bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract PR07: A biosensor mouse to predict the dissociation and spread of pancreatic cancer
Authors: Herrmann David , Erami Zahra , Warren Sean , Nobis Max , Magenau Astrid , Lucas Morghan , Vennin Claire , McGhee Ewan J. , Leung Wilfred , Reischmann Nadine , Mrowinska Agata , Schwarz Juliane P. , Kadir Shereen , Karim Saadia A. , Campbell Andrew D. , Gallego-Ortega David , Evans Jeffry , Sansom Owen J. , Morton Jennifer P. , Anderson Kurt I. , Timpson Paul
Published: March 2017

E-cadherin-mediated cell-cell junctions play a physical role in maintaining normal epithelial architecture. The disruption or deregulation of these adhesions in cancer can lead to the collapse of tumor epithelia that precedes invasion and subsequent metastasis. Here, we have generated an E-cadherin-GFP(FRAP) biosensor mouse, which enables intravital photobleaching and quantification of E-cadherin mobility in live tissue, without affecting normal biology. We demonstrate using FRAP or FLIP, the broad applications of this mouse to examine E-cadherin regulation in multiple tissues including mammary, brain, liver and kidney, while specifically monitoring E-cadherin mobility during disease progression in the pancreas. We assess E-cadherin stability in native pancreatic tissue, upon genetic manipulation involving Kras and p53 or in response to anti-invasive drug treatment, and reveal new insights into the dynamic remodeling of E-cadherin during in situ cancer progression. Photobleaching in the E-cadherin-GFP(FRAP) mouse correlate directly with epithelial integrity and mechanical strength making the biosensor mouse a valuable tool to fundamentally expand our understanding of E-cadherin-mediated events in native micro-environments.

This abstract is also being presented as Poster B23.

Citation Format: David Herrmann, Zahra Erami, Sean Warren, Max Nobis, Astrid Magenau, Morghan Lucas, Claire Vennin, Ewan J. McGhee, Wilfred Leung, Nadine Reischmann, Agata Mrowinska, Juliane P. Schwarz, Shereen Kadir, Saadia A. Karim, Andrew D. Campbell, David Gallego-Ortega, Jeffry Evans, Owen J. Sansom, Jennifer P. Morton, Kurt I. Anderson, Paul Timpson. A biosensor mouse to predict the dissociation and spread of pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr PR07.
Abstract BS1-2: Epigenetic targets in breast cancer
Authors: Polyak K
Published: March 2017

Epigenetic regulators are emerging therapeutic targets in various human cancer types including breast cancer. Histone modification (e.g., methylation and acetylation) regulates chromatin structure and transcription, and abnormalities in this process lead to perturbed development and differentiation. Similarly, DNA methylation patterns are commonly perturbed in tumors and this can increase genetic instability and also cellular heterogeneity within tumors. The demonstration of frequent somatic mutations in histones and epigenetic regulators factors in a wide range of human cancer types underscores the importance of epigenetic regulation in tumorigenesis. In breast cancer, genes encoding transcriptional regulators (e.g., FOXA1, GATA3) are among the most frequently mutated genes, suggesting a key role for perturbed epigenetic programs in tumorigenesis. Epigenetic regulators are broadly categorized into writers – enzymes that catalyze the placement of modifications in histones or DNA such as histone and DNA methyltransferases, erasers – enzymes that remove histone or DNA modifications including histone and DNA demethylases, and readers – proteins that recognize a specific histone or DNA modification to help concentrate an enzymatic or structural protein complex. BET bromodomain family of chromatin regulators (e.g., BRD4) recognize acetylated histones and play a key role in the assembly of active transcription complexes. Targeting of these proteins by BET bromodomain inhibitors (BBDIs) have been shown to inhibit the growth of several cancer types and they appear promising novel therapeutic agents in breast cancer as well. However, a significant fraction of breast cancer cells is not sensitive to BBDIs and even some of the initial responsive ones relatively quickly acquire resistance due to activation of anti-apoptotic pathways and bromodomain-independent recruitment of BRD4 to the chromatin. Thus, inhibitors of BET bromodomain proteins alone or in combination with other compounds provide a promising novel therapeutic strategy for the treatment of breast tumors.

Citation Format: Polyak K. Epigenetic targets in breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr BS1-2.
Abstract DL-1: Targeting breast cancer stem cells: Challenges and opportunities
Authors: Wicha MS
Published: March 2017

Breast cancers contain cell populations that display hierarchical organization at the apex of which are cells that display stem cell properties. These cancer stem cells (CSCs) mediate metastasis and contribute to treatment resistance. CSC's display cellular plasticity , a property that allows them to transition between mesenchymal and epithelial states, facilitating metastasis. Although different therapeutic strategies have been developed for the treatment of the various molecular subtypes of breast cancer, CSCs driving these cancers may share common regulatory pathways including those maintaining cellular plasticity. This suggests that therapeutic strategies targeting these CSC pathways may be complementary to subtype specific therapeutic agents targeting bulk cell populations. Furthermore, since CSCs constitute a minor fraction of total tumor cell populations classical clinical endpoints such as tumor regression are inadequate to assess the efficacy of CSC targeting therapeutics. Neoadjuvant trial designs allow for the direct assessment of treatment on biological targets and as well as the therapeutic effectiveness of CSC targeting agents. Molecular analysis of circulating tumor cells at single cell resolution provides an alternative method of accessing the effects of CSC targeting therapies.

CSCs are regulated by the tumor micro environment and recent studies suggest that the immune microenvironment plays a crucial role in CSC regulation. Immunotherapeutic approaches may provide a means to target heterogeneous CSC's as well as bulk tumor populations. Early phase clinical trials currently in progress have demonstrated the safety of CSC targeting agents. Future randomized trials will be required to determine whether addition of CSC targeting therapeutics to current agents targeting bulk cell populations improves the efficacy of these therapeutic agents.

Citation Format: Wicha MS. Targeting breast cancer stem cells: Challenges and opportunities [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 DL-1.
Abstract ES1-2: Paracrine signaling and intratumoral heterogeneity
Authors: Rosen JM
Published: March 2017

Breast cancer is no longer considered a single disease, but instead comprises multiple subtypes with genetically and most likely epigenetically heterogeneous tumors composed of numerous clones. Both the hierarchical cancer stem cell (CSC) and clonal evolution models have been invoked to help explain this intratumoral heterogeneity. Several recent studies have helped define the functional interactions among the different cellular subpopulations necessary for the evolution of this complex ecosystem. These interactions involve paracrine interactions that include locally acting Wnt family members, reminiscent of the signaling pathways important for normal mammary gland development and stem cell self-renewal. In addition, they involve interactions between breast cancer cells and the immune microenvironment. In this presentation, we will discuss the interactions among various cell populations in both normal and tumor tissues. A better understanding of these interactions, especially in the metastatic setting, will be important for the development of improved combinatorial therapies designed to prevent relapse and to ultimately decrease mortality.

Citation Format: Rosen JM. Paracrine signaling and intratumoral heterogeneity [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 ES1-2.
Abstract ES4-1: Basic science of immunotherapy
Authors: Knutson KL
Published: March 2017

While it remains unclear whether the immune system naturally evolved to prevent cancer, it is clear that many of its constituent cells and factors can greatly influence the clinical course of the disease in many different cancers, including breast cancer. Generally speaking, the immune system is a double edged sword and produces a broad array of both pro-tumor and anti-tumor factors. Of those which demonstrate anti-tumor activity, antigen-specific T cells (including both cytotoxic and helper T cells) are the most important as several studies have now shown that increased T cell infiltration is generally, and markedly, protective. More recent evidence also suggests that B cells can also be protective, particularly when producing tumor-specific antibodies or associated with intratumoral tertiary lymphoid structures. Thus, newer therapeutics being developed in academia and industry are being designed to directly augment adaptive immunity. The methods to manipulate the numbers of lymphocytes is growing and includes direct clonal expansion approaches such as vaccination and adoptive T cell therapy as well as more indirect methods that modulate cell intrinsic regulatory mechanisms (e.g. checkpoint and co-stimulatory pathways). In contrast, the pro-tumor activity of the immune system is largely mediated by the myeloid compartment of the immune system. While normal myeloid cells are not generally pro-tumorigenic, most tumors impair proper myeloid differentiation inducing intratumoral and systemic accumulation of defective myeloid cells which have profound tumor-promoting activity. This tumor-promoting activity of myeloid cells is mediated either through direct tumor growth-promoting activity (e.g. growth and angiogenic factors) or through blockade of adaptive immune response. Mechanisms by myeloid cells promote tumor growth appear to be diversified and are now only recently becoming understood, but nonetheless represent unique targets for therapeutic manipulation either alone in combination with other therapeutic modalities (e.g. checkpoint blockade). The basic underpinnings of tumor immunology are being rapidly identified and applied clinically to treat a variety of cancers and more recently breast cancer. This educational lecture will be a general overview of tumor immunology focusing on recent basic and therapeutic advances, highlighting those relevant to the field of breast cancer.

Citation Format: Knutson KL. Basic science of immunotherapy [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 ES4-1.
Abstract ES5-1: Breast cancer risk assessments: Who is high risk?
Authors: Nangia J
Published: March 2017

What is my risk for breast cancer? This is a common question physicians are asked, and with the changing guidelines for breast cancer screening it is very important to have a good understanding of what a woman's risk for breast cancer is. Breast cancer risk assessments can be done based on family history, risk factors and personal history of prior breast biopsies. During this educational session we will review different models used to determine breast cancer risk as well as other factors that can increase or reduce breast cancer risk.

Citation Format: Nangia J. Breast cancer risk assessments: Who is high risk? [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 ES5-1.
Abstract ES5-2: ES5-2 Non-endocrine strategies: Beyond the estrogen receptor
Authors: Brown P
Published: March 2017

Powel Brown, Parijatham Thomas, Abhijit Mazumdar, Diane Weber, Robin Coyne, Lana Vornik, Terry Bevers, and Abenaa Brewster

Department of Clinical Cancer Prevention; University of Texas MD Anderson Cancer Center; Houston, TX.

Breast cancer prevention has been demonstrated to be possible using anti-estrogen drugs. However, these drugs only prevent the development of estrogen receptor-positive breast cancers, and are often not acceptable to women. Therefore, there has been a major effort to develop more acceptable breast cancer preventive strategies. In this presentation I will review the current approaches to breast cancer prevention, with a focus on risk-based preventive interventions, including behavioral measures to reduce breast cancer risk in average risk individuals, and drug-based interventions in high risk individuals. While anti-estrogen hormonal therapies are still the most effective preventive therapy other than prophylactic breast surgery, other strategies are being tested that offer great promise. Interventions that have been shown to be effective in preclinical studies include novel molecularly targeted drugs (such as PARP inhibitors, mTOR inhibitors, and RXR-selective retinoids), re-purposed drugs (such as metformin and statin drugs), and vaccines. In addition, novel schedules and formulations are being tested to avoid the toxicity of traditionally used drugs such as tamoxifen and aromatase inhibitors. High-risk individuals who may particularly benefit from preventive therapy include women with premalignant lesions (atypical hyperplasia and lobular carcinoma-in-situ lesions), ductal carcinoma-in-situ breast cancers, or a genetic predisposition to breast cancer. With continued advances in molecularly targeted drug development and improved personalized risk assessment, effective, safe, and acceptable breast cancer preventive strategies will soon be available.

Citation Format: Brown P. ES5-2 Non-endocrine strategies: Beyond the estrogen receptor [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 ES5-2.
Abstract ES7-2: ES7-2 Mechanisms of resistant to therapy in ER positive cancer
Authors: Turner NC
Published: March 2017

Recent years have seen substantial advances in our understanding of ER positive/ HER2 negative breast cancer, both in the genetics of this subtype of breast cancer and the biological processes the drive tumor growth and resistance to therapy. Diverse targetable mutations have been identified in studies of primary breast cancer, along with acquired mutations in the estrogen receptor (ESR1) found in 30% of advanced breast cancers that progress on aromatase inhibitors. The therapeutic significance of this genetic diversity is being explored in ongoing studies. Therapies that target mTOR and CDK4/6 have entered routine clinical practice, demonstrating substantial improvements in progression free survival for patients with advanced cancer. The ongoing challenge is to identify biomarkers of sensitivity, to assist in selecting patients who benefit, and identify mechanisms of resistance to therapy to identify the optimal schedule of therapies and identify novel therapeutic approaches for resistant disease.

Citation Format: Turner NC. ES7-2 Mechanisms of resistant to therapy in ER positive cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr ES7-2.
Abstract OT1-02-01: Phase II neoadjuvant trial of nanoparticle almumin-bound paclitaxel and trastuzumab in patients with node-negative, Her-2 positive breast cancer (OMC-BC04)
Authors: Iwamoto M , Tanaka S , Koda C , Kawaguchi K , Terasawa R , Sato N , Fujioka H , Kimura K , Uchiyama K
Published: March 2017

Background: Neoadjuvant chemotherapy plus trastuzumab results in a 30% to 50% pathologic complete response (pCR) rate in HER-2 positive breast cancer and has been associated with improved therapeutic outcomes. Thus, the pCR rate can be useful in evaluating novel agents in this patient population. Albumin-bound (nab)-paclitaxel can reduce the toxicity of Paclitaxel while maintaining its efficacy. We reported that neoadjuvant therapy using Anthracycline based regimens (EC,AC,FEC) followed by a combination with nab-Paclitaxel and Trastuzumab was effective and safe by OMC-BC01 Study (Tanaka et al. Clin Breast Cancer 15:191-196). The pCR rate was 36% and 71% in the patients with estrogen receptor-positive and negative cancer, respectively. In addition, Tolaney et al. showed that adjuvant Paclitaxel and Trastuzumab for node-negative, HER-2 positive tumors measuring up to 3 cm in greatest dimension was associated with patients outcomes that were better than expected on the basis of historical data (Tolaney et al. N Engl J MED.2015 Jan 8:372(2):134-141). We conducted a clinical Phase II, multicenter, neoadjuvant trial of combination with nanoparticle albumin-bound Paclitaxel and Trastuzumab in patients with node-negative, Her-2 positive, estrogen receptor-negative breast cancer measuring up to 3 cm in greatest dimension.

Patients and Methods: nab-Paclitaxel and Trastuzumab as neoadjuvant therapy in patients with Her-2 positive, node-negative, estrogen receptor-negative breast cancer measuring up to 3 cm in greatest dimension. Patients are treated with neoadjuvant nab-Paclitaxel (260mg/m2) and Trastuzumab q21d x 4, and undergo surgery 4-6 weeks later from completing chemotherapy. The primary endpoint, pCR is defined as no evidence of invasive tumors in the final surgical sample both in the breast and axillary lymph nodes. Secondary endpoints include objective clinical response rate, histological response rate, disease-free interval, rate of breast conserving surgery, and the safety of the treatment.

Accrual: Presently, a total number of 1 patient have been included since start of the study. The expected end of accrual of 30 patients will be the last quarter 2018.

Citation Format: Iwamoto M, Tanaka S, Koda C, Kawaguchi K, Terasawa R, Sato N, Fujioka H, Kimura K, Uchiyama K. Phase II neoadjuvant trial of nanoparticle almumin-bound paclitaxel and trastuzumab in patients with node-negative, Her-2 positive breast cancer (OMC-BC04) [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 OT1-02-01.
Abstract OT3-03-02: Maximising recruitment and retention of patients into UK-ANZ POSNOC trial
Authors: Goyal A , Coleman RE , Dodwell D , Fallowfield L , Jenkins VA , Mann B , Reed MW ,   POSNOC Trial Management Group
Published: March 2017

The success of a clinical trial is often dependant on whether recruitment targets can be met in the required time frame. Surgeons want to gather robust evidence but may experience considerable discomfort in relation to their clinical instincts and concerns about patient eligibility and safety. The ongoing POSNOC study design is pragmatic to maximise recruitment. A patient information DVD is used as an adjunct to patient information leaflet. The protocol allows for either axillary radiotherapy or axillary node clearance. Here we report recruitment and retention of participants into POSNOC, the associated barriers and challenges, and various strategies employed to overcome these barriers.

A total of 368 participants were recruited till May 2016. A total of 90%(331) of participants were recruited via non intra-operative pathway, and 10%(37) from intra-operative pathway. The most common known reasons for non-participation of eligible women were - woman wanting axillary treatment and clinician/MDT deciding woman needs axillary treatment. The mean randomisation yield from screening was 30% (range 6 to 100%). The highest recruiting sites were Derby, Manchester, Oxford, Belfast and Bristol.

The screening logs identified barriers as: fewer than estimated eligible women, clinicians not offering trial to all eligible patients and patient acceptability.

To reach recruitment targets in a timely fashion, a multifaceted approach is being employed. a) Protocol amendments to widen the inclusion criteria, b) 250 patients to be recruited by Australia and New Zealand sites, c) additional 50 sites to be opened in the UK, d) encourage OSNA centres to follow the non intra-operative pathway, e) communication workshops, f) POSNOC poster in breast units to raise awareness, g) questionnaire survey - sites to identify local issues and their perceptions about recruitment, h) social media - POSNOC WhatsApp group i) newsletters and briefings, j) competitions, k) tips to maximise recruitment document that includes a template script of one way to introduce the study l) regional telephone conferences for research nurses, m) investigator meeting.

The success of these strategies remains to be assessed and shall be reported separately.

Citation Format: Goyal A, Coleman RE, Dodwell D, Fallowfield L, Jenkins VA, Mann B, Reed MW, POSNOC Trial Management Group. Maximising recruitment and retention of patients into UK-ANZ POSNOC trial [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 OT3-03-02.
Abstract P1-01-14: Nuclease-activated oligonucleotide probes for detection of breast cancer circulating tumor cells (CTCs): Early clinical results
Authors: Giangrande PH , Kruspe S , Dickey DD , Kamboj S , Clark KC , Urak K , Burghardt E , Smith B , Thomas A , McNamara JO
Published: March 2017

Introduction:

A challenge for CTC-based diagnostic tests has been the development of methods with sufficient sensitivity to detect low levels of CTCs. Expense, accuracy and complexity have also limited clinical uptake of CTCs. To overcome these limitations we explored detecting CTCs by measuring their nuclease activity with nuclease-activated probes. We present the development of a rapid and highly-sensitive CTC detection assay based on probes that are selectively digested (activated) by target nucleases expressed in breast cancer cells.

Methods:

Nuclease activity in samples from women with Stage IV breast cancer and healthy donors was determined and correlated with clinical data. Patients seen at University of Iowa Clincis were eligible for this IRB-approved study. Blood samples were processed using microfilter (ScreenCell) units for CTC enrichment and converted into cell lysates that were examined by means of three different chemically-optimized oligonucleotide probes. CTC-derived nuclease activity was quantified using a fluorometer. The presence of CTCs was confirmed using established CTC detection methods (e.g. RT-PCR, immunohistostaining).

Results:

Sensitivity of the probe assay was 5 cancer cells in buffer solution and ~200 cancer cells in 1 mL of healthy donor blood. The final study cohort included 28 breast cancer patients and 10 healthy donors. The averaged signal intensities from patient samples were significantly higher compared to the healthy donor control group, presumably arising from CTCs in the blood. Statistical analysis further reveald short incubations in the assay (<20 min) to be optimal. From an ROC analysis we obtained AUC values of 0.8821, 0.8103 and 0.9356 for the three different probes. The oligonucleotide probe being the best predictor of disease yielded 100% sensitivity in the patient samples with a specificity of 70%. The dsDNA 20 minute probe was correlated negatively with tumors being ER+/PR+ (p=0.03). The 2'f-RNA 0 minute probe correlated significantly with HER2- tumors (p=0.04). In this smaller series other trends were also suggested.

Conclusion:

We describe a novel diagnostic for the detection of CTCs that could overcome limitations of CTC detection assays and could provide a robust diagnostic tool for breast cancer. Future clinical assays derived from this technology could require minimal training and infrastructure and might be developed into a point-of-care testing format.

Citation Format: Giangrande PH, Kruspe S, Dickey DD, Kamboj S, Clark KC, Urak K, Burghardt E, Smith B, Thomas A, McNamara JO. Nuclease-activated oligonucleotide probes for detection of breast cancer circulating tumor cells (CTCs): Early clinical results [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 P1-01-14.
Abstract P1-01-17: Establishment and preliminary clinical application of breast cancer CTC detection kit based on immune magnetic lipid microsphere/human breast mammaglobin
Authors: Yang B , Wu J , Liang X , Mei S , Zhou B
Published: March 2017

Objective

To explore the effect of breast cancer CTC detection kit based on immune magnetic lipid microsphere (IML) separation and human breast mammaglobin (hMAN) identification, we combined epithelial cell adhesion molecule (EpCAM) IML enrichment and immune fluorescence staining of CK/hMAN (IML/hM-BCD) method.

Methods

74 patients with metastatic breast cancer (MBC) were selected to validate the performance of our integrated CTC capture platform by carrying out side-by-side comparisons with the Cellsearch assay using the same sample. In each study, 15 mL blood was divided equally to identify CTC numbers by employing either Cellsearch and our platform.

Results

In MBC patients, the rates of diagnostic positive detection of Cellsearch and IML/hM-BCD method were 50% and 83.4%, respectively. The IML/hM-BCD method presented a greater ability to capture CTCs from MBC patients. A significant difference in the number (1~5) of CTCs captured by IMLM was observed in the images (2-fold more for IMLM vs CellsearchTM, P<0.001). Furthermore, the morphology and footprint sizes of the cells detected by IML/hM-BCD method offer another approach to validating these observations from the perspectives of cell pathology and cytology. The combined information was utilized to delineate CTCs (DAPI+/CK+/CD45-, cell size > 5 µm) from WBCs (DAPI+/CK-/CD45+, cell size < 15 µm) and cellular debris. Our immunomagnetic lipid microsphere captured significantly different CTC numbers that corresponded to the patients' clinical data.

Conclusions

The panel of IML separation and combined CK/hMAN identification may serve as representative enrichment and biomarkers for CTCs, thus it presents potentially significant valve for monitoring early metastasis, therapeutic efficacy and prognosis for the patients with breast cancer.

Citation Format: Yang B, Wu J, Liang X, Mei S, Zhou B. Establishment and preliminary clinical application of breast cancer CTC detection kit based on immune magnetic lipid microsphere/human breast mammaglobin [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 P1-01-17.
Abstract P1-03-16: Tumor-infiltrating lymphocyte (TIL) assessment distilled into two binary parameters in triple-negative breast cancer (TNBC)
Authors: Cui X , McIntire PJ , Ginter PS , Irshaid L , Chen Z , Shin SJ
Published: March 2017

This abstract was withdrawn by the authors.
Abstract P1-04-05: RNA immunoprecipitation reveals lncRNA-protein interactions in basal-like breast cancer
Authors: Northwood K , Saunus J , Milevskiy M , Lakhani S , Brown M
Published: March 2017

Interactions between long non-coding RNAs (lncRNAs) and proteins contribute to the epigenetic regulation of gene expression, and defects in such interactions have been implicated in several diseases, including cancer. Basal-like breast cancer accounts for approximately 15% of all breast cancer and is a major clinical problem given its poor survival and lack of responsiveness to targeted breast cancer treatments. DNA methylation is non-random and is much more pronounced in basal-like breast cancer (BLBC) compared to other molecular subtypes of breast cancer, raising the possibility that hypermethylation could be important in the genesis of BLBCs. LncRNAs are aberrantly expressed in multiple subtypes of breast cancer, including BLBC, and are considered to have significant prognostic potential. In order to explore the potential roles of DNA methylation and lncRNAs in BLBC, we investigated lncRNA-protein interactions using bioinformatics and molecular techniques, focusing on proteins that actively perform DNA methylation - the DNA methyltransferase (DNMT) family. Our novel bioinformatic methods revealed that BLBC may be sub-classified according to methylation profile in a way that could predict disease survival. We then identified candidate lncRNAs that are over-expressed in BLBC and statistically predicted to interact with DNMT proteins. Using RNA immunoprecipitation of BLBC cell lines, we have identified potential lncRNA-protein interactions that may be involved in epigenetic remodelling in BLBC. The role of these lncRNAs in epigenetic gene regulation and BLBC is currently being explored.

Citation Format: Northwood K, Saunus J, Milevskiy M, Lakhani S, Brown M. RNA immunoprecipitation reveals lncRNA-protein interactions in basal-like breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-04-05.
Abstract P1-05-21: A comparison of oncotype DX recurrence scores in a screen detected vs a symptomatic cohort of patients with breast cancer: A UK experience
Authors: Khawaja S , Parab A , Thomas D , Huws A , Munir A , Udayasankar S , Sharaiha Y , Holt S
Published: March 2017

Background:

In the Western World, it has been stated that breast cancers detected on a screening program are indolent. There have been many recent publications stating that breast screening is overdiagnosing and therefore overtreating patients with breast cancer. With the advent of genomic testing, it can now be determined which patients have an aggressive tumor requiring systemic chemotherapy. We therefore conducted a retrospective study in the UK on patients having oncotype DX testing in both screen detected and symptomatic cancers.

Materials and Methods:

Patients in our institution undergoing oncotype DX testing for invasive breast cancer which was ER positive and node negative were part of this study. The detection of the breast cancer was documented as either a screening case or a symptomatic one. The recurrence scores of the oncotype DX testing was then compared in the screening versus the symptomatic cohort.

Results:

155 patients were included in this study. They underwent Oncotype DX testing between 2008 to 2016. The age of the patients ranged from between 31 years to 78 years. Eighty-nine patients were reported to have a low recurrence score; 45 had an intermediate score; and 21 had a high result. Fifty eight patients were screen detected, while 97 patients were symptomatic presentations. In the screening population, 32 patients had a low recurrence score; 22 had an intermediate result and 4 had a high recurrence score resulting in the latter groups being considered for chemotherapy. In the symptomatic cohort, 57 had a low recurrence score; 23 had an intermediate result; and 17 had a high score.

Conclusion:

The results of our study depict that even patients in a screeining cohort will have a high number of intermediate recurrence scores and some with a high recurrence score. This shows that the hypothesis that screening detects a majority of breast cancers which are indolent not requiring further systemic treatment should be looked at again in light of our results with genomic testing.

Citation Format: Khawaja S, Parab A, Thomas D, Huws A, Munir A, Udayasankar S, Sharaiha Y, Holt S. A comparison of oncotype DX recurrence scores in a screen detected vs a symptomatic cohort of patients with breast cancer: A UK experience [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 P1-05-21.
Abstract P1-05-29: Genomic variants in 5 male breast cancers using whole exome sequencing
Authors: Agrawal V , Zhong M , Huang W , Kewarpu P , Dimitrova N , Fallon JT
Published: March 2017

This abstract was not presented at the symposium.
Abstract P1-05-30: Genomic and microenvironmental intra-tumor heterogeneity in DCIS
Authors: Fortunato A , King L , Mallo D , Kovacheva V , Yuan Y , Boddy A , Graham T , Aktipis A , Mardis ER , Hall A , Marks JR , Hwang S , Maley CC
Published: March 2017

Intra-tumor heterogeneity drives neoplastic progression by supplying the fuel for natural selection among neoplastic cells. It also complicates screening and treatment of neoplasms. We hypothesize that the degree of intra-tumor heterogeneity in DCIS should predict which tumors are likely to become invasive and metastatic. We initiated a pilot project to test this hypothesis by comparing 9 cases of pure DCIS to 9 cases of DCIS with adjacent invasive disease. For each case, we sequenced the exome from two spatially distinct regions of DCIS as well as normal tissue taken from a lymph node with no tumor involvement. This required the development of new methods to extract high quality sequencing data from small amounts of DNA extracted from FFPE samples. We calculated the genetic divergence between the two tumor regions, defined as percent of the sequenced regions of the genome showing differences between the two samples that had sufficient sequencing coverage and quality scores for confident scoring. We also employed automated imaging analysis to score microenvironmental differences between the two tumor regions. These microenvironmental measures are based on ecological methods for measuring organismal interactions and habitats. We will present initial data on differences in phenotypic and genotypic intra-tumor heterogeneity comparing pure DCIS to DCIS associated with invasive breast cancer. Our methods can be readily translated to large tissue banks of FFPE samples from DCIS.

Citation Format: Fortunato A, King L, Mallo D, Kovacheva V, Yuan Y, Boddy A, Graham T, Aktipis A, Mardis ER, Hall A, Marks JR, Hwang S, Maley CC. Genomic and microenvironmental intra-tumor heterogeneity in DCIS [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 P1-05-30.
Abstract P1-06-05: Breast cancer organoid cultures preserve intra-tumor heterogeneity and reveal intrinsically resistant phenotypes to standard chemotherapies
Authors: Sowder ME , Ludwik KA , Pasic L , Brenin DR , Stricker TP , Macara IG , Lannigan DA
Published: March 2017

Breast cancer intra-tumor heterogeneity contributes to chemotherapy resistance and decreased patient survival, yet no reliable in vitro models exist to study this phenomenon. To address this need we developed an in vitro 3D organoid culture system using primary human breast cancer tissue. A major difficulty in the development of such models is to identify robust in vitro conditions that preserve the breast cancer phenotypes observed in situ. To address this challenge we used quantitative immunofluorescence imaging to compare the cellular phenotypes in the starting tumor tissue with those observed in the tumor organoids cultured in 3D. We utilized a clustering algorithm and utility function to quantitatively assess whether tumor organoids generated in vitro faithfully recapitulated intra- and inter-tumor heterogeneity of the tumor tissue in situ. This approach generated a normalized score that reflects tissue-organoid similarity. To test the sensitivity of our method to overall changes in tissue phenotype we focused on three distinct breast cancer subtypes distinguished by expression of estrogen receptor (ER), progesterone receptor (PR) and amplification of ERBB2/HER2 (HER2). Using our approach, we successfully recapitulated the tumor phenotypes present in ER+, ER+/HER2+ and triple negative breast cancer. We discovered that EGF preserves the TNBC phenotype, whereas AREG is required for recapitulating the phenotype of ER+ and ER+/HER2+ breast cancers. Additionally, our data demonstrate that HER1 ligands drive inter- and intra-tumor heterogeneity. To investigate how intra-tumor heterogeneity contributes to therapy responses we treated organoids with standard agents used clinically to treat each of the distinct subtypes. For all tumor subtypes we observed differential vulnerabilities between patients to drug treatments. Importantly, our analysis identified divergent cellular phenotypes that have various sensitivities to chemotherapies. Taken together, our methodology provides an unprecedented view of intra-tumor heterogeneity and allows for the investigation of chemo-resistance mechanisms. Further, this approach will provide a powerful tool, which will enhance the identification of novel therapies and facilitate personalized medicine.

Citation Format: Sowder ME, Ludwik KA, Pasic L, Brenin DR, Stricker TP, Macara IG, Lannigan DA. Breast cancer organoid cultures preserve intra-tumor heterogeneity and reveal intrinsically resistant phenotypes to standard chemotherapies [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 P1-06-05.
Abstract P1-06-06: Evidence for tumor heterogeneity and clonal evolution during invasive progression of breast cancer
Authors: Ding Y , Marks JR , King LM , Hall AH , Mardis ER , Rodrigo AG , Maley CC , Hwang E-S
Published: March 2017

Purpose: Intratumoral heterogeneity is well recognized to be an important driver of treatment resistance and metastasis. We undertook this N of one study to measure the degree of heterogeneity in a single large preinvasive lesion with an invasive component to determine the relationship between tumor heterogeneity, spatial distribution, clonal evolution, and invasive progression.

Methods: We identified a patient with extensive DCIS measuring 7.5 cm, associated with 1.5 cm of an invasive component. We segregated the tumor sample into 32 unique blocks with precise geospatial localization; invasive cancer was identified in 3 of 32 blocks. NGS libraries were made from FFPE derived DNA (20-40ng) for full exome sequencing and hybridization to a 4.8 million element SNP array. All data were analyzed and a phylogentic tree was constructed.

Results: The sequence data was analyzed with Platypus[1] and 3922 somatic mutation sites were found in total. These sites were concatenated into one sequence for each sample. Then a Neighbor-Joining tree was built with a Jukes-Cantor model and 1000 bootstrap replicates using FastME 2.0[2], to assess the reliability of the tree (Figure 1). Phylogenetic analysis revealed that invasive cancer evolved twice, independently. Dense sampling allowed reconstruction of the temporal order of mutations that accumulated in the cell lineage of the invasive cancers. Furthermore, the phylogeny revealed that distant regions may be closely genetically related, the oldest parts of the tumor were in the interior of the tumor, and that the invasive tumors evolved near the oldest parts of the tumor, rather than at the expanding front.

Conclusions: Extensive sampling and sequencing of a single tumor yields important insights about tumor heterogeneity and tumor progression for DCIS to invasive cancer. Foci of invasion were geospatially associated with preinvasive regions of progressively higher mutational load.

1. Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SR, Wilkie AO, McVean G, Lunter G, Consortium W: Integrating mapping-, assembly-and haplotype-based approaches for calling variants in clinical sequencing applications. Nature genetics 2014, 46(8):912-918.

2. Lefort V, Desper R, Gascuel O: FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Molecular biology and evolution 2015:msv150.

Citation Format: Ding Y, Marks JR, King LM, Hall AH, Mardis ER, Rodrigo AG, Maley CC, Hwang E-S. Evidence for tumor heterogeneity and clonal evolution during invasive progression of breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-06.
Abstract P1-08-07: Assessing the impact of loss of NF1 protein on endocrine therapy resistance
Authors: Cakar B , Chan D , Yan P , Zheng Z , Singh P , Lei JT , Haricharan S , Ellis M , Chang E
Published: March 2017

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

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

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

Citation Format: Cakar B, Chan D, Yan P, Zheng Z, Singh P, Lei JT, Haricharan S, Ellis M, Chang E. Assessing the impact of loss of NF1 protein on endocrine therapy resistance [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-08-07.
Abstract P1-10-09: Delineation of internal mammary nodal target volumes in breast cancer radiotherapy
Authors: Jethwa KR , Kahila MM , Hunt KN , Brown LC , Corbin KS , Park SS , Yan ES , Boughey JC , Mutter RW
Published: March 2017

Purpose/Objectives: The optimal clinical target volume (CTV) for internal mammary node irradiation (IMNI) is uncertain in an era of increasingly conformal volume-based treatment planning for breast cancer. We mapped the location of gross internal mammary lymph node (IMN) metastases in order to identify areas at highest risk for harboring occult disease.

Methods and Materials: Patients with axial imaging of IMN disease, including fluorodeoxyglucose F-18 (FDG18) positron emission tomography (PET-CT) and magnetic resonance imaging (MRI), were identified from a breast cancer registry. The IMN location was transferred by a radiation oncologist and breast radiologist onto the corresponding anatomic position on representative axial CT images of a patient in the treatment position. Distribution of lymph nodes, and their location was compared with consensus group guidelines of IMN target delineation.

Results: Sixty-seven patients with 130 IMN metastases were mapped. The location was in the first three intercostal spaces in 102 of 130 (78%) nodal metastases. Eighteen of 130 (14%) IMN were located caudal to the third intercostal space, while 10 of 130 (8%) IMN were located cranial to the first intercostal space, including 3 patients with isolated IMN metastases at that location in the absence of distant disease. Of the 102 nodal metastases within the first three intercostal spaces, 54 (53%) were located within the RTOG consensus volume. Relative to the internal mammary (IM) vessels, 19 (19%) nodal metastases were located medially with a mean distance of 2.2 mm (SD 2.9 mm), while 29 (28%) were located laterally with a mean distance of 3.6 mm (SD 2.5 mm). Ninety and ninety-five percent of lymph nodes within the first three intercostal spaces would have been encompassed within a 4 mm and 6 mm medial and lateral expansion on the IM vessels, respectively.

Conclusions: For women with indications for elective IMNI, a 4 mm medial and lateral expansion on the IM vessels within the first 3 intercostal spaces may be appropriate. In women with known IMN involvement, cranial extension to the confluence of the IM vein with the brachiocephalic vein +/- caudal extension to the 4th or 5th interspace with a 6 mm medial and lateral expansion may be considered, provided that normal tissue constraints are met.

Citation Format: Jethwa KR, Kahila MM, Hunt KN, Brown LC, Corbin KS, Park SS, Yan ES, Boughey JC, Mutter RW. Delineation of internal mammary nodal target volumes in breast cancer radiotherapy [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 P1-10-09.