological assessment). Univariate and multivariable statistical analyses were performed.

Results: The number of sentinel nodes biopsied varied significantly between operating surgeon (p&lt;0.0001) and was significantly associated with the number of positive nodes (p&lt;0.0001), patient age (p=0.037), tumour size (p=0.011) and the use of NACT (p&lt;0.003) in multivariable analysis. More nodes were removed in patients who had node-positive disease, were younger, had larger tumours and had neoadjuvant chemotherapy. Within the subset who received NACT (n=40), separate multivariable analyses were performed for both the 30% of these patients who were lymph-node positive at diagnosis and the 70% who were not. No factors were found to be significant explanatory variables for the number of SLNs biopsied in the group who were lymph-node negative at diagnosis. In contrast, although the number of patients who received NACT and were lymph-node positive at diagnosis was small, surgeon was found to be a statistically significant explanatory variable for the number of SLNs taken at biopsy.

Discussion:

• This study shows that the surgeon plays an important and significant role in determining the number of sentinel nodes removed by sentinel lymph node biopsy.

• The number of positive nodes was also found to be an important factor, likely due to greater numbers of nodes being taken by surgeons who suspect positive nodes on intraoperatively inspection.

• Higher numbers of nodes were removed in younger patients, patients with larger tumours and patients who received NACT.

• In conclusion, either some surgeons remove too many nodes or others are removing too few and there needs to be more consistency in surgical SNB practices.

Citation Format: J Michael Dixon, Julia Grewar, Dominique Twelves, Charlene Kay, Carlos Martinez-Perez, James Meehan, Mark Gray, Arran K Turnbull. Factors affecting the number of sentinel lymph nodes removed in the treatment and staging of breast cancer? [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 P4-02-09.

Abstract P1-01-03: Association of cardiac energetics and plasma biomarkers with anthracycline-based chemotherapy in breast cancer patients

BACKGROUND Anthracyclines are widely used in the treatment of breast cancer and are well recognised to carry increased risk of cardiotoxicity. This can occur as an early, acute manifestation or many years after treatment as late onset cardiomyopathy. It is increasingly apparent that there may be a chronic subclinical phase associated with low grade cardiac injury with no apparent clinical impact on the contractile function of the heart. This period may remain latent for many years with the patient remaining asymptomatic and with apparently normal cardiac function. Identification of early and subtle cardiac dysfunction during this period could provide a window of opportunity for therapeutic intervention if those at risk or those experiencing this low-grade decline could be accurately identified. This study explores the potential utility of phosphorus magnetic resonance spectroscopy (31P-MRS) to identify very early anthracycline-induced cardiac toxicity and baseline predisposition to cardiac injury. This technique measures the phosphocreatine/adenosine triphosphate concentration ratio (PCr/ATP), which reflects cardiac cellular energetics. The normal range of PCr/ATP is approximately 1.8 - 2.2, whereas decreased PCr/ATP is associated with a drop in available energy reserve in the heart, associated with many forms of heart failure. Conventional cardiac investigations of electrocardiogram, multiple gated acquisition radionuclide scans (MUGA) and ultra-high sensitivity plasma cardiac troponin-I (cTn-I) have also been applied. METHODS 20 newly diagnosed breast cancer patients, receiving anthracycline-based chemotherapy, had magnetic resonance imaging to assess left ventricular ejection fraction and 31P magnetic resonance spectroscopy (31P MRS) to assess phosphocreatine to adenosine triphosphate concentration ratio (“PCr/ATP”). Measurements were performed pre-chemo, mid-chemo and post-chemo. Plasma high sensitivity cardiac troponin-I (cTn-I) and electrocardiograms were performed. RESULTS There was a significant negative correlation between change in PCr/ATP pre- to mid- chemo and change mid- to post-chemo (r=-0.68, p=0.04). Mean ejection fraction reduced significantly (5.1%) pre- to post-chemo (p=0.02). Change in PCr/ATP ratios pre- to post-chemo correlated inversely with changes in LVEF over the same period (r=-0.65, p=0.006) and mid- to post-chemotherapy (r=-0.77, p=0.002). Plasma cTn-I increased pre- to mid-chemo (1.35±0.81 to 4.40±2.64 ng/L; p=0.0001) and mid to post-chemo (4.40±2.64 to 18.33±13.23 ng/L; p=0.0001). CONCLUSIONS This study has demonstrated the use of 31P MRS in exploring cardiac energetics of breast cancer patients undergoing chemotherapy. Pre-chemotherapy PCr/ATP ratios were in line with healthy control values obtained using our system. This technique detected a pattern of recovery of PCr/ATP ratios following an initial 3 cycles of anthracyclines. Changes in PCr/ATP ratios were found to be significantly negatively correlated with changes in LVEF from pre to post chemotherapy. The significant decrease in LVEF from pre-post chemo may be due to the delayed response of LVEF to the initial 3 cycles of anthracyclines. Small but significant increases in plasma levels of cardiac troponin-I were observed early after initiation of anthracyclines. PCr/ATP ratios were not found to be related to cTn-I values but LVEF and cTn-I were found to be positively correlated. Future studies should take account of background factors that could influence cardiac PCr/ATP ratio such as age, physical fitness and regular medication whilst the improved sensitivity of 7T MRI scanners may also help in detecting earlier changes in cardiac energetics in this patient group.

Citation Format: Olga Oikonomidou, Gillian Macnaught Macnaught, Christopher T Rodgers, William Clarke, Annette Cooper, Heather McVicars, Arran K Turnbull, Saeed Mirsadraee, Scott Semple, Martin Denvir. Association of cardiac energetics and plasma biomarkers with anthracycline-based chemotherapy in breast cancer patients [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 P1-01-03.

Abstract P6-04-03: In-depth genomic analysis of acquired resistance to multiple sequential lines of endocrine therapy in breast cancer

Background: 80% of all breast cancers (BCs) are ER+. Not all respond to endocrine therapy (ET) and many eventually develop resistance. An in-depth genomic analysis of cancers that acquired resistance (aR) to multiple sequential lines of ET after an initial period of response has been performed.

Patients: A unique cohort of tissues from 20 post-menopausal women with ER+ BC was collected. All patients initially responded to neoadjuvant ET; 19/20 received an aromatase inhibitor (AI): letrozole (LET) (n=18) or anastrozole (AN) (n=1), 1 patient received fulvestrant followed by adjuvant tamoxifen (TAM) (mean treatment duration 22 months, range 4-67) before developing resistance. Patients were then treated by surgery or 2nd line ET. Overall, 13/20 received 2nd line ET either AN (n=1), TAM (n=10) or exemestane (EX) (n=1); 6 went on to receive 3rd line ET with EX (n=5) or LET (n=1).

Methods: Serial RNA & DNA from 3-5 cancer samples per patient (89 samples) had Ribo0-RNAseq and DNA exome sequencing. Somatic mutations and copy number alterations (CNA) were determined. Fisher’s exact test was used to compare mutation frequencies (MFs). Differential gene expression analysis was performed using two-class unpaired Significance Analysis of Microarrays (SAM).

Results:

Mutations: Comparisons of MFs between all sensitive vs resistant tumours identified mutations in SAAL1 and SLC9A9 as being enriched in sensitive tumours while mutations in GATA3 and ZFPM2 were enriched across tumours with acquired resistance to ET. Only KMT2C was identified as enriched in resistant tumours when comparing sensitive to only those that acquired resistance to 1st line LET. When comparing sensitive tumours to only those that had acquired resistance to multiple lines of ET (LET and TAM +/- AN and EX), sensitives were significantly enriched for mutations in CCDC141 and SLC9A9 and multi-drug resistant (MDR) tumours were significantly enriched for mutations in 11 genes including ESR1 and GATA3, and genes involved in cell adhesion (CDH1, FLG, FLG2 and FREM2). ESR1 mutations were identified in 6/20 patients; 5 patients had D538G mutations, 2 appeared during resistance to 1st line LET and 3 in MDR tumours. 1 patient had an ESR1 frame-shift mutation which appeared during resistance to 1st line LET. GATA3 was mutated in 7/20 patients, of which 4 had mutations in all samples including baseline, 2 had mutations uniquely present in MDR tumours and 1 had mutations that appeared during resistance to 1st line LET.

CNA: No significant gains or losses were identified when comparing sensitive tumours to those resistant to 1st line LET alone, but significant gains were identified across multiple chromosomes in MDR tumours. Gain of ESR1 was seen in 8/20 patients; in 3 patients there was ESR1 gain at diagnosis which persisted through initial response and subsequent aR. 5 patients developed ESR1 gain during MDR but not during initial resistant to 1st line LET.

Gene Expression: Analysis comparing sensitive and MDR tumours identified 82 differentially expressed genes (FDR=0). MDR tumours had higher proliferation and higher expression of transcriptional regulators including FOS and FOSB, histone cluster genes and genes involved in oxidative phosphorylation. MDR tumours also had higher expressions of GATA3 induced genes.

Discussion: In contrast to 1st line ET resistance, aR to multiple lines was characterised by significant gains across multiple chromosomes including ESR1 gain in a quarter of tumours. MDR tumours were also characterised by enrichment of mutations in particular genes including ESR1 (D538G in particular) which occurs in one-third of patients with aR. GATA3 is expressed in &gt;90% of BCs, is reported to be mutated in up to 10% of all BCs may be integral to the functions of ESR1; mutations in GATA3 were enriched in MDR tumours and may highlight a new area of ET resistance.

Citation Format: Arran K Turnbull, Youli Xa, Carlos Martinez-Perez, Olga Oikonomidou, James Meehan, Mark Gray, Lisa A Carey, Charles M Perou, J Michael Dixon. In-depth genomic analysis of acquired resistance to multiple sequential lines of endocrine therapy in breast cancer [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 P6-04-03.

Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches

BACKGROUND

High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.

METHODS

This study describes our experiences of nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples.

RESULTS

The number of genes represented and reliability varied between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material.

CONCLUSIONS

Overall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.

Estrogen Receptor Pathway Activity Score to Predict Clinical Response or Resistance to Neoadjuvant Endocrine Therapy in Primary Breast Cancer

Endocrine therapy is important for management of patients with estrogen receptor (ER)-positive breast cancer; however, positive ER staining does not reliably predict therapy response. We assessed the potential to improve prediction of response to endocrine treatment of a novel test that quantifies functional ER pathway activity from mRNA levels of ER pathway-specific target genes. ER pathway activity was assessed on datasets from three neoadjuvant-treated ER-positive breast cancer patient cohorts: Edinburgh: 3-month letrozole, 55 pre-/2-week/posttreatment matched samples; TEAM IIa: 3- to 6-month exemestane, 49 pre-/28 posttreatment paired samples; and NEWEST: 16-week fulvestrant, 39 pretreatment samples. ER target gene mRNA levels were measured in fresh-frozen tissue (Edinburgh, NEWEST) with Affymetrix microarrays, and in formalin-fixed paraffin-embedded samples (TEAM IIa) with qRT-PCR. Approximately one third of ER-positive patients had a functionally inactive ER pathway activity score (ERPAS), which was associated with a nonresponding status. Quantitative ERPAS decreased significantly upon therapy (P < 0.001 Edinburgh and TEAM IIa). Responders had a higher pretreatment ERPAS and a larger 2-week decrease in activity (P = 0.02 Edinburgh). Progressive disease was associated with low baseline ERPAS (P = 0.03 TEAM IIa; P = 0.02 NEWEST), which did not decrease further during treatment (P = 0.003 TEAM IIa). In contrast, the staining-based ER Allred score was not significantly associated with therapy response (P = 0.2). The ERPAS identified a subgroup of ER-positive patients with a functionally inactive ER pathway associated with primary endocrine resistance. Results confirm the potential of measuring functional ER pathway activity to improve prediction of response and resistance to endocrine therapy.

On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer

Background

Neoadjuvant chemotherapy is increasingly given preoperatively to shrink breast tumours prior to surgery. This approach also provides the opportunity to study the molecular changes associated with treatment and evaluate whether on-treatment sequential samples can improve response and outcome predictions over diagnostic or excision samples alone.

Methods

This study included a total of 97 samples from a cohort of 50 women (aged 29–76, with 46% ER+ and 20% HER2+ tumours) with primary operable breast cancer who had been treated with neoadjuvant chemotherapy. Biopsies were taken at diagnosis, at 2 weeks on-treatment, mid-chemotherapy, and at resection. Fresh frozen samples were sequenced with Ion AmpliSeq Transcriptome yielding expression values for 12,635 genes. Differential expression analysis was performed across 16 patients with a complete pathological response (pCR) and 34 non-pCR patients, and over treatment time to identify significantly differentially expressed genes, pathways, and markers indicative of response status. Prediction accuracy was compared with estimations of established gene signatures, for this dataset and validated using data from the I-SPY 1 Trial.

Results

Although changes upon treatment are largely similar between the two cohorts, very few genes were found to be consistently different between responders and non-responders, making the prediction of response difficult. AAGAB was identified as a novel potential on-treatment biomarker for pathological complete response, with an accuracy of 100% in the NEO training dataset and 78% accuracy in the I-SPY 1 testing dataset. AAGAB levels on-treatment were also significantly predictive of outcome (p = 0.048, p = 0.0036) in both cohorts. This single gene on-treatment biomarker had greater predictive accuracy than established prognostic tests, Mammaprint and PAM50 risk of recurrence score, although interestingly, both of these latter tests performed better in the on-treatment rather than the accepted pre-treatment setting.

Conclusion

Changes in gene expression measured in sequential samples from breast cancer patients receiving neoadjuvant chemotherapy resulted in the identification of a potentially novel on-treatment biomarker and suggest that established prognostic tests may have greater prediction accuracy on than before treatment. These results support the potential use and further evaluation of on-treatment testing in breast cancer to improve the accuracy of tumour response prediction.

Electronic supplementary material

The online version of this article (10.1186/s13058-019-1159-3) contains supplementary material, which is available to authorized users.

Development and characterisation of acquired radioresistant breast cancer cell lines

BACKGROUND

Radiotherapy plays an important role in the multimodal treatment of breast cancer. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Development of effective cancer treatments will require further molecular dissection of the processes that contribute to resistance.

METHODS

Radioresistant cell lines were established by exposing MDA-MB-231, MCF-7 and ZR-751 parental cells to increasing weekly doses of radiation. The development of radioresistance was evaluated through proliferation and colony formation assays. Phenotypic characterisation included migration and invasion assays and immunohistochemistry. Transcriptomic data were also generated for preliminary hypothesis generation involving pathway-focused analyses.

RESULTS

Proliferation and colony formation assays confirmed radioresistance. Radioresistant cells exhibited enhanced migration and invasion, with evidence of epithelial-to-mesenchymal-transition. Significantly, acquisition of radioresistance in MCF-7 and ZR-751 cell lines resulted in a loss of expression of both ERα and PgR and an increase in EGFR expression; based on transcriptomic data they changed subtype classification from their parental luminal A to HER2-overexpressing (MCF-7 RR) and normal-like (ZR-751 RR) subtypes, indicating the extent of phenotypic changes and cellular plasticity involved in this process. Radioresistant cell lines derived from ER+ cells also showed a shift from ER to EGFR signalling pathways with increased MAPK and PI3K activity.

CONCLUSIONS

This is the first study to date that extensively describes the development and characterisation of three novel radioresistant breast cancer cell lines through both genetic and phenotypic analysis. More changes were identified between parental cells and their radioresistant derivatives in the ER+ (MCF-7 and ZR-751) compared with the ER- cell line (MDA-MB-231) model; however, multiple and likely interrelated mechanisms were identified that may contribute to the development of acquired resistance to radiotherapy.

Abstract P3-12-24: Tumor-secreted predictive biomarkers of response to radiotherapy in breast cancer

Background:In breast cancer (BC), radiotherapy (RT) is used adjuvantly to prevent recurrence and also in the palliative setting. Clinical signs of RT response are often not apparent for several weeks post-treatment and we currently lack tools to predict or monitor tumor response to RT early during treatment. The aim was to identify tumor-secreted biomarkers whose release reflects response to RT, which could be monitored during treatment in the blood or intratumorally by an implantable biosensor, currently under development within the Implantable Microsystems for Personalised Anti-Cancer Therapy (IMPACT) program.

Methods: A series of experiments assessed the effect of different radiation doses (2-10Gy) on 3 human BC cell lines – MDA-MB-231 (ER-), MCF-7 (ER+) and HBL-100 (ER-) –, 1 canine breast cancer and 2 sheep lung cancer lines. Culture media was collected from each dose experiment at a range of post-radiation time-points (1-24 hours). Proteins were isolated from collected media for secretome mass spectrometry (MS) analysis. A subset of treatment/time conditions were repeated in the same BC cell lines and radioresistant (RR) derivatives from which RNA was extracted and analysed using Lexogen QuantSeq for whole-genome transcriptomics.In-lab candidate biomarker validation was carried out using immuhistochemistry (IHC), immunofluorescence (IF) and western blotting (WB) using validated antibodies. Levels of candidate biomarkers were also assessed in normal and untreated BC tissues using IHC. ELISA-based methods are currently under investigation for detection of the lead candidate biomarkers in the blood of large animal cancer models treated with RT.

Results: Biomarker discovery using the MS data revealed 4 promising candidates: EIF3G, SEC24C, YBX3 and TK1. These are released from BC and animal cancer cells sensitive to radiation in a dose-dependent manner 24 hours after treatment. Analysis of the transcriptomic data showed an 8-fold higher expression of the genes encoding the 4 candidates in the radio-sensitive parental cell lines compared to the RR cell lines. IF and WB confirmed lower intracellular expression of the 4 proteins in RR cells compared to the parental lines. WB of collected culture media confirmed release of each of the 4 candidates 24 hours after a 2Gy dose of radiation in only the parental lines. GAPDH was not found in these media samples, demonstrating that protein release was not due to cell lysis.

Conclusions:

· We have identified 4 promising biomarkers which are released from cancer cells sensitive to RT and not released from RR derivatives.

· All 4 candidates are released 24 hours after a 2Gy radiation dose, which fits with the current clinical dosing schedule where radiation is administered at 24 hour intervals. Ongoing work will elucidate if these biomarkers can be reliably detected in blood or intratumorally using implantable biosensors.

· There are currently no validated predictive tools to monitor RT response during treatment. If successfully validated, these biomarkers could have a clinical role in personalising RT dosing schedules and durations for solid tumors in the neoadjuvant and palliative setting, thus optimising treatment and preventing the administration of ineffective RT and its associated side effects.

Citation Format: Meehan J, Gray M, Turnbull AK, Martinez-Perez C, Bonello M, Ward C, Langdon SP, McLaughlin S, MacLennan M, Dixon JM, Wills J, Quinn N, Finich AJ, von Kriegsheim A, Cameron D, Kunkler IH, Murray A, Argyle D. Tumor-secreted predictive biomarkers of response to radiotherapy in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-12-24.

Abstract P4-15-04: Neoadjuvant endocrine therapy for ER+ DCIS can lead to disease regression and allows BCS in up to a third of patients with disease &gt;40mm at diagnosis

Background: The role of neoadjuvant endocrine therapy (NET) for ER+ DCIS is an area of evolving study. It may allow down-sizing prior to surgery, converting DCIS requiring mastectomy to disease suitable for breast conservation surgery (BCS). Here we report the results from the first European single-institution series of its type.

Methods: Data were prospectively collected from patients diagnosed with ER+ DCIS and treated with NET prior to surgery, at a single unit between 2009 -2015. The size of the tumour on initial imaging (mammography) was compared to the size of the tumour on final imaging and pathology using RECIST criteria to determine disease progression. Blocks from initial core biopsy and final pathology are being interrogated by immunohistochemistry and DNA and RNA comparisons.

Results: 42 patients diagnosed with ER+ DCIS received NET with median age at diagnosis of 63y (range 37-94y). 7/42 premenopausal women were treated with tamoxifen, 35/42 post-menopausal women were treated with letrozole.

36/42 (85.7%) patients underwent surgery with 18/36 (50%) requiring mastectomy and 18/36 (50%) treated by BCS. 3/18 (16.7%) of the BCS patients required re-excision for positive margins. The median time to operation was 72d (range 15-308d). In total 12/42 (28.6%) had invasive disease on final pathology.

2/36 (5.6%) patients had a pathological complete response (PCR), 14/36 (38.9%) had a partial response (PR), 17/36 (47.2%) had stable disease and 3/36 (8.3%) had larger disease on pathology than imaging; this is a common feature of many lower grade DCIS lesions.

26/42 (61.9%) patients initially had DCIS &gt;40mm (largest 240mm) and yet 9/26 (34.6%) of these patients still underwent successful BCS.

There was a significant correlation between length of endocrine therapy and reduction in size of disease. Immunohistochemical and molecular analyses are ongoing.

Conclusions:

•NET is an effective treatment for ER+ DCIS. It reduces the rate of re-excision to 16.7% in this series - substantially lower than the national (UK) figures for DCIS at 30%.

•It produces path CRs (5.6%) and high response rates that relate to the duration of treatment.

•This unique study shows that the optimal duration of NET is of the order of 6 months, achieving high rates of conversion for mastectomy to BCS.

Citation Format: Cartlidge CW, Johns N, Hackney RJ, Turnbull AK, Dixon JM. Neoadjuvant endocrine therapy for ER+ DCIS can lead to disease regression and allows BCS in up to a third of patients with disease &gt;40mm at diagnosis [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 P4-15-04.

Abstract P5-04-27: Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents

Background: Around 70% of all breast cancers (BCs) are estrogen receptor positive (ER+), but some do not respond to endocrine therapy (ET) and many eventually develop resistance. ESR amplification (ESRA) linked to an increase in ESR1 gene expression is known to occur in some cancers that are endocrine resistant. However, the incidence of ESRA has been the object of debate and its clinical significance remains unclear. This study aimed to investigate the incidence of ESRA in BCs resistant to multiple sequential ETs and optimise a fluorescence in-situ hybridisation (FISH) methodology to robustly detect ESRA.

Methods: Two unique cohorts have been studied:

(A) 20 post-menopausal women with ER+ BC with acquired resistance to letrozole, subsequently treated with up to 4 different lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq and DNA exome sequencing;

(B) 18 post-menopausal women who developed ER+ BC recurrences on 1st line adjuvant letrozole, then on 2nd line tamoxifen and subsequently on 3rd line exemestane. Tissues were collected at the time of each surgery.

We have optimised a FISH method to assess ESRA in these tissues.

Results: In cohort A, 6/20 patients developed ESR1 gene amplification (ESRA) at some point during treatment. In 5 of these cases, ESRA was only found while on 2nd or 3rd line exemestane but was not present on acquired resistance to previous letrozole or tamoxifen. 1 patient had ESRA at the time of first recurrence on letrozole.

The FISH method showed concordance with the genomic analysis. This suggests that ESRA may be associated with BCs that are treated with and then become resistant to exemestane.

ESRA is also evident in samples from Cohort B, which includes 18 exemestane resistant cases. The complete analysis is ongoing.

Conclusions:

· ESRA can be seen in ER+ recurrent BCs.

· ESRA may be associated with BCs treated with 2nd or 3rd line exemestane.

· The frequency of ESRA in endocrine and exemestane resistance can now be ascertained using an optimised FISH-based method, which is more cost-effective than alternative genomic and biochemical methods.

Citation Format: Turnbull AK, Martinez-Perez C, Mok S, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-27.

Abstract P5-04-14: Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection

Background: Approximately 70% of breast cancers (BCs) are estrogen receptor positive (ER+). Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop acquired resistance. Next-generation sequencing (NGS) has shown ESR1 mutations (ESRMs) are present in 10-50% of recurrent/metastatic cancers treated with aromatase inhibitors (AIs). Many of these mutations are located in the ligand-binding domain of ER, so they can lead to constitutive activation. This suggests ESRMs are a major mechanism of acquired resistance to endocrine therapy (ET) and numerous studies have shown a link between ESRMs and reduced sensitivity to 2nd line ET. The aim of this project was to investigate the incidence and clonal evolution of common ESRMs in BCs resistant to multiple sequential ETs using NGS, as well as novel PCR and in situ mutation detection methods.

Methods: We have optimised an allele-specific real-time PCR (rtPCR) assay and an in situ mutation detection method (ER-ISMD) for the assessment of ESRMs. Both have been designed to identify a missense gain-of-function D538G mutation with a single nucleotide-resolution in formalin-fixed paraffin-embedded (FFPE) BC tissues.

Two unique cohorts have been studied:

(A) 20 post-menopausal women (PMW) with ER+ BC who acquired resistance to letrozole and were treated with up to 4 subsequent lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq, DNA exome sequencing, rtPCR and ER-ISMD.

(B) 150 PMW with ER+ BC who developed local (n=79), lymph node (n=59) or distant (n=12) recurrences on 1st line adjuvant letrozole, anastrozole or tamoxifen. Of these, 48 patients developed subsequent recurrences on 2nd line ET. Tissue samples from each recurrence and matched primary BC were collected.

Results: In cohort A, 5/20 patients (20%) had expansion of a D538G ESR1 mutation clone at time of resistance 1st line ET (3:letrozole, 1:anastrozole, 1:tamoxifen). The mutant allele frequency (MAF) increased further in the 4 BCs treated with 2nd line ET (2:tamoxifen, 2:exemestane) and further still in the 1 BC who received 3rd line exemestane. 0/6 patients with ESRM responded to subsequent ET. Allele-specific rtPCR and ER-ISMD have been used to validate these findings and also identified low frequency ESRM clones in the sequential samples prior to the development of clinical resistance, that were not reported by NGS. Both methods have also been applied to screen tissues from patients in cohort B, where ESRMs have also been identified in recurrent samples. Complete analysis is currently ongoing.

Conclusions:

· ESRMs develop and expand in some BCs as a mechanism for acquired resistance to ET and are associated with a lack of response to subsequent standard ETs.

· Allele-specific rtPCR can detect ESRMs and is more cost-effective and easier to use than NGS for ER mutation analysis.

· Some ESRMs predate clinical resistance.

· ER-ISMD is a novel approach that allows for identification and visualisation of the distribution of mutant clones in morphologically intact FFPE tissue.

· ER-ISMD has the potential to become a clinically useful tool to help direct the use of 2nd line ET in routine care.

Citation Format: Martinez-Perez C, Turnbull AK, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-14.

Abstract P5-18-03: A predictive model for local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS)

Background: Ductal carcinoma in situ (DCIS) is a heterogeneous precursor, non-invasive breast lesion. There is a lack of specific DCIS molecular predictors of in breast tumour recurrence (IBTR) or progression to invasive breast cancer (IBC) after breast conserving surgery (BCS) +/- radiotherapy (RT). The aim of this was to identify novel biomarkers and combine these with clinical parameters to develop a new model to predict IBTR in patients treated by BCS for DCIS.

Methods: A single institution DCIS biomarker discovery study included a case-control matched series of 180 patients (median age 61, range 35-94) treated at the Edinburgh Breast Unit between 2000 and 2010:

· 88 patients with low/intermediate grade DCIS treated with BCS alone; 18 recurred within 10 years.

· 92 patients with high grade DCIS treated by BCS and RT; 22 recurred within 10 years.

Median follow-up was 7.4 years. RNA was extracted from DCIS lesions and whole-genome transcriptomics analysis was performed using Lexogen QuantSeq. Predictive models were generated based upon the most informative genes. Independent validation cohorts are also available and are currently being used for validation.

Results: The models developed predict risk of IBTR in patients with low or intermediate grade DCIS treated with BCS alone and high grade DCIS treated with DCIS plus RT. The models were found to be independent of grade and stratify patients into binary groups of high and low risk of recurrence.

A promising model was developed based on the expression of 5 genes combined with tumour diameter ≤15mm or &gt;15mm.

• In low/intermediate grade DCIS expression levels of a solute carrier family gene, kinetochore associated gene and an immunomodulatory gene are predictive of recurrence.

• In high grade DCIS an additional solute carrier and a glutathione S-transferase related gene are predictive of recurrence.

• In the training sets the models have 96% (high-grade) and 92% (low/intermediate grade) accuracy of prediction of subsequent recurrence and estimates of IBTR-free survival were highly significant in both groups (&lt;0.0001). Validation of the model by RT-PCR and immunohistochemistry is underway in both the training cohort and an independent validation cohort.

Conclusions:

· Promising models to predict risk of IBTR in patients treated for DCIS have been developed.

· Novel biomarkers that predict recurrence have been identified using new technologies that may have clinical potential.

· Independent validation is currently underway.

Citation Format: Martinez-Perez C, Turnbull AK, Fernando A, Ekatah GE, Arthur LM, Cartlidge CW, Johns N, Sims AH, Thomas JS, Dixon JM. A predictive model for local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-18-03.

Abstract P3-11-13: On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer

Purpose: Neo-Adjuvant chemotherapy treatment is increasingly being used in breast cancer to preoperatively shrink tumour volumes and facilitate surgical plans. These datasets however, are still scarce, making it difficult to assess the relative value of multiple time point biopsies compared to diagnostic only sampling. This study aims to identify sequential samplings intrinsic value.

Method: A total of 97 samples from a cohort of 50 neoadjuvant chemotherapy treated primary breast cancer patients (aged 29-76 at diagnosis, Allred status 47:53% +/-, Her2 status 80:20% +/-, mixed grade and menopausal status) taken pre- treatment, at 2 weeks on-treatment, mid chemotherapy and at resection were sequenced with Ion Ampliseq transcriptome yielding expression values for 12,635 genes. Differential expression analysis was performed across response groups (16 Responders, 34 Non-Responders) as defined by Pathological Complete Response and over treatment time to identify significantly differentially expressed genes, pathways and markers indicative of response status.

Results: An on-treatment marker for response was identified (AAGAB), which resulted in a testing accuracy of 100% and a validation accuracy of 78% in the I-SPY 1 Trial. AAGAB was predictive of long term survival (p = 0.048 testing, p = 0.031 validation) in both chemotherapy cohorts at the same expression level as defined for treatment response. The single gene on-treatment biomarker, AAGAB proves more performant than established prognostic tests, Mammaprint (Edinburgh NEO trial, pre-treatment 61%, on-treatment 63%. I-SPY 1 trial, pre-treatment 60%, on-treatment 66%) and Pam50 RORS (neo trial pre-treatment 50%, on treatment 58%, Magbanua trial pre-treatment 56%, on-treatment 64%)

Conclusion: Changes in gene expression of on-treatment chemotherapy breast cancer resulted in the identification of a novel gene marker that was as effective in predicting prognostic status as established prognostic tests. These results support the use of on-treatment testing in breast cancer to improve the accuracy of tumour response prediction.

Citation Format: Bownes RJ, Turnbull AK, Cameron D, Sims AH, Oikonomidou O. On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-11-13.

Abstract P5-04-03: Molecular characterisation of ER+ breast cancer dormancy and acquired resistance using a clinical model: Potential involvement of epigenetic regulation

Background: The risk of recurrence for oestrogen receptor positive (ER+) breast cancer patients treated with 5 years of adjuvant endocrine therapy persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate. Therefore, previous efforts have been limited to in vitro or in vivo approaches. In this study sequential tumour samples from patients receiving extended neoadjuvant endocrine treatment were characterised as a novel clinical model of ER+ breast cancer dormancy and acquired resistance.

Methods: Consecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant letrozole therapy were subjected to transcriptomic and proteomic analysis, representing pre- (before treatment), early-on (13-120 days) and long-term (&gt;120 days) neoadjuvant letrozole treatment. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as “dormant”, and the remaining 20 patients as “acquired resistant”. Expression analysis was performed by using Illumina BeadChips. R and BioConductor packages were used for analysis. Differentially expressed genes were determined by using paired Rank Products (FDR, 5%).

Results: Multidimensional scaling using most variant 500 genes demonstrated that long-term treated dormant samples clustered separately from their matched pre- and early-on samples whereas long-term treated resistant samples were indistinguishable from their pre-treatment counterparts. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared to dormant tissues after extended letrozole treatment. Decrease in 5-hydroxymethylcytosine were significant early-on.

Conclusions: This is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumors exhibit distinct molecular changes under extended treatment whereas acquired resistant tumors are more similar to matched diagnostic samples supporting the molecular concordance between primary tumors and metastases. Global loss of DNA methylation was observed in resistant tumours under extended treatment which can be predicted within first 4 months of therapy. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients supporting a potential role for therapy targeted at these epigenetic alterations in the management of endocrine resistant breast cancer.

Funding: This work was supported by Marie Skłodowska-Curie Individual Fellowship [H2020-MSCA-IF, 658170] and Welcome Trust Institutional Fund (ISSF3) to CS and AHS, Breast Cancer Now to AHS.

Citation Format: Selli C, Turnbull AK, Pearce D, Fernando A, Renshaw L, Thomas JS, Dixon MJ, Sims AH. Molecular characterisation of ER+ breast cancer dormancy and acquired resistance using a clinical model: Potential involvement of epigenetic regulation [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-03.

Abstract P3-10-26: Predicting benefit from HER2-targeted therapies in patients with ER+/HER2+ breast cancer

Background: ER+/HER2+ accounts for up to 10% of all breast cancers (BCs) and most are treated with endocrine therapy (ET) after surgery to reduce the recurrence risk. We developed and validated an immunohistochemistry (IHC) based test (EA2Clin) that incorporates baseline IL6ST, clinical variables and on-treatment measurement of MCM4. Responders (Rs) and non-responders (NRs) to ET are identified and it accurately estimates recurrence-free survival (RFS) and BC-specific overall survival (BCSS). The aim was to determine if EA2Clin could accurately predict ER+/HER2+ patients likely to benefit from ET and to determine if it can identify those for whom HER2-targeted therapies are required.

Methods: 3 cohorts were studied:

A: 32 post-menopausal women (PMW) with large ER+/HER2+ BC treated with neoadjuvant (3-6 months) then adjuvant letrozole. 5 also received adjuvant chemotherapy plus Herceptin. Neoadjuvant clinical response was assessed by changes in tumour volume. Tumour core biopsies were taken at 0, 14 days and 3 months. Gene expression analysis using Illumina HT12 whole-genome beadarrays was performed on a subset (n=17) where fresh tissue was available.

B: 13 PMW with ER+/HER2+ BC who were treated by surgery without neoadjuvant therapy. RNA was extracted from excision tissues and analysed using whole-genome Affymetrix U133A microarrays.

C: 15 PMW with ER+/HER2+ BC treated with 2-weeks of pre-operative letrozole (n=7) or anastrozole (n=8). All received adjuvant letrozole. Tissues were collected at pre-treatment and at surgery. None received Herceptin or chemotherapy.

All patients were followed-up after surgery (median follow-up = 6.4 years).

Results: In cohort A, half (16/32) of the patients responded to ET with tumour volume reductions of &gt;70% with neoadjuvant treatment. Innate resistance was apparent in 3 patients with continued tumour growth on ET, whereas 13 patients developed resistance after a period of response. EAClin2 predicted neoadjuvant response with a 92% accuracy. There was increased expression of phospho-AKT and phospho-ERK in NRs, not seen in Rs. Half (8/16) of the NR cancers expressed phospho-ER; but was not seen in any responsive cancer. Gene expression analysis in 17 patients showed increased MAPK and PI3K pathway activity in the 9 NR compared with the 8 R tumours. These results were recapitulated in cohort B where MAPK and PI3K activity were associated with low levels of IL6ST.

In the 16/32 patients who responded well to neoadjuvant ET the actuarial recurrence rate was 0% at 5 and 10 years. The rate of recurrence in the NR was 30% at both 5 and 10 years. Of the 5 patients who received chemotherapy plus Herceptin, none recurred despite a poor response to neoadjuvant letrozole (median length to last follow-up was 6.1 years). Initial data suggest that in cohort B EA2Clin identifies a group of ER+/HER2+ cancers that can be managed by ET alone.

Conclusions:

· The EA2Clin test identifies ER+/HER2+ BCs who respond well to ET alone and those with a poor clinical response who have higher risk of recurrence.

· NR to ET have increased expression of PI3K and MAPK pathways, consistent with active HER2 signalling.

· There is potential role for EA2Clin in selecting ER+/HER2+ patients that require and benefit from HER2-targeted therapies.

Citation Format: Turnbull AK, Webber V, McStay D, Arthur L, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Clarke R, Sims AH, Dixon JM. Predicting benefit from HER2-targeted therapies in patients with ER+/HER2+ breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-26.

Abstract P3-06-17: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis

Background: Transcriptomic analyses of clinical samples can help improve our understanding of disease aetiology, drug effectiveness, assign molecular subtypes and derive prognostic signatures for clinical decision-making. The success of early microarray studies relied heavily on sample quality and predominantly fresh frozen (FF) tissues to generate reliably robust data. The emergence of next-generation microarray and sequencing-based technologies from formalin-fixed paraffin-embedded (FFPE) tissues provides an opportunity to study archival clinical tissues with long-term follow-up. Here we assess 9 technologies, which vary in resolution, cost and RNA requirements, with matched FF and FFPE tissues from the same patient.

Methods: Sequential tumour biopsies were taken pre-treatment and on-treatment (at 14-days and 3-months) from 11 postmenopausal patients with oestrogen receptor positive breast cancer treated with 3 months of neoadjuvant letrozole. Half of each sample was snap frozen in liquid nitrogen and half was FFPE, RNA was extracted from both. Transcriptomic analyses were performed using 9 technologies: Illumina Beadarray, Affymetrix U133A, Affymetrix Clariom S, NanoString nCounter, AmpliSeq Transcriptome, Lexogen QuantSeq and IonXpress RNAseq, Tempo-Seq BioSpyder and Qiagen UPX3'.

Results: Success rates for generating robust expression profiles from FFPE tissues were 100% all except the Illumina BeadChip (22%) and AmpliSeq Transcriptome (83%) , which varied by the age of tissue. With the total number and position of probes/primers/counts varying widely between approaches, in total 7305 genes were represented across all of the whole-genome technologies tested.

Clear batch effects were evident when comparing data from FF and FFPE tissues and when comparing between different technologies. Standard batch correction approaches such as XPN and ComBat minimised technical bias effect and increased the correlations between matched samples (FF and FFPE) to R&gt;0.9, irrespective of the technology used.

When analysed by multi-dimensional scaling following batch correction, samples clustered by treatment time-point. When ranked by expression of 60 proliferation genes, reported by us to change with letrozole treatment, samples ordered again by time-point, consistent with our previous findings, and paired samples clustered together.

Conclusions:

· Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches.

· A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution and RNA requirements to fit the user's needs.

· Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis.

Citation Format: Turnbull AK, Selli C, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Figueroa JD, He X, Tanioka M, Munro A, Murphy L, Fawkes A, Clark R, Coutts A, Perou CM, Carey LA, Dixon JM, Sims AH. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis [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 P3-06-17.

Abstract P5-11-03: Measurement of on-treatment proliferation biomarkers in nodal metastasis improves prediction of endocrine therapy response using the EA2CliN test

Background: The majority of patients with early-stage estrogen receptor positive (ER+) breast cancer (BC) are treated with adjuvant endocrine therapy (ET) after surgery to reduce the risk of recurrence. Recently, we have developed and validated an immunohistochemistry (IHC) based assay (EndoAdjuvant2 Clinical; EA2Clin) that measures pre-treatment IL6ST level together with clinical variables and on-treatment MCM4 to assess proliferation. We have previously shown that it can accurately identify responders and non-responders to ET and predicts recurrence-free survival (RFS) and BC-specific overall survival (BCSS). We postulated that measuring on-treatment proliferation in lymph node metastases (LN+) rather in the primary cancer might further improve the accuracy of the test for these patients. The aim was to test and validate this in cohorts of pre- and post-menopausal women (preMW & PMW) treated with preoperative ET (tamoxifen (T), fulvestrant (F), letrozole (L) or anastrozole (A)) and subsequent adjuvant ET.

Methods: Cohorts: (1) 137 PMW with ER+ BC, 59 were LN+, treated with neoadjuvant L (median duration 4.8 months, range 1-33), then surgery followed by adjuvant L (n=109) or other ET (n=28); (2) 148 PMW with ER+ BC, 55 were LN+, treated with 2 weeks of preoperative L (n=76) or A (n=72), then surgery followed by adjuvant L (n=69) or T (n=79); (3) 52 preMW with ER+ BC, 24 were LN+, treated with 2 weeks of preoperative T (n=26) or 1x750mg dose of F (n=26), then surgery followed by adjuvant T. All LN+ patients had sentinel node biopsies or clearance. The median follow-up was 6.5 years (cohort 1), 6.3 years (cohort 2) and 10.2 years (cohort 3).

EA2Clin: Patients are classified as:

· Low risk: ER+ and LN-negative and &lt;2cm or pre-treatment IL6ST 2+/3+ (IHC) and post-treatment MCM4 in the primary has &lt;20% positive nuclear staining.

· High risk: ER+ LN+ grade 3 BCs &gt;2cm or pre-treatment IL6ST is 0 or 1+, or IL6ST is 2+ or 3+ and MCM4 in the primary has &gt;10% positive nuclear staining.

EA2CliN uses the post-treatment level of MCM4 in the nodes, rather than the primary cancer.

Results: In cohort 1, EA2Clin (using primary tumour MCM4) was significantly associated with both RFS (P=0.0003, HR=13.17, 95%CI=5.48-13.61) and BCSS (P=0.005, HR=11.91, 95%CI=8.73-31.42). The 5 and 10 year actuarial recurrence rates were 5%/5% and 48%/64% for the low and high-risk groups respectively.

In the same cohort, using the MCM4 level in the node (EA2CliN) there was an even more significant association with both RFS (P&lt;0.00009, HR=18.16, 95%CI=12.59-19.46) and BCSS (P=0.002, HR=12.93, 95%CI=5.43-25.62). The 5 and 10 year actuarial recurrence rates were 0%/0% and 48%/72% for the low and high-risk groups respectively. Further validation of EA2CliN in cohorts 2 and 3 is underway.

Discussion:

· Direct measurement of on-treatment proliferation biomarkers in LN metastases improves prediction of outcomes to ET in women with BC.

· This tests identifies a group of low risk women that are node negative and node positive with a 100% RFS and BCSS.

· This is the most impressive predictive test for patients with ER+ breast cancer yet developed.

Citation Format: Turnbull AK, Mok S, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Sims AH, Dixon JM. Measurement of on-treatment proliferation biomarkers in nodal metastasis improves prediction of endocrine therapy response using the EA2CliN test [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-11-03.

HER2 regulates HIF-2α and drives an increased hypoxic response in breast cancer

Background

Tumour hypoxia is a driver of breast cancer progression associated with worse prognosis and more aggressive disease. The cellular response to hypoxia is mediated by the hypoxia-inducible transcription factors HIF-1 and HIF-2, whose transcriptional activity is canonically regulated through their oxygen-labile HIF-α subunits. These are constitutively degraded in the presence of oxygen; however, HIF-1α can be stabilised, even at high oxygen concentrations, through the activation of HER receptor signalling. Despite this, there is still limited understanding on how HER receptor signalling interacts with HIF activity to contribute to breast cancer progression in the context of tumour hypoxia.

Methods

2D and 3D cell line models were used alongside microarray gene expression analysis and meta-analysis of publicly available gene expression datasets to assess the impact of HER2 overexpression on HIF-1α/HIF-2α regulation and to compare the global transcriptomic response to acute and chronic hypoxia in an isogenic cell line model of HER2 overexpression.

Results

HER2 overexpression in MCF7 cells leads to an increase in HIF-2α but not HIF-1α expression in normoxia and an increased upregulation of HIF-2α in hypoxia. Global gene expression analysis showed that HER2 overexpression in these cells promotes an exaggerated transcriptional response to both short-term and long-term hypoxia, with increased expression of numerous hypoxia response genes. HIF-2α expression is frequently higher in HER2-overexpressing tumours and is associated with worse disease-specific survival in HER2-positive breast cancer patients. HER2-overexpressing cell lines demonstrate an increased sensitivity to targeted HIF-2α inhibition through either siRNA or the use of a small molecule inhibitor of HIF-2α translation.

Conclusions

This study suggests an important interplay between HER2 expression and HIF-2α in breast cancer and highlights the potential for HER2 to drive the expression of numerous hypoxia response genes in normoxia and hypoxia. Overall, these findings show the importance of understanding the regulation of HIF activity in a variety of breast cancer subtypes and points to the potential of targeting HIF-2α as a therapy for HER2-positive breast cancer.

Electronic supplementary material

The online version of this article (10.1186/s13058-019-1097-0) contains supplementary material, which is available to authorized users.

Molecular changes during extended neoadjuvant letrozole treatment of breast cancer: distinguishing acquired resistance from dormant tumours

BACKGROUND

The risk of recurrence for endocrine-treated breast cancer patients persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate; previous efforts have been limited to in-vitro or in-vivo approaches. In this study, sequential tumour samples from patients receiving extended neoadjuvant aromatase inhibitor therapy were characterised as a novel clinical model.

METHODS

Consecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant aromatase inhibitor therapy with letrozole were subjected to transcriptomic and proteomic analysis, representing before (≤ 0), early (13-120 days), and long-term (> 120 days) neoadjuvant aromatase inhibitor therapy with letrozole. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as "dormant", and the remaining 20 patients as "acquired resistant".

RESULTS

Changes in gene expression in dormant tumours begin early and become more pronounced at later time points. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to the resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. The DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared with dormant tissues after extended letrozole treatment.

CONCLUSIONS

This is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumours continue to change during treatment whereas acquired resistant tumours more closely resemble their diagnostic samples. Global loss of DNA methylation was observed in resistant tumours under extended treatment. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients, supporting a potential role for therapy targeted at these epigenetic alterations in the management of resistance to oestrogen deprivation therapy.

The evolving role of receptors as predictive biomarkers for metastatic breast cancer

INTRODUCTION

In breast cancer, estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) are essential biomarkers to predict response to endocrine and anti-HER2 therapies, respectively. In metastatic breast cancer, the use of these receptors and targeted therapies present additional challenges: temporal heterogeneity, together with limited sampling methodologies, hinders receptor status assessment, and the constant evolution of the disease invariably leads to resistance to treatment. Areas covered: This review summarizes the genomic abnormalities in ER and HER2, such as mutations, amplifications, translocations, and alternative splicing, emerging as novel biomarkers that provide an insight into underlying mechanisms of resistance and hold potential predictive value to inform treatment selection. We also describe how liquid biopsies for sampling of circulating markers and ultrasensitive detection technologies have emerged which complement ongoing efforts for biomarker discovery and analysis. Expert commentary: While evidence suggests that genomic aberrations in ER and HER2 could contribute to meeting the pressing need for better predictive biomarkers, efforts need to be made to standardize assessment methods and better understand the resistance mechanisms these markers denote. Taking advantage of emerging technologies, research in upcoming years should include prospective trials incorporating these predictors into the study design to validate their potential clinical value.

Novel histopathologic feature identified through image analysis augments stage II colorectal cancer clinical reporting

A number of candidate histopathologic factors show promise in identifying stage II colorectal cancer (CRC) patients at a high risk of disease-specific death, however they can suffer from low reproducibility and none have replaced classical pathologic staging. We developed an image analysis algorithm which standardized the quantification of specific histopathologic features and exported a multi-parametric feature-set captured without bias. The image analysis algorithm was executed across a training set (n = 50) and the resultant big data was distilled through decision tree modelling to identify the most informative parameters to sub-categorize stage II CRC patients. The most significant, and novel, parameter identified was the ‘sum area of poorly differentiated clusters’ (AreaPDC). This feature was validated across a second cohort of stage II CRC patients (n = 134) (HR = 4; 95% CI, 1.5– 11). Finally, the AreaPDC was integrated with the significant features within the clinical pathology report, pT stage and differentiation, into a novel prognostic index (HR = 7.5; 95% CI, 3–18.5) which improved upon current clinical staging (HR = 4.26; 95% CI, 1.7– 10.3). The identification of poorly differentiated clusters as being highly significant in disease progression presents evidence to suggest that these features could be the source of novel targets to decrease the risk of disease specific death.

Abstract P4-08-03: EA2Clin: A novel immunohistochemical prognostic and predictive test for patients with estrogen receptor-Positive breast cancer

Background: The majority of patients with early-stage estrogen receptor positive (ER+) breast cancer (BC) are treated with adjuvant endocrine therapy (ET) after primary surgery to reduce the risk of recurrence. A variety of tests are available to predict outcomes on ET but most require gene-level measurements and are expensive. Recently, we developed an immunohistochemistry (IHC) based test (EA2Clin) using levels of pre-treatment IL6ST together with clinical variables and on-treatment proliferation. The aim was to validate this test in cohorts of both pre- and post-menopausal women treated with two weeks of a variety of endocrine treatments (tamoxifen, fulvestrant or an aromatase inhibitor) prior to surgery.

Methods: The cohorts are: (A) 186 post-menopausal women (PMW) with ER+ BC treated with at least 2 weeks of preoperative or neoadjuvant letrozole or anastrozole, then surgery followed by adjuvant letrozole (n=132) or tamoxifen (n=54); (B) 51 pre-menopausal women (preMW) with ER+ BC treated with 2 weeks of either neoadjuvant tamoxifen (n=24) or one 750mg dose of faslodex (n=27), then surgery followed by adjuvant tamoxifen. The median follow-up was 5.4 years for cohort A and 10.2 years for cohort B. IHC analysis was performed using a Leica BOND III autostainer and the EA2Clin algorithm was used to stratify patients in binary high or low-risk groups.

Results: In the cohort of PMW, EA2Clin was highly significantly associated with both recurrence-free survival (RFS) (P&lt;0.0001, HR=13.26, 95%CI=5.59-13.46) and breast cancer specific survival (BCSS) (P&lt;0.0001, HR=12.93, 95%CI=4.43-37.72). The 5 and 10 year actuarial recurrence rates were 7%/22% and 46%/73% for the low and high risk groups, respectively. The actuarial breast cancer-related death rate for the low risk group was 5% at both 5 and 10 years, whereas for the high risk group was 33%/38%. Confounding factors were not found to be significant.

In the cohort of preMW, our test was significantly associated with both RFS (P=0.002, HR=5.71, 95%CI=1.91-17.05) and BCSS (P=0.016, HR=4.81, 95%CI=1.34-17.26). The 5 and 10 year actuarial recurrence rates were 12%/29% and 27%/77% for the low and high risk groups, respectively. The 5 and 10 year actuarial breast cancer-related death rates were 7%/19% and 9%/58% for low and high risk groups, respectively.

Discussion:

· This study has validated EA2Clin as the first predictive tool to incorporate clinical data with pre and on-treatment immunohistochemical biomarkers to predict accurately the outcome of patients with ER positive breast cancer treated with adjuvant ET.

· This test predicts both RFS and BCSS in pre- and PMW treated with a variety of endocrine agents.

· Because this test incorporates clinical variables with simple IHC, it can be performed locally in any pathology lab.

Citation Format: Turnbull AK, Fernando A, Renshaw L, Keys J, Thomas JS, Sims AH, Dixon JM. EA2Clin: A novel immunohistochemical prognostic and predictive test for patients with estrogen receptor-Positive breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-08-03.

Abstract P5-11-02: Predicting local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS)

Background: Ductal carcinoma in situ (DCIS) of the breast represents a heterogeneous group of precursor, non-invasive breast lesions. Currently we lack accurate tools to stratify DCIS patients according to inherent risk of in breast tumour recurrence (IBTR) or progression to invasive breast cancer (IBC).Most DCIS patients are treated by breast-conversing surgery (BCS), followed by whole-breast radiotherapy (RT) for the majority of high-grade DCIS. The aim of this study was to identify novel biomarkers which predict recurrence after BCS +/- RT.

Methods: A single institution study of 466 consecutive patients (median age 61, range 35-94) with DCIS treated by BCS between 2000 and 2010 was carried out. 271 patients with grade 3 DCIS received RT and 155 with grade 1/2 DCIS did not receive RT.

For biomarker discovery, a case-control matched series of 200 patients (mean age = 61, range = 36-84) from the above audit that met the following criteria was selected:

· 120 with low/intermediate-grade DCIS treated with BCS alone: 30 have recurred, 90 patients matched 3:1 have not recurred by 10 years.

· 80 with high-grade DCIS treated by BCS plus RT: 20 have recurred, 60 patients matched 3:1 have not recurred by 10 years.

Median follow-up was 7.4 years. RNA has been extracted and Affymetrix Clariom S whole-genome analysis has been performed and is currently being analysed.

Results:

In the cohort of 466 patients, 271 patients with high grade DCIS had BCS plus RT. Actuarial IBTR and IBC-IBTR in this group were 10% and 4% at 5 years and 18% and 6% at 10 years, respectively. 155 patients with low/intermediate grade DCIS had BCS alone. Actuarial overall IBTR and IBC-IBTR in this group were 6% and 2% at 5 years and 13% and 2% at 10 years respectively.

In the high-grade, RT treated group, lesion size (P&lt;0.001, P=0.003), presence of comedo necrosis (P=0.018, P=0.025) and the Van Nuys Prognostic Index (VNPI) (P=0.02, P=0.004) were significantly associated with overall IBTR and DCIS-IBTR. No factor was significantly associated with IBS-IBTR in the high grade group and no factor predicted for any IBTR in the low/intermediate group.

Full genomic analysis of the 240 patient case-control matched cohort is underway and will be presented.

Discussion:

· This is the first DCIS biomarker discovery study using whole genome analysis and the matched cohort design looking separately at BCS + RT for high-grade DCIS and BCS only for low/intermediate grade DCIS.

· Clinical parameters alone may have insufficient sensitivity to identify high-grade, RT-treated patients at risk of developing IBC-IBTR.

· While recurrence rates in the low/intermediate grade DCIS group are lower than in the high-grade group, some patients do recur and there is a need to develop new tools which can identify low grade patients with a sufficiently high risk of recurrence to warrant additional treatment.

Citation Format: Martinez-Perez C, Turnbull AK, Ekatah GE, Arthur LM, Fernando A, Sims AH, Thomas JS, Dixon JM. Predicting local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS) [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-11-02.

Abstract P4-08-02: Understanding the mechanisms of action underlying the role of IL6ST, a key biomarker for prediction of response to endocrine therapy

Introduction: IL6ST is regarded as a putative ER target gene. Recently it has been recognised as a key biomarker for prediction of response to endocrine therapy (ET), having been included as the primary biomarker in our EA2Clin test and as an ER-signalling gene in the EndoPredict test. In both tests higher IL6ST expression is associated with a better response to ET and better prognosis. Despite its importance as a biomarker, little is known about its functional role in breast cancer (BC).

Methods: Pre- and on-treatment (at 14-days and at surgery) samples were collected from 102 post-menopausal women with ER+ BC, treated with 3-6 months of neoadjuvant ET. RNA was extracted for whole-genome expression analysis. From a subset with available fresh frozen tissue (28 patients, 83 samples) protein was extracted and proteome analysis using mass spectrometry is currently underway – results available for SABCS 2017. Immunohistochemistry was performed on FFPE tissue microarrays (TMAs) comprising pre-treatment samples from 102 patients. Cytoplasmic/membrane staining was scored using a graduated scale (0-3+) and nuclear staining was graded using an Immunoscore.

Results: IL6ST exists in membrane-bound and soluble forms of varying size. The full-length membrane bound molecule comprises 8 domains: 6 extracellular, 1 transmembrane and 1 cytoplasmic. In the EA2Clin test, pre-treatment BC tissues are stained for IL6ST with an antibody specific for a region spanning the transmembrane and cytoplasmic domains. TMAs were stained for IL6ST with both this and a second antibody binding the extracellular part, detecting both full-length and most soluble isoforms. Levels of both were correlated (R=0.82, P&lt;0.0001).

IL6ST is known to mediate the action of cytokines including IL6, OSM and LIF via downstream regulation of pathways such as JAK/STAT. TMAs were stained for antibodies against IL6ST, OSM, IL6, total STAT3, pSTAT3 (Tyr705) and pSTAT3 (Ser727). IL6ST was scored as low (0/1+) or high (2+/3+). There was a positive association between levels of IL6ST and IL6 (P=0.02) and total STAT3 (P=0.003). There was no association between IL6ST and OSM or either pSTAT3.

Supervised gene expression analysis comparing pre-treatment samples with high and low IL6ST levels revealed increased levels of STAT3-regulated genes: cell cycle (CEBPD, CDKN1B), apoptosis (NFIL3, ATF3, BCL2), extracellular matrix remodelling (ADM, SEPRINE1-3) and interferon signalling (IFIT1, IFI44, IFI27). Unsupervised gene enrichment analysis revealed increased expression of genes involved with JAK/STAT, PI3K, mTOR and ERBB1 signalling in tumours expressing higher IL6ST levels. Lower levels were associated with increased energy generation, cellular metabolism and epithelial-mesenchymal transition.

Conclusions:

• This is the first matched whole-genome and mass spectrometry proteome analysis of sequential ET-treated BC patients

• IL6ST predicts response to ET – it is used in2 independent assays

• Levels of full-length IL6ST appear to be the most important for ET response prediction

• IL6ST may have an active role in BC cells, mediating signalling of cytokines such as IL6 through the JAK/STAT pathway and subsequent downstream transcriptional regulation.

Citation Format: Turnbull AK, Fernando A, Martinez-Perez C, Finch AJ, von Kriegsheim A, Wills J, Quinn N, Selli C, Mosley D, Langdon SP, Sims AH, Dixon JM. Understanding the mechanisms of action underlying the role of IL6ST, a key biomarker for prediction of response to endocrine therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-08-02.

Abstract P3-13-05: Long-term outcome of neoadjuvant endocrine therapy followed by breast conserving surgery

Background:Neoadjuvant therapy (NET) in women with large or locally advanced estrogen receptor(ER)-rich breast cancers (BC) allows the option of breast-conserving surgery (BCS) + radiotherapy (RT). The aim was to study the long term safety of this strategy.

Methods: 280 postmenopausal women (median age 77, range 50-95, table 1) with ER-rich BC had BCS after NET (median duration 4.8 mths, range 1.7-42.8 mths). 221 (79%) received only letrozole. 59 (21%) began on letrozole and were switched to anastrozole, exemestane or tamoxifen due to adverse events or lack of clinical response. 200 patients (71%) had adjuvant RT (RTgroup) and 25 (9%), adjuvant chemotherapy. Median follow-up = 5.5 years.

Table 1: Clinical characteristics of patients.CharacteristicNo. PatientsTumour SizeT131 (11%)T2169 (60%)T314 (5%)T456 (20%)Unknown10 (4%)Grade136 (13%)2153 (55%)370 (25%)Unknown21 (7%)Nodes+ve101 (36%)-ve177 (63%)Unknown3 (1%)ER Allred615 (5%)762 (22%)8203 (73%)

Results:

254 patients had NET response data. 74% had a clinical response. NET response was higher for grade 1 (84%) than for 2 (73%) or 3 (72%) cancers.

Actuarial local recurrence rates (LRR) were 8% (95%CI±0.04) and 12% (95%CI±0.06) at 5 & 10 years. Actuarial overall BC recurrence rates were 14% (95%CI±0.04) and 27% (95%CI±0.12) at 5 & 10 years, with BCS death rates of 7% (95%CI±0.04) and 14% (95%CI±0.10) at 5 & 10 years, showing only half with recurrence died from BC. Crude all-cause mortality but not BC-specific survival (BCSS) favoured those who had adjuvant RT (P&lt;0.001) or chemotherapy (P=0.006). The 15-year rate was 50.9%, while BCS death rate was only 7.3%.

Positive nodes were associated with worse overall recurrence free survival (RFS) (P=0.007) but not local RFS or BCSS. Tumour size was not associated with RFS or BCSS. Tumour grade was not associated with RFS but grade 3 patients had a lower BCSS (P=0.002) compared to patients grade 1/2 cancers.

RT was associated with improved LRR (P&lt;0.0001) and overall RR (P=0.038): 5 & 10 year in RTgroup were 5% (95%CI±0.04) + 7% (95%CI±0.04) vs 9% (95%CI±0.12) + 31% (95%CI±0.24) in no-RTgroup. The 5 & 10 year ORR in the RTgroup was 14% (95%CI±0.06) and 39% (95%CI±0.16) vs 28% (95%CI±0.16) + 38% (95%CI±0.24) in the no-RTgroup. Although differences were not significant, BCSS was higher in the no-RTgroup: 5 & 10 yearly BCSS rates were 10% (95%CI±0.04) and 20% (95%CI±0.12) vs 6% (95%CI±0.08) + 12% (95%CI±0.14) in RTgroup.

16/67 patients with T3/4 cancers with no RT had lower overall RFS (P=0.018) but no difference in local RFS. 13/98 patients with node +ve disease with no RT had lower LRR (P=0.002) and overall RR (P=0.024). 54/169 node -ve patients with no RT had lower LRR (P=0.019) but similar overall RR. 50/183 patients with grade 1/2 cancers had no RT and had lower LRR (P&lt;0.0001) and overall RR (P=0.049). BCSS was not associated with RT use in subgroups related to tumour size, node status or grade.

Discussion:

· Response to NET is not worse in ER rich grade 3 or node positive cancers.

· After NET, BCS and RT provides excellent LRR.

· BCSS rates were low; most died of other causes.

· NET followed by BCS and RT is safe even for grade 3 and node positive cancers.

· BCS alone provides adequate disease control for majority with significant co-morbidities.

Citation Format: Yau JD, Turnbull AK, Renshaw L, Keys J, Leeper A, Thomas JS, Dixon JM. Long-term outcome of neoadjuvant endocrine therapy followed by breast conserving surgery [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-13-05.

Abstract P4-04-02: Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis

Background: Approximately 40% of ER+ breast cancer present with nodal metastasis. To date, there has been no comparison of the molecular response of primary cancers and metastases to ET. Recent evidence suggests that nodal metastases have different clones and subclones compared to the primary tumour. The aim of this study is to characterise the molecular response of primaries and nodal metastases to ET.

Methods: A unique set of 7 post-menopausal women with ER-positive breast cancer had biopsies taken from the primary tumour and a positive lymph node at diagnosis and at surgery following 3-12 months of neoadjuvant letrozole. 14-day and 3-6 month on-treatment biopsies from the primary tumour and involved nodes were also taken from the same patients, giving a total of 75 samples. Lymph node FFPE blocks were stained for cytokeratin and macro-dissected to enrich for tumour tissue. RNA and DNA were extracted and Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR performed. Whole-transcriptome AmpliSeq targeted-sequencing has been analysed for 4 patients.

Results: Multi-dimensional scaling and hierarchical clustering analysis based on all transcripts and the 500 most variably expressed genes revealed that primaries and nodal metastases are strongly associated at diagnosis but some nodes diverge during ET treatment. Analysis of estrogen-responsive proliferation-associated genes (n=60) in nodal metastasis revealed a reduction in expression of the majority of genes with ET. However, the expression levels of some remained high in the on-treatment node samples in all 4 patients analysed compared with the matched primary tumour on treatment. In particular, expression of genes involved in DNA replication and regulation of cell cycle including MCM6 and RRM2 (DNA replication), ASPM and CEP55 (mitosis) and CDKN3 (regulation of cell cycle) persisted at high levels in nodal metastases, but reduced in the primary cancers. Similarly, primary tumours had increased levels of ECM remodeling genes (n=60) as treatment continued, while levels in the nodal metastasis were heterogeneous on-treatment. Full genome sequencing results will be available by December 2017.

Discussion

· This is the first study to investigate genomic and transcriptomic changes with ET in both primary cancers and nodal metastases.

· On-treatment changes in nodal disease are heterogeneous between patients and within the same patient.

· Nodal metastases do respond to ET with reduced levels of proliferation-associated genes.

· Some proliferation-associated genes appear to maintain higher expression in nodal disease.

· Patterns of gene expression observed in some nodal metastases are consistent with profiles previously described by us for ET resistance and recurrent disease.

· Nodal metastases may accumulate mutations during treatment with ET and on-going analysis will clarify this.

Citation Format: Dixon JM, Turnbull AK, Tanioka M, Parker J, He X, Fernando A, Renshaw L, Keys J, Thomas JS, Sims AH, Carey LA, Perou CM. Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-04-02.

Abstract P4-03-01: Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ breast cancers

Background: 70% of all breast cancers (BCs) are ER+. Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop resistance. The aim was to perform in-depth genomic analysis of both primary resistant BCs, that do not respond to ET, and cancers which progress (&gt;40% increase in size) after an initial response as they acquire resistance (AQR) to ET.

Methods: A unique series of 48 post-menopausal women with ER+ BC received neoadjuvant ET using letrozole (L) or anastrozole (A) (mean treatment duration 17 months, range 3-67). 13/48 received up to 4 lines of ET.

12/48 responded to A or L, 16/48 had primary resistance and 20/48 had AQR.

Of 20 with AQR, 13 had 2nd line ET with A or tamoxifen (T). 6 had 3rd line ET with exemestane (E) and 1 had 4th line megestrol acetate (MA). Serial RNA & DNA from 3-5 cancer samples/patient (226 samples) had Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR. We have data so far on 29 patients: 5 responders, 4 with primary resistance and 20 AQR, the full cohort will be complete shortly.

Results:

ESR1 Mutations (ESRM): 1/5 responders had an ESRM (E380Q) at diagnosis. This clone disappeared with response to L. 5/20 patients with AQR (25%) had clonal expansion of an ESRM during 1st line ET (L:4, A:1). 4 had a chr6:152419926[lowbar]A:G (D538G) ESRM and 1 had a novel ESRM. Of the 5 with ESRM acquired during 1st line ET, the mutant allele fraction (MAF) increased further in the 4 who had 2nd ET (3:T, 1:E) and increased further for the 2 who had 3rd line E.

ESR1 Amplification (ESRA):

5 patients developed ESRA. 3/5 developed ESRA on 2nd or 3rd line E that was not present on AQR to 1st line L or A and 2nd line T. The other 2 developed ESRA on L. 2/5 with ESRA had concomitant CYP19A1 amplification. One patient with ESRA that developed on 3rd line E subsequently responded to MA. No patients with primary resistance to 1st line ET had an ESRM or ESRA.

PIK3CA mutations (PIK3M): 5/20 with AQR had PIK3M (25%). 3/7 had PIK3M at diagnosis and in 3 MAF increased between 1st and 2nd line ET. 2/7 developed PIK3M when resistant to 2nd line ET, 1 of the 2 had ESRA. 2 patients responsive to L had PIK3M at diagnosis and MAF decreased with therapy.

Other Mutations: Unique mutations with limited commonality developed and new clones expanded in the remaining cancers during primary and acquired resistance. Clonality analysis of AQR samples to different ETs showed proliferation of specific clones, characterised by novel sets of mutations, which typically became the dominant clone at the time of resistance to a particular agent.

Summary: 13/20 with acquired resistance had ESRM, ESRA, or PIK3M in resistant tumours: 1 had all 3, 2 ERSM + ESRA, 1 ERSA + PIK3CA, 4 ESRM only, 2 ESRA only and 3 had PIK3M only.

Conclusions:

• Endocrine resistance is complex

• ESRM or ESRA is uncommon at diagnosis and does not explain primary ET resistance

• ESRM (in particular the D538G mutation) occurs in one-third of patients with acquired resistance. 2nd line ET results in clonal selection and expansion of ESRM cells. Assessing recurrences for ESRM by in situ detection has clinical utility

• ESRA is only seen in heavily ET-pre-treated tumours, with its significance being unknown.

Citation Format: Dixon JM, Turnbull AK, Tanioka M, Wheless A, Garrett A, Martinez-Perez C, Parker J, He X, Sims AH, Thomas JS, Carey LA, Perou CM. Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-03-01.

Margin width and local recurrence after breast conserving surgery for ductal carcinoma in situ

INTRODUCTION

Ductal Carcinoma in situ (DCIS) represents 5% of symptomatic and 20-30% of screen detected cancers. Breast conserving surgery (BCS) ± radiotherapy is performed in over 70% of women with DCIS. What constitutes an adequate margin for BCS remains unclear.

METHODS

A single institution follow up study has been conducted of 466 patients with pure DCIS treated by BCS between 2000 and 2010 of whom 292 received whole breast radiotherapy and 167 did not. Patients were selected for radiotherapy based on perceived risk of in breast tumour recurrence (IBTR). Distance to nearest radial margin was measured; 10 patients had a margin width of <1 mm, 94 had widths of 1-2 mm and 362 had widths of >2 mm. There was no association of margin width and the use of radiotherapy.

RESULTS

At a median follow up of 7.2 years there were 44 IBTR (27 DCIS and 17 invasive). There was no evidence that margin widths >2 mm resulted in a lower rate of IBTR than margin widths of 1-2 mm. The actuarial IBTR rates at 5 and 10 years for margins of 1-2 mm were 9.0% (95% CI ± 5.9%) and 9.0% (95% CI ± 5.9%) respectively and for margins of >2 mm were 8.0% (95% CI ± 3.9%) and 13.0% (95% CI ± 3.9%) respectively. Odds Ratio for IBTR 1-2 mm vs >2 mm was 0.839 (95% CI 0.392-1.827) p = 0.846. In a multivariate analysis only DCIS size predicted for IBTR (HR 2.73 p < 0.0001).

CONCLUSION

1 mm appears a sufficient margin width for BCS in DCIS irrespective of whether patients receive radiotherapy.

Abstract P1-06-04: Molecular characterisation, subtype concordance and prognostic group assignment between patient-matched primary breast tumours and axillary lymph node metastases

Introduction

Currently the primary breast tumour is used for prognostic profiling and as a monitor of response to therapy but how often does the molecular profile of the primary cancer reflect the molecular profile of nodal metastases? No previous study has investigated in detail the genomic profile of matched primary breast cancer (P) and nodal metastases (N) and correlated these with outcome. The aim of this study was to investigate whether the mRNA profiles of matched P and N differ significantly.

Methods

RNA was extracted from core biopsies from primary breast tumours and paired metastatic axillary lymph node samples from both FFPE blocks and fresh frozen samples. RNA was labelled and hybridised to Illumina HT-12 BeadChips to create a dataset consisting of one primary and one or two matched nodal metastasis, totalling 68 samples from 31 patients. Data was processed and corrected for batch effects, then analysed using the statistical programming language R. Clinical data on progression free and overall survival was collected from electronic and medical case note review.

Results

Unsupervised hierarchical clustering of the 500 most variable genes in each sample grouped only 12 of 31 P&Ns (39%) together, meaning in the majority of patients their P or N more resembled a cancer from another patient than its own paired P or N.

The number of genes with greater than 2 fold change (&gt;2FC) between P&N was used to categorise paired samples into 'least changed' (&lt;130 genes with &gt;2 FC) and 'most changed' (&gt;370 genes with &gt;2FC) groups. Multidimensional scaling of the 500 most variable genes in the most changed group (n-=10) showed consistently that nodal metastases differed molecularly from the primary cancer.

When categorised by Sorlie centroid, 12 of 31 patients (39%) had a different molecular subtype in N compared with P. N tended to be a poorer prognostic subtype than P. 50% had luminal A primaries paired with luminal B nodes. The remaining 50% changed in other non-consistent patterns.

6 patients had 2 N samples to analyse alongside P. 4 of these (67%) had the same subtype in all 3 samples, and a further 1 the same 2Ns (luminal B) which differed from P (luminal A). The final had luminal A P paired with 1 luminal A and 1 luminal B Ns.

There was no evident correlation between the least changed and most changed groups and progression free and overall survival. This may however reflect the short term follow up.

Discordance between P and N in expression of ESR1 was 32%; PGR 19% and ERBB2 16%.

Conclusions

This study of gene expression change in matched primary breast cancers and synchronous metastatic paired axillary lymph nodes shows that molecular subtype differs in 39%. 50% of nodes had a poorer prognostic subtype than their primary. Expression of ESR, PGR and ERBB2 differs in up to 32%

Classifying cancer molecular phenotype and estimating prognosis based only on the primary cancer misclassifies significant numbers of patients. Classification of prognosis, and treatment based on the nodal metastasis may provide better information on which to base treatment.

Citation Format: Arthur LM, Turnbull AK, Pearce DA, Renshaw L, Thomas JS, Sims AH, Dixon JM. Molecular characterisation, subtype concordance and prognostic group assignment between patient-matched primary breast tumours and axillary lymph node metastases [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-04.

A PAM50-Based Chemoendocrine Score for Hormone Receptor-Positive Breast Cancer with an Intermediate Risk of Relapse

.