Breast Cancer Research Community Research Articles

Perimenopausal and Menopausal Mammary Glands In A 4-Vinylcyclohexene Diepoxide Mouse Model

As both perimenopausal and menopausal periods are recognized critical windows of susceptibility for breast carcinogenesis, development of a physiologically relevant model has been warranted. The traditional ovariectomy model causes instant removal of the entire hormonal repertoire produced by the ovary, which does not accurately approximate human natural menopause with gradual transition. Here, we characterized the mammary glands of 4-vinylcyclohexene diepoxide (VCD)-treated animals at different time points, revealing that the model can provide the mammary glands with both perimenopausal and menopausal states. The perimenopausal gland showed moderate regression in ductal structure with no responsiveness to external hormones, while the menopausal gland showed severe regression with hypersensitivity to hormones. Leveraging the findings on the VCD model, effects of a major endocrine disruptor (polybrominated diphenyl ethers, PBDEs) on the mammary gland were examined during and after menopausal transition, with the two exposure modes; low-dose, chronic (environmental) and high-dose, subacute (experimental). All conditions of PBDE exposure did not augment or compromise the macroscopic ductal reorganization resulting from menopausal transition and/or hormonal treatments. Single-cell RNA sequencing revealed that the experimental PBDE exposure during the post-menopausal period caused specific transcriptomic changes in the non-epithelial compartment such as Errfi1 upregulation in fibroblasts. The environmental PBDE exposure resulted in similar transcriptomic changes to a lesser extent. In summary, the VCD mouse model provides both perimenopausal and menopausal windows of susceptibility for the breast cancer research community. PBDEs, including all tested models, may affect the post-menopausal gland including impacts on the non-epithelial compartments.

LAMIS-DMDB: A new full field digital mammography database for breast cancer AI-CAD researches

The current state of machine learning (ML) and deep learning (DL) shows that they are powerful tools that can be used to glean knowledge from a huge amount of data. While a great deal of research in this area has centered around improving the accuracy and efficiency of training and inference algorithms, there has been relatively little attention paid to the equally important problem of monitoring the quality of data. To tackle this challenge, we have created a cutting-edge breast database capable of employing ML and DL algorithms to detect and classify breast cancer. It is noteworthy that compared to other digital mammogram databases (DMDB), the Laboratory of Mathematics, Informatics and System (LAMIS) images have better resolution and are in full-field digital mammography (FFDM) format. Furthermore, the images can be accessed according to their abnormality (normal, benign, malignant), lesions classification (mass, calcification, architectural distortion, multiple finding), American College of Radiology (ACR) density classification (ACR1, ACR2, ACR3, ACR4) and Breast Imaging Reporting and Data System (BI-RADS). Specifically, the database is designed to provide a variety of metadata as well as clinical data in simple comma separated values (CSV) format that can be really beneficial to the breast cancer research community and to the development of computer-aided diagnosis (CADx) tools that rely on artificial intelligence (AI) algorithms, such as those based on DL models.

Abstract A081: Testing the effect of culturally targeted, normative messaging on Black women’s intentions to participate in a breast cancer clinical trial

Abstract Despite increasing disease incidence and remarkably high mortality rates, Black women are underrepresented in breast cancer (BC) clinical trials (CTs), likely limiting the generalizability of BC research findings to Black patients. Evidence demonstrates that the BC research community could exert more effort to ensure the recruitment of Black women into CTs. Although Black and white women have similar BC incidence rates, Black women are 40% more likely than all other races and ethnicities to die of the disease. Clear disparities exist even after controlling for socioeconomic inequalities. Black participation in CTs has been declining, which is particularly unfortunate given the increasing health problem of a lack of Black representation in medical research. Successfully swelling the percentages of Black women who participate in BC research is important and likely reliant on increasing group members’ motivations to surmount existing historical, cultural, and social barriers. Guided by normative and cultural theoretical frameworks, this study examined the effects of culturally informed messaging on Black women’s intention to participate in a preventive BC CT. Six hundred thirty-five Black women aged 18 and over were recruited through Qualtrics to participate in an online, posttest only, control-group design message testing study using random assignment to condition (the control or one of four injunctive-, descriptive-, and/or legacy norm-focused messages). They answered survey questions designed to measure the messages’ effects on the women’s intention to participate in the CT. The study employed univariate and multivariate logistic regression and yielded statistically nonsignificant results; none of the four hypotheses were supported. However, the findings trended overall toward having higher probability of intending to perform the behavior (overall intention M = 3.35). All conditions had means higher than three (out of a five-point scale) and the relatively high resulting intention outcome variables were promising. Important knowledge was gained from this study showing that dissemination of culturally targeted, norms-based messaging to Black women could elicit positive intentions in their willingness to donate healthy breast tissue. The most important implication is that message content is affected by the medium through which it is delivered. Additional implications include the importance of overlaying cultural factors onto normative theories, and that Black women really need culturally aware, norms-focused relational communication to enable an understanding that CT participation is something in which they and others like them have interest and—despite other research that implies otherwise—really want to do, particularly after having been comprehensively informed. Given that previous successful recruitment methods to this CT for this population were grounded in research practices involving face-to-face, interpersonal interactions, future research should consider employing a multi-level approach in testing these messages. Citation Format: Katherine E. Ridley-Merriweather. Testing the effect of culturally targeted, normative messaging on Black women’s intentions to participate in a breast cancer clinical trial [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr A081.

Breast Cancer Brain Metastases: Achilles' Heel in Breast Cancer Patients' Care.

Brain metastases (BM) significantly affect the prognosis as well as the quality of life of breast cancer (BC) patients. Although advancements in neurosurgical and radiotherapy techniques improve local control and symptom management, BM remains associated with a poor prognosis. In addition, the efficacy of currently approved systemic therapies in central nervous system (CNS) compartment is still limited, especially after progression on local therapy. The blood-brain barrier (BBB) has been recognized as amechanism of primary resistance to many chemotherapeutic agents and targeted therapies due to low drug penetration. Other mechanisms of primary and secondary resistance are still unclear and may vary across the BC subtypes. New small molecules have demonstrated efficacy in BM, in particular for the HER2-positive subtype, with a benefit in survival. A new era has begun in the field of BM, and many trials specifically designed for this population are currently ongoing. The BC research community needs to address this call with the final aim of improving the efficacy of systemic therapy in CNS compartment and ultimately preventing the occurrence of BM.

Distribution of breast cancer molecular subtypes within receptor classifications: Lessons from the I-SPY2 Trial and FLEX Registry.

592 Background: Expression-based molecular subtypes of breast cancer (BC) predict tumor behavior and therapeutic response. Subtype distributions by age and sociodemographics can inform strategies for BC screening, treatment, and prognosis. The conventional approach, adopted by NCI’s Surveillance, Epidemiology, and End Results (SEER) Program, uses HR and HER2 to label: “triple negative” (HR-HER2-), “HER2-enriched” (HR-HER2+), “luminal A” (HR+HER2-), and “luminal B” (HR+HER2+). However, immunohistochemical (IHC)-based receptor labels may not reflect clinically and epidemiologically relevant molecular subtypes that share the same nomenclature, e.g., luminal B. Methods: We compared IHC labels by HR/HER2 to molecular subtypes by MammaPrint (MP) and BluePrint (BP) for patients in the phase II neoadjuvant I-SPY2 TRIAL for high-risk, stage II-III BC (NCT01042379, n = 981) and in the multicenter, prospective FLEX Registry for stage I-III BC (NCT03053193, n = 5,679). Results: IHC labels were discordant with MP/BP in 52% of I-SPY2 and 43% of FLEX cases (Table 1). HR-HER2- had the highest concordance with basal-type (99% in I-SPY2, 88% in FLEX). HR+ labels had the least agreement with MP/BP: HR+HER2- tumors were molecularly luminal B and basal in 71% and 29% of I-SPY2 and 40% and 4% of FLEX cases, respectively. HR+HER2+ tumors were molecularly luminal A and HER2-type in 10% and 60% of I-SPY2 and 15% and 36% of FLEX cases, respectively. Of molecularly luminal B cases, only 14% in I-SPY2 and 7% in FLEX were HR+HER2+. Conclusions: IHC markers collected by population-based registries (SEER) enable BC surveillance. However, IHC labels cannot be used as surrogates for molecular subtypes by MP/BP, especially for luminal B tumors. Given the unmet need to improve management of luminal B BC, we anticipate the growing importance of molecular subtyping to inform treatment and epidemiological research. We propose that the BC research community work with SEER to update its IHC labels to avoid overlap with molecular subtype nomenclature and incorporate such modern classifications when available. [Table: see text]

The MCF10 Model of Breast Tumor Progression.

The MCF10 cell lines first described by Soule and colleagues in 1990 have been a great resource for the breast cancer research community, facilitating research on the regulation of normal breast epithelial phenotypes and progressive changes in this regulation during malignancy. Here we review the development of the MCF10 parental and subsequent sublines and highlight a few of the major contributions of MCF10 model systems to breast cancer research.See related article by Soule and colleagues, Cancer Res 1990;50:6075-86.

Breast Cancer Reconstruction: Design Criteria for a Humanized Microphysiological System

International regulatory agencies such as the Food and Drug Administration have mandated that the scientific community develop humanized microphysiological systems (MPS) as an in vitro alternative to animal models in the near future. While the breast cancer research community has long appreciated the importance of three-dimensional growth dynamics in their experimental models, there are remaining obstacles preventing a full conversion to humanized MPS for drug discovery and pathophysiological studies. This perspective evaluates the current status of human tissue-derived cells and scaffolds as building blocks for an "idealized" breast cancer MPS based on bioengineering design principles. It considers the utility of adipose tissue as a potential source of endothelial, lymphohematopoietic, and stromal cells for the support of breast cancer epithelial cells. The relative merits of potential MPS scaffolds derived from adipose tissue, blood components, and synthetic biomaterials is evaluated relative to the current "gold standard" material, Matrigel, a murine chondrosarcoma-derived basement membrane-enriched hydrogel. The advantages and limitations of a humanized breast cancer MPS are discussed in the context of in-process and destructive read-out assays. Impact statement Regulatory authorities have highlighted microphysiological systems as an emerging tool in breast cancer research. This has been led by calls for more predictive human models and reduced animal experimentation. This perspective describes how human-derived cells, extracellular matrices, and hydrogels will provide the building blocks to create breast cancer models that accurately reflect diversity at multiple levels, that is, patient ethnicity, pathophysiology, and metabolic status.

Breast cancer biobank from a single institutional cohort in an urban setting in india: Tumor characteristics and survival outcomes

A breast cancer biobank with retrospectively collected patient data and FFPE tissue samples was established in 2018 at Prashanti Cancer Care Mission, Pune, India. It runs a cancer care clinic with support from a single surgeon's breast cancer practice. The clinical data and tissue sample collection is undertaken with appropriate patient consent following ethical approval and guidelines. The biobank holds clinical history, diagnostic reports, treatment and follow-up information along with FFPE tumor tissue specimens, adjacent normal and, in few cases, contralateral normal breast tissue. Detailed family history and germline mutational profiles of eligible and consenting patients and their relatives are also deposited in the biobank. Here, we report the first audit of the biobank. A total number of 994 patients with breast disease have deposited consented clinical records in the biobank. The majority of the records (80%, n=799) are of patients with infiltrating ductal carcinoma (IDC). Of 799 IDC patients, 434 (55%) have deposited tumor tissue in the biobank with consent. In addition, germline mutation profiles of 84 patients and their family members are deposited. Follow-up information is available for 85% of the 434 IDC patients with an average follow-up of 3 years. The biobank has aided the initiation of translational research at our center in collaboration with eminent institutes like IISER Pune and SJRI Bangalore to evaluate profiles of breast cancer in an Indian cohort. The biobank will be a valuable resource to the breast cancer research community, especially to understand South Asian profiles of breast cancer.

Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures.

Invasive lobular carcinoma (ILC) is the second most common subtype of breast cancer following invasive ductal carcinoma (IDC) and characterized by the loss of E-cadherin-mediated adherens junctions. Despite displaying unique histologic and clinical features, ILC still remains a chronically understudied disease, with limited knowledge gleaned from available laboratory research models. Here we report a comprehensive 2D and 3D phenotypic characterization of four estrogen receptor-positive human ILC cell lines: MDA-MB-134, SUM44, MDA-MB-330, and BCK4. Compared with the IDC cell lines MCF7, T47D, and MDA-MB-231, ultra-low attachment culture conditions revealed remarkable anchorage independence unique to ILC cells, a feature not evident in soft-agar gels. Three-dimensional Collagen I and Matrigel culture indicated a generally loose morphology for ILC cell lines, which exhibited differing preferences for adhesion to extracellular matrix proteins in 2D. Furthermore, ILC cells were limited in their ability to migrate and invade in wound-scratch and transwell assays, with the exception of haptotaxis to Collagen I. Transcriptional comparison of these cell lines confirmed the decreased cell proliferation and E-cadherin-mediated intercellular junctions in ILC while uncovering the induction of novel pathways related to cyclic nucleotide phosphodiesterase activity, ion channels, drug metabolism, and alternative cell adhesion molecules such as N-cadherin, some of which were differentially regulated in ILC versus IDC tumors. Altogether, these studies provide an invaluable resource for the breast cancer research community and facilitate further functional discoveries toward understanding ILC, identifying novel drug targets, and ultimately improving the outcome of patients with ILC.Significance: These findings provide the breast cancer research community with a comprehensive assessment of human invasive lobular carcinoma (ILC) cell line signaling and behavior in various culture conditions, aiding future endeavors to develop therapies and to ultimately improve survival in patients with ILC. Cancer Res; 78(21); 6209-22. ©2018 AACR.

Normal Breast-Derived Epithelial Cells with Luminal and Intrinsic Subtype-Enriched Gene Expression Document Interindividual Differences in Their Differentiation Cascade.

Cell-type origin is one of the factors that determine molecular features of tumors, but resources to validate this concept are scarce because of technical difficulties in propagating major cell types of adult organs. Previous attempts to generate such resources to study breast cancer have yielded predominantly basal-type cell lines. We have created a panel of immortalized cell lines from core breast biopsies of ancestry-mapped healthy women that form ductal structures similar to normal breast in 3D cultures and expressed markers of major cell types, including the luminal-differentiated cell-enriched ERα-FOXA1-GATA3 transcription factor network. We have also created cell lines from PROCR (CD201)+/EpCAM- cells that are likely the "normal" counterpart of the claudin-low subtype of breast cancers. RNA-seq and PAM50-intrinsic subtype clustering identified these cell lines as the "normal" counterparts of luminal A, basal, and normal-like subtypes and validated via immunostaining with basal-enriched KRT14 and luminal-enriched KRT19. We further characterized these cell lines by flow cytometry for distribution patterns of stem/basal, luminal-progenitor, mature/differentiated, multipotent PROCR+ cells, and organogenesis-enriched epithelial/mesenchymal hybrid cells using CD44/CD24, CD49f/EpCAM, CD271/EpCAM, CD201/EpCAM, and ALDEFLUOR assays and E-cadherin/vimentin double staining. These cell lines showed interindividual heterogeneity in stemness/differentiation capabilities and baseline activity of signaling molecules such as NF-κB, AKT2, pERK, and BRD4. These resources can be used to test the emerging concept that genetic variations in regulatory regions contribute to widespread differences in gene expression in "normal" conditions among the general population and can delineate the impact of cell-type origin on tumor progression.Significance: In addition to providing a valuable resource for the breast cancer research community to investigate cell-type origin of different subtypes of breast cancer, this study highlights interindividual differences in normal breast, emphasizing the need to use "normal" cells from multiple sources as controls to decipher the effects of cancer-specific genomic aberrations. Cancer Res; 78(17); 5107-23. ©2018 AACR.

Abstract P5-10-01: Patient advocates as partners in breast cancer research at Georgetown University Lombardi Comprehensive Cancer Center

Abstract The integration of patient advocate input into biomedical research grant proposals is a relatively new phenomenon and represents a paradigm shift for basic, translational and clinical researchers seeking funding for their proposed studies. In 2011, the Lombardi Comprehensive Cancer Center (LCCC) at Georgetown University (GU) established the Georgetown Breast Cancer Advocates (GBCA) to facilitate collaboration between researchers and advocates. The mission of GBCA is to ensure research is patient-centered, innovative, evidence-based, and accessible. Working with researchers and clinicians at GU-LCCC early in proposal development, the members of the GBCA evaluate the feasibility of research, emphasizing the need for bench-to-bedside studies, the importance of quality of life, health care disparities and a reduction in breast cancer mortality. This integrated and early approach has resulted in GU-LCCC researchers being awarded a PCORI Grant, a DOD Idea Expansion Award, and a prestigious NIH U01 award. The GBCA consists of survivors and community stakeholders from diverse ethnic, racial, and age groups. It ranges from women at high risk for breast cancer to both short- and long-term survivors of various sub-types of breast cancer and those with recurrent disease. Several advocates were trained by the National Breast Cancer Coalition's scientific education program, Project LEAD, and others participate in the Susan G. Komen for the Cure Advocates in Science Program. Members have served as consumer reviewers for the DOD's Breast Cancer Research Program at both the peer review and programmatic review levels, and as patient representatives on American Society of Clinical Oncology (ASCO) clinical practice guideline panels. GU-LCCC researchers and oncologists serve as advisors for the group. This poster describes the evolution and work of the GBCA and how the group has influenced breast cancer research at GU-LCCC. GBCA works with researchers in the pre-award phase, providing input to investigators regarding methodologies to increase participant recruitment, retention, and adherence to research protocols. The advocates also provide input on study designs and patient education strategies. Through their contributions, the advocates have become an integral and respected part of the breast cancer research community at GU-LCCC. Citation Format: Brundage S, Charles Chisholm D, Holloway JN, Lucas W, Salamone J, Winarsky S, London M, Greenwood N, Stahl S, Carbine N, Goyes R, Price E, Ernst E, Leventhal K-G, Isaacs C, Clarke R, Shajahan-Haq AN. Patient advocates as partners in breast cancer research at Georgetown University Lombardi Comprehensive Cancer Center. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-10-01.

Disparities in breast cancer care and research: report from a Breast Cancer Research Foundation sponsored workshop, 9-10 October 2014.

The purpose of this workshop was to bring together diverse stakeholders from the breast cancer research community to discuss critical issues related to disparities in breast cancer care and to identify potential strategies for reducing disparities and inequities in care through research. The workshop format included a series of formal content presentations, participation in break out groups that focused on specific topics highlighted in the content presentations, reporting back of findings and a facilitated discussion that focused on shaping a research agenda. The workshop members concluded that numerous groups of women are at increased risk for disparities in breast cancer care: many patients and survivors suffer disproportionately from inadequate access to high-quality diagnosis and treatment, resulting in more frequent and severe adverse outcomes from the disease. Research on breast cancer disparities provides a major opportunity for reducing the burden of breast cancer. Thus, it is important for the Breast Cancer Research Foundation and other research funders to consider how to best promote research focused on ensuring breast cancer health equity.

Abstract P4-19-02: Early experience of patient donation and researcher use of tissues donated to a national breast cancer tissue bank

Abstract The need for a specialist breast cancer biobank was recognised through a Gap Analysis conducted by the UK charity, Breast Cancer Campaign (Thompson AM et al., Breast Cancer Res 2008: 10(2); R26). As a result The Breast Cancer Campaign Tissue Bank (www.breastcancertissuebank.org) was launched in 2010 as a coalition of 4 centres of excellence for breast cancer research in the UK. Breast cancer patients presenting to these centres are offered the opportunity to donate surplus tissue and bloods to The Breast Cancer Campaign Tissue Bank. Researchers can apply for these samples by completing a simple on line application form. Here we describe our early experience of patient donation to The Breast Cancer Campaign Tissue Bank and outline the sample requests received from researchers to date. Most of the first year of operation (2010) was spent developing SOPs and ensuring collection protocols were robust, with some limited prospective collection. The collection was pump-primed from existing resources. By 2011 all sites were operational and working to the same standards. Over a 2 year period (Jan 2011 - Dec 2012), over 90% of suitable patients (1803) consented to tissue donation. From these we derived 3951 frozen tissue aliquots, 1517 formalin-fixed paraffin-embedded cases and 2012 blood derivatives (serum, plasma and whole blood). Asian patients were less likely to consent while younger patients tended not to donate blood, but were happy to donate tissue. All male patients consented to tissue and blood donation. At Dec 2012, the total numbers of sample aliquots derived from these donated tissue and blood samples was 22, 127. This includes frozen and formalin-fixed paraffin-embedded tissues, serum, plasma and whole blood. At present, application for tissue samples is restricted to the UK and Ireland but we aim to open to international applications in the near future. All applications are reviewed by an international Tissue Access Committee which includes appropriate clinical and scientific expertise plus representation by patient advocates. At 1st June 2013, seventeen applications had been received, of which 14 were approved. Three applications were rejected, made on the basis that the applicants were not making the best use of the donated material. Thus far, tissues have been dispatched to 9 researchers with 5 in preparation. These include 465 formalin-fixed paraffin-embedded cases and 158 frozen samples, all provided with a basic minimum dataset. Early experience of patient consent was encouraging with patients overall very enthusiastic and willing to donate to our biobanking programme. More research is needed to help understand the barriers in preventing ethnic minorities to donate and the reluctance in some young people to donate blood samples. Interest by the breast cancer research community in accessing samples is steadily rising as the resource becomes more widely known and increased website traffic is translating into applications for tissues. This has been an ambitious multidisciplinary endeavour but we are building a valuable resource to service the needs of the breast cancer research community with the goal of helping translate laboratory results into clinical benefit. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-19-02.

ROCK: a resource for integrative breast cancer data analysis

Given the steady increase in breast cancer rates in both the developed and developing world, there has been a concerted research effort undertaken worldwide to understand the molecular mechanisms underpinning the disease. The data generated from numerous clinical trials and experimental studies shed light on different aspects of the disease. We present a new version of the ROCK database (rock.icr.ac.uk), which integrates such diverse data types allowing unique analyses of published breast cancer experimental data. We have added several new data types and analysis modules to ROCK, which allow the user to interactively query and research the huge amounts of available experimental data and perform complex correlations across studies and data types such as gene expression, genomic copy number aberrations, micro RNA expression, RNA interference, survival analysis, clinical annotation and signalling protein networks. We present the recent and major functional updates and enhancements to the ROCK resource, including new analysis modules and microRNA and NGS data integration, and illustrate how ROCK can be used to confirm known experimental results as well as generate novel leads and new experimental hypotheses using the Wnt signalling cell surface receptor FZD7 and the Myc oncogene. ROCK provides a unique breast cancer analysis platform of integrated experimental datasets at the genomic, transcriptomic and proteomic level. This paper presents how ROCK has transitioned from being simply a database to an interactive resource useful to the broader breast cancer research community in our effort to facilitate research into the underlying molecular mechanisms of breast cancer.

Abstract 800: Simultaneous methylation and mutational analysis of breast cancer genomes using droplet-based targeted sequencing.

Abstract Targeted sequencing using droplet-based PCR provides an established method to selectively and uniformly amplify thousands of genomic regions of interest for deep, cost-effective next generation sequencing. Recently, this approach has been adapted for the analysis of bisulfite-treated DNA, enabling both quantitative epigenomic analysis (strand-specific determination of cytosine methylation status with single-base pair resolution) and genomic mutation detection. Simultaneous collection of both methylation and genomic aberration information with a single method makes efficient use of precious clinical material and allows both researchers and clinicians to use this information to sub-type cancers. Here we report on our sequencing results using a single breast cancer targeted panel for sequence specific analysis of both epigenomic methylation and genomic mutation in breast tumor samples. The Breast Cancer MethylSeq Panel includes PCR primer pairs designed to amplify 1000 targets, leaving room for an additional 3000 target loci of interest to be added by individual researchers in the future. This single panel provides information about both loci-specific CpG methylation and genomic mutations, enabling analysis of multiple content types including: A) cell subtype (CELL); B) genomic mutation (MUT); C) surrogate gene expression subtypes using promoter CpG islands or other methylation marks (EXP); D) copy-number variation (CNV); E) Loss of Heterozygosity (LOH); and F) methylation-mediated gene silencing and loss of imprinting (IMP). In addition, miRNA associated with breast cancer will be targeted for analysis (MIR). The Breast Cancer MethylSeq Panel was tested and validated with a set of 64 bisulfite-converted DNA samples that included breast cancer cell lines, a range of ER positive and negative tumors and TCGA samples, and a set of 8 metastatic tumors from a single individual. Overall Illumina HiSeq sequencing success metrics, concordance with metadata on the various target classes (A-F above) using validated controls, and results from the patient samples will be presented. The Breast Cancer MethylSeq Panel allows simultaneous analysis of epigenomic and genomic sequence alterations associated with breast tumor samples, enabling tumor sub-typing and correlation with clinical outcomes. This ‘core’ panel provides a unique (expandable) screening tool for the breast cancer research community, and a paradigm for efficient analysis of multiple endpoints from a single assay for other diseases. Citation Format: Michael L. Samuels, Matt Roth, Preethi Srinivasan, Kevin Riehle, Adam Brufsky, Ryan Hartmaier, David Boone, R. Alan Harris, Chia-Chin Wu, Steffi Oesterreich, Adrian Lee, Aleksandar Milosavljevic. Simultaneous methylation and mutational analysis of breast cancer genomes using droplet-based targeted sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 800. doi:10.1158/1538-7445.AM2013-800

Abstract PL01-04: Stress and the social environment: Impact on cancer risk

Abstract The breast cancer research community has long considered the impact of exogenous estrogen exposure, nutrition, alcohol consumption, and exercise on breast cancer biology. More recently, experimental studies of exposure to chronic stressors in the social environment and the resulting stress response have suggested that epinephrine- and glucocorticoid-mediated signaling pathways might potentiate breast cancer growth both at primary and metastatic tumor sites. To study this hypothesis in more detail, we initiated a transdisciplinary study of a well-established social stressor for female rodents- chronic social isolation. We found that exposing a young female rodent to chronic socially isolation for 12 weeks (compared to group living/social interaction with three other female mice) was associated with increased mammary tumor growth in genetically predisposed rodents. For example, in the C3(1)/SV40 T-antigen (Tag) FVB/N mouse model of “triple-negative” (ER,PR and ErbB-negative breast cancer) the heightened stress response elicited by chronic social isolation was associated with increased expression of metabolic genes in the mammary gland before invasive tumors develop (i.e. during the in situ carcinoma stage when the animals are 15 weeks of age). This suggested that metabolic changes within the mammary gland could affect breast cancer biology. To further understand how accelerated mammary tumor growth may be associated with the physiological response to social isolation, we separated the mammary gland adipose tissue from its adjacent ductal epithelial cells and then analyzed individual cell types for changes in metabolic gene expression. We found that the major increase in expression of the key metabolic genes Acaca, Hk2 and Acly was primarily in the adipocyte (fat cell) fraction of the mammary gland. In contrast, metabolic gene expression was not significantly increased in visceral or gonadal adipose depots of socially isolated female mice, suggesting that the stress response affects individual fat depots differently in this model. We confirmed that the increased metabolic gene expression in the mammary adipocytes of socially isolated mice coincided with increased glucose metabolism, lipid synthesis, and local leptin production; interestingly, systemic leptin levels were not significantly altered. Furthermore, compared to the group housed mammary fat, application of media that had been cultured with isolated mouse mammary adipose tissue resulted in relatively increased proliferation of mammary cancer cells. These results suggest that the physiological response to a chronic social stressor (isolation) results in metabolic changes in mammary gland adipocytes that in turn contribute to increased proliferation of pre-invasive malignant epithelial cells. Adipocyte-secreted metabolites and/or tumor growth-promoting proteins could identify biomarkers and/or targets for preventive intervention in breast cancer. We are currently examining the mammary fat of the isolated versus group-housed mice to identify differential production of adipokines and lipid species that may influence early breast cancer growth in this model. Citation Format: Suzanne Conzen. Stress and the social environment: Impact on cancer risk. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr PL01-04.

P5-21-03: The Breast Cancer Campaign Tissue Bank.

Abstract The breast cancer research community has recognised that access to a source of carefully collected well-annotated human breast tissue is essential for translational research. Research institutions often face barriers in gaining access to this resource as collections typically have restrictive access policies or an over burdensome application process. This was formally recognised by around 50 prominent breast cancer researchers through a Gap Analysis conducted in London, UK in 20061. As a direct result of this report, 4 leading UK centres (Barts Cancer Institute, the Universities of Dundee, Leeds and Nottingham) with multi disciplinary expertise in pathology, basic science, bioinformatics and computer science have collaborated with a leading breast cancer charity to form the Breast Cancer Campaign Tissue Bank (BCCTB; http://www.breastcancercampaigntissuebank.org). BCCTB is a unique resource of biological materials and supportive clinical data, efficiently and ethically collected from patients with breast cancer, to provide researchers with high quality, relevant materials, helping to raise the standard of breast cancer research and facilitating the co-ordinated translation of scientific findings into the clinical setting. A wide range of biological materials are banked, including fresh frozen tumour and surrounding tissue, isolated purified cell populations (which can be provided for culture or DNA/RNA/protein extraction), whole blood and serum samples, as well as formalin-fixed paraffin-embedded material. Specialised collections are also available through the Bank on a collaborative basis. BCCTB has a centralised IT system allowing efficient tracking of samples and recording of raw data from studies, and providing a user-friendly web-based search portal to view material available. A purpose-built Bioinformatics platform allows mining breast cancer literature data from multiple sources and integrating different types of -omics and clinical data alongside publically relevant annotations from a growing number of biological resources such as NCBI, Ensembl, UniProt and Reactome. This platform is also fully interoperable with the International Cancer Genome Consortium (ICGC) and can be automatically cross-queried from the ICGC data portal which allows direct cross-comparison of experimental findings generated from the ICGC breast cancer projects with literature-derived information stored in our portal. Together this results in the highly efficient and co-ordinated use of samples, reducing duplication of effort and facilitating data mining and analysis. As science is constantly evolving we have an inbuilt R&D program, including cell immortalisation, investigating improved sample storage and collection methods and on-going IT development, all of which will ensure the bank remains cutting-edge. Tissue is released following review by a Tissue Access Committee comprising clinical and non-clinical breast cancer researchers and patient advocates. Direct interaction with end users ensures the materials and data supplied meets the researcher needs. Currently BCCTB is accepting applications from UK based researchers with projects funded by Breast Cancer Campaign. It will launch to the wider breast cancer community in the next 18 months. 1Thompson A et al., Breast Cancer Research 2008, 10:R26. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-21-03.

Breast Cancer Research– the first ten years

Breast Cancer Research was launched in 1999 with the aim of providing a home for translational research in breast cancer [1]. The field of translational research has advanced considerably over the past ten years, and the journal has evolved over this time to meet the changing needs of the breast cancer research community. As we celebrate Breast Cancer Research's 10th birthday, we take this opportunity to reflect on the journal's growth over the last decade. Breast Cancer Research is committed to open access publication of research articles, and remains the only journal in the breast cancer field dedicated to open access. Open access means research is universally and freely available via the Internet. Authors retain their own copyright, allowing them to grant any third party the right to use, reproduce and disseminate the article. Open access has broad benefits both for scientists and the general public. Anyone with an Internet connection is able to read the research for free without having to rely on access to a library with a subscription. For example, the 2006 paper by Scutt et al. [2] received wide coverage [3] and was instantly available for any interested patients or clinicians – something that is much more difficult for articles published in subscription based journals. Over the last ten years, there have been massive leaps forward in open access publishing. Many more journals now offer open access options, and there is more support for this publishing model within the scientific community. In particular, many funders now advocate open access by making it a condition of funding that a version of the accepted article is made available in a public repository such as PubMed Central. A recent exciting development has been the announcement of the National Institutes of Health (NIH) Public Access Policy [4], which comes into place in April this year. Open access allows our research to be accessible to a vast potential audience, with over 80,000 articles downloaded from our website every month. Indeed, our most highly accessed article from Arpino and colleagues [5] has been downloaded over 35,000 times since publication. Our highly visible research is complemented by educational reviews and timely opinion pieces. The type of articles published has changed over the years, expanding in 2003 to encompass endocrinology [6], and adding new sections such as clinical trial updates [7]. Breast Cancer Research has always aimed to make the most of the advantages available online over the traditional print format, and in 2005 the print version of the journal was discontinued. This reflects a general publishing trend away from print in the way readers now find articles of interest. The journal's online functionality means you can search PubMed or Google Scholar for related articles, post and read comments, email articles to colleagues and even post articles directly to social networking sites such as Facebook. In the pipeline are online tools for our referees, and a revamped design for the homepage, which will give the website a cleaner, easy-to-navigate new look. In addition to developing online functionality, the journal has always strived to provide access to the latest research as quickly as possible. Our average time from submission to giving authors a first decision is less than 6 weeks, and for the past year we have published all research articles as soon as they are accepted. Articles now have their final citation and are listed in PubMed on the day they are accepted – a service unique to Breast Cancer Research amongst our competitor breast cancer journals. All our research articles are immediately archived in repositories such as PubMed Central to ensure that our articles will be permanently available. Of course, one measure of a journal's success that is highly valued amongst our authors and readers is that of the Impact Factor. Breast Cancer Research currently has an impact factor of 4.16, ranking us the second most cited breast cancer journal, according to the 2006 Journal Citation Report [8]. Breast Cancer Research also compares very favourably using the new SCImago Journal Rank [9]. SCImago takes into account the citation record of the journal you are being cited by and ranks Breast Cancer Research 26th out of all 139 oncology journals, an impressive placing for a niche journal. Breast Cancer Research has had a very impressive first ten years. As we celebrate the journal's continued growth, we would like to thank our Editorial Board for their ongoing support, as well as our authors and reviewers who all contribute to the journal's success. We hope to continue to evolve, and look forward to the journal's progress over the next decade!

A Bayesian derived network of breast pathology co-occurrence

In this paper, we present the validation and verification of a machine-learning based Bayesian network of breast pathology co-occurrence. The present/not present occurrences of 29 common breast pathologies from 1631 pathology reports were used to build the network. All pathology reports were developed by a single pathologist. The resulting network has 25 diagnosis nodes interconnected by 40 arcs. Each arc represents a predicted co-occurrence or null co-occurrence. Model verification involved assessing the robustness of the original network structure after random exclusion of 25%, 50%, and 75% of the pathology report dataset. The structure of the network appears stable as random removal of 75% of the records in the original dataset leaves 81% of the original network intact. Model validation was primarily assessed by review of the breast pathology literature for each arc in the network. Almost all network identified co-occurrences (95%) have been published in the breast pathology literature or were verified by expert opinion. In conclusion, the Bayesian network of breast pathology co-occurrence presented here is both robust with respect to incomplete data and validated by consistency with the breast pathology literature and by expert opinion. Further, the ability to utilize a specific pathology observation to predict multiple co-current pathologies enables exploration of pathology co-occurrence patterns in an intuitive manner that may have broader application in both the breast pathologist clinical community and the breast cancer research community.

In Search of Breast Cancer Culprits: Suspecting the Suspected and the Unsuspected

I would like to welcome breast cancer research community to the first editorial of our newest journal “Breast Cancer: Basic and Clinical Research”. In pursuit of breast cancer culprits, we have come a long way since the early 90's when the first breast cancer susceptibility gene BRCA1 was mapped and cloned. In the past few years, several new loci associated with the various degree of breast cancer risk have been identified using “Candidate Gene Association Study (CGAS) and Genome-Wide Association Study (GWAS)” approaches. This editorial is meant to quickly glance over recent findings of these population-based association studies.