bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract P4-01-15: A high-throughput three-dimensional cell migration assay (BiO assay) for toxicity screening for breast cancer applications
Authors: Tseng H , Sabino LG , Haisler WL , Gage JA , Neeley SK , Souza GR 
Published: August 2014

Abstract
Common in vitro assays for drug toxicity screening are not accurate predictors of human in vivo toxicity as they are performed on two-dimensional (2D) surfaces that do not mimic native cellular environments. Three-dimensional (3D) cell culture systems, like magnetic levitation, offer representative culture environments, with spatial control to design assays for drug toxicity applications. In this study, a label-free 3D in vitro assay for high-throughput toxicity screening (BiO Assay) of breast cancer cells was developed.
Confluent flasks of cancerous and non-cancerous mammary gland epithelial cells (MDA-231 and MCF-10A) were incubated overnight with a magnetic nanoparticle assembly, to which they bind. The next day, these cells were detached from the flask, and with the external application of a magnetic field, levitated to the air-liquid interface, where cells aggregated and interact to form larger 3D structures. These 3D structures were levitated for 24 hours to induce extracellular matrix formation. Afterwards, the structures were mechanically disrupted and patterned into rings using ring-shaped magnets. The magnetic field was removed, drugs, like doxorubicin, were added at varying concentrations, and the rings were allowed to close. This assay was validated against a 2D viability assay. A mobile device was programmed to capture the rings at specified timepoints, and image analysis was performed to track ring closure as a function of drug concentration and time.
MDA-231s and MCF10As were successfully formed into 3D cultures using magnetic levitation, and patterned into rings. We found significantly different results in drug sensitivity between cells grown in 2D and 3D. In conclusion, the BiO Assay is a simple assay that measures drug toxicity in a culture system similar to the native cellular environment.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-01-15.
Abstract P4-01-22: Measurement of tumour lesion glycolysis by FDG-PET in triple negative breast cancer
Authors: Antony Tharayil I , Harada N , Patel N , Varghese V , Kenny L 
Published: August 2014

Abstract
Background:
Triple negative breast cancer (TNBC) has been associated with a high glycolytic rate. As a surrogate measure, the SUV of FDG uptake is found to be higher both in the TNBC and her2 positive phenotypes. Tumour lesion glycolysis (TLG) is a product of the mean SUV value and tumour volume. We wished to evaluate the role of combined volume and metabolic measurements of glycolysis in patients with TNBC.
Methods: 300 FDG-PET scans were performed in patients with breast cancer, of whom 25 were found to have TNBC over a 4 year period, in 19 patients there were suitable lesions identified for analysis. Patients were scanned on the same Siemens PET/CT scanner in the local hospital, static images were acquired 60 minutes post-injection. SUV was corrected for injected activity and body weight, TLGMAX50 was also calculated considering SUV50 isocontour instead of SUV mean. ∑TLG was the sum of TLG for an individual patient.
Results: 117 lesions in total from 19 different patients were analyzed (mean = 6.15 lesions per patient). SUVMEAN, TLG mean, SUVMAX and TLGMAX were calculated for each lesion. SUVMEAN per patient varied from 2.69 to 15.48 while SUV50 varied from 5.45 to 48.23. ∑TLGMEAN and ∑TLGMAX ranged from 13.06 to 364.072 and 18.29 to 575.627, respectively. There was significant variation between patients and within different tumor lesions within patients. SUVPEAK for all lesions of patients ranged from 4.8 to 36.4.
Conclusions: TLG varies widely in patients with triple negative breast cancer, further studies are required to determine if this will be a useful prognostic/predictive measure in the future.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-01-22.
Abstract P4-01-24: Positron emission mammography (PEM) does increase specificity in diagnosis of breast cancer
Authors: Müller FHH , Hentschel M , Müller AG , Farahati J 
Published: August 2014

Abstract
Purpose:
To determine the diagnostic performance of PEM, a HR-PET with intrinsic resolution of 1.6 mm in detection of breast cancer (B-Ca).
Methods and Material:
PEM was performed in 122 lesions with suspicious breast lesions 90 min after i.v. application of 3.5 MBq F-18-FDG per KG body weight. A ROI marked the target lesion, measured the maximum PEM uptake value (PUVmax) and was correlated with a corresponding non-target ROI in the contra lateral healthy breast determining the target/non-target ratio. Two independent readers analysed images of all 122 lesions and compared the results to histopathology (11 PEM-Biopsies/8 Breast-Cancers) later. The group analyses for all malignant, benign, corresponding non-target lesions and the mean target/non-target ratio were calculated by paired Student t-Test.
Results:
22 out of 122 lesions were malignant. Mean of PUVmax was measured 4.3±2,7 in malignant lesions and 1.1±0.4 for the contra-lateral healthy breast (p = 0.001). The mean target/non-target ratio in patients with B-Ca of 3.7±1.5 was also significantly higher compared to benign lesions 1.1±0.4 (p = 0.001).
Considering a PUVmax &gt;1.9, PEM was true-positive in all 22 cancers resulting in a sensitivity of 100%, specificity of 97%, PPV of 88% and NPV of 100%.
Detecting of B-Ca by PEM was at it´s best observed with a PUVmax cut-off level of &gt;1.9 combined with a target/non-target ratio of &gt;1.4.
Conclusion:
PEM can detect breast cancer with high accuracy using PUVmax as well as target/non-target ratio with high specificity. The results shown have to be confirmed in larger patient cohort. The higher specificity causes a lower rate of biopsies, surgery, chemotherapy and costs, therefore a evidence based medicine study will start in Germany.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-01-24.
Abstract P4-03-03: Determination of lymph node status using the primary tumor’s gene expression signature
Authors: Gyorffy B , Sztupinszki Z , Weltz B , Chen S-C , Quay S 
Published: August 2014

Abstract
Introduction:Lymph node status is one of the most important clinical parameters of breast cancer. Axillary lymph node dissection and sentinel lymph node biopsy have considerable morbidity associated with them and a method to accurately predict lymph node positivity would be clinically useful. To date, no gene expression signature has been established that is capable ofestimatin lymph node positivity. Our aim was to develop a new predictor using a large set of patient samples and compare its performance to known clinical variables.
Methods: An integrated database was constructed using publicly available Affymetrix microarrays with known lymph node status. The patients were divided into the four molecular subtypes of basal, luminal A, luminal B and HER2 positive using the St. Gallen criteria and the gene chip based gene expression data of estrogen receptor, HER2 receptor and MKI67. ROC analysis was performed for each gene within each subtype. Then, the top 10 genes of each list were combined, and using the expression data of these 40 genes across all patients, Manhattan or Euclidean distanceswere computed to calculate the distance between each sample. All the patients were ranked, and lymph node status was defined by using the proportional lymph node positivity of “x” nearest ranked patients. Multiple regression was performed to compare the classification using the gene expression data to known clinical variables. Statistical significance was set at p&lt;0.01.
Results: The database includes 2756 patients, of whom 983 are lymph node positive. To optimize the classification, different number of genes (all/top100/top40) and different number of closest patients (x = 1/2/5/10/25/25/100/250/500) and two different distance metrics (Euclidean and Manhattan distance) were assessed. The best performance was achieved using the top40 genes with Manhattan distance to the 100 nearest patients. This setting reached a sensitivity of 0.70, specificity of 0.73 and accuracy of 0.72 across all patients. When compared to ESR1 status, HER2 status, MKI67 expression, grade, size, and agein the multiple regression, only the gene-expression based classification (1.56E-31) and size (1.7E-24) were significant.
Discussion:We have established a pipeline capable of determining lymph node positivity using the gene expression data of 40 genes.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-03-03.
Abstract P4-03-09: Time points to diagnosis and treatment of invasive breast cancer in southwestern Ontario
Authors: Vandenberg TA , Ballantyne B , Diaz Rodriguez LA , Whiston FJ , Stitt LW 
Published: August 2014

Abstract
Background Delays in breast cancer diagnosis and treatment are associated with increased tumour size at presentation, higher incidence of lymph node metastasis, higher relapse rates and lower 5-year survival rates in some studies. Diagnosis and treatment of breast cancer is complex, involving many health care practitioners at multiple locations. New advances in diagnostic and prognostic indicators make the process ever more complex. We reviewed the timing of crucial events in breast cancer diagnosis and treatment in Southwestern Ontario. Methods: Two time periods (2001, 2011) were assessed. Patients with new early invasive breast cancer with specific TNM criteria (T1c or greater plus any N, or any T plus N1-3; M0) were included. Data collection and analysis explored significant time points from first suspicion of malignancy, to diagnosis and definitive treatment, as well as patient demographic information. Results: 300 and 451 eligible patients were identified in 2001 and 2011 cohorts. Distribution of T and N status by cohort was compared by Chi-square test and time from first suspicion to diagnosis by Wilcoxon testing. The proportion of patients in which the time from first suspicion (clinical by lay person or health professional or by imaging) to pathological diagnosis exceeded two months increased from 20.4% in 2001 to 42.1% in 2011. There were no differences in time from first suspicion to diagnosis when analyzed by age (p = 0.54) or location (p = 0.50). Pathological T2-4 status at diagnosis increased from 48.4% in 2001 to 56.8% in 2011, and N2-3 status increased from 7.3% to 12.6%. Patients who had mammograms increased from 52.7% to 59.4%. A positive or suspicious mammogram was the first sign in 36% and 39.1% of cases. There was a trend towards more pathological diagnoses and definitive surgeries at tertiary centers compared to community hospitals. Conclusions: There is a longer time interval from first suspicion of malignancy to pathological diagnosis in 2011 compared to 2001 for both urban and rural populations. The number of non-low risk, non-metastatic cancers at diagnosis increased by 50% over the time interval studied (300 v 451), but number of T2-T4 non-metastatic cancers increased by 77% (145 v 256) and N2,3 cancers by 136% (22 v 52). This is despite more patients receiving mammograms (52.7% v 59.4%). Delays in breast cancer treatment are multifactorial, including both system-, and patient-related factors. This is an under-researched area and more investigation is needed to understand the reasons for the diagnostic delays and more serious cancers at presentation in order to improve outcomes. Reasons for higher proportions of advanced cancers will be discussed.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-03-09.
Abstract P4-04-03: A microgenomic approach using LCM procured breast cancer cells to identify clinically relevant gene signatures that underlie favorable response of ILC to aromatase inhibitors
Authors: Sanders MA , Andres SA , Wittliff JL 
Published: August 2014

Abstract
Based on CGH analyses, invasive lobular carcinoma (ILC) is closely related to low grade invasive ductal carcinoma (IDC), and is genetically unrelated to intermediate and high grade invasive carcinomas (Pathol Res Pract 2005; 201:713). Results from the BIG 1-98 trial, showed that patients with ILC and luminal B (intermediate/high grade) IDC treated with Letrozole, an aromatase inhibitor (AI), had a significant improvement in overall survival, whereas patients with luminal A (low grade) IDC did not (Cancer Res 2012; 72(24 Suppl):Abstract nr S1-1). Despite genetic evidence suggesting a close relationship between ILC and low grade IDC, and disparity between ILC and intermediate and high grade IDC, a clinically relevant gene set underlying a tumor's biologic responsiveness to AIs likely exists. We are deciphering a gene subset that would differ in expression between low grade IDC and ILC, and would be shared by ILC and luminal B IDC. Identification of such a gene set should lead to a more robust marker for identifying AI responsive tumors rather than relying solely on histomorphology and/or immunohistochemistry for the pathologic diagnosis of ILC, since the distinction between ILC and IDC is not always straight forward in pathology practice.
Using 247 de-identified human breast carcinoma biopsies collected under standardized, stringent conditions, total RNA was extracted from carcinoma cells procured by laser capture microdissection to perform microarray analyses of approximately 22,000 genes to identify expression signatures associated with breast cancer characteristics. Of the 247 samples, 169 samples were used for the analysis and included 16 ILCs, 13 low grade IDCs, 55 intermediate grade IDCs and 85 high grade IDCs.
Preliminary analyses identified 1267 genes that were differentially expressed (p&lt;0.01) between cell samples from patients with IDC compared to those with ILC. Gene expression levels in breast cancer cells from patients with low grade IDC compared to those with ILC yielded 200 genes that were statistically differentially expressed (p&lt;0.01). When comparing high grade IDC to ILC, 149 of these genes were not differentially expressed indicating that this gene set may serve as a panel of candidate genes for identifying cancers responsive to AIs. Pathway analysis software (Ingenuity®) identified that these genes were associated with key molecular and cellular functions, e.g., cell-to-cell signaling, cell morphology, cell death and survival, cellular assembly and organization and carbohydrate metabolism. qPCR analyses are used to validate and refine the gene subset distinguishing ILC from low grade IDC. Our approach is revealing subtle molecular features that discriminate these lesions based on clinical behavior. Supported in part by a grant from the Phi Beta Psi Charity Trust.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-03.
Abstract P4-04-15: UC San Diego molecular tumor board: Experience in breast cancer
Authors: Parker BA , Schwab RB , Helsten TL , Sarah BG , Ojeda-Fournier H , Datnow B , Schwaederle MC , Coutinho AC , Kurzrock R 
Published: August 2014

Abstract
Background: To realize the promise of personalized medicine, it is important to build the infrastructure to match patients to the most promising therapies using evolving genomic information to inform clinical trial and treatment recommendations.
Methods: A molecular tumor board was established in December 2012 consisting of representatives of medical oncology, surgery, radiation, pathology, radiology, clinical genetics, molecular genetics and diagnostics, basic and translational science, and bioinformatics and pathway analysis. Patients with metastatic breast cancer signed consent for collection of data in a registry format related to clinical history, genomic analysis, treatment recommendations, and response. Tumor specimens from patients with metastatic breast cancer were subjected to a next generation sequencing diagnostic test (Foundation One™) in a CLIA-certified lab (Foundation Medicine) and analyzed for genomic alterations in a 182 gene panel or a 236 gene panel. Clinical cases and genomic alterations were discussed at Molecular Tumor Board where clinical trials and treatment recommendations were considered, with the final decision made by the treating oncologist.
Results: Genomic analyses of metastatic breast cancer specimens from 17 consented patients had at least one genomic alteration and no tumors had the same genomic alterations. 12/17 had ≥ 2 and 4/17 had 6 or 7 genomic alterations. The most common genomic alterations were in PIK3CA observed in tumors from 6/17 patients. 1/17 tumor specimens had only a single genomic alteration for which there are no current targeted drugs in clinical studies or available commercially (GATA3). Radiographic and/or tumor marker response have been observed to date in 3/4 heavily pretreated patients following treatment with a targeted therapy or a targeted therapy informed by the genomic data in combination with other drugs.
Conclusions: The strategy of matching targeted clinical trial and commercially available therapies to genomic alterations of tumor specimens from individual patients with metastatic breast cancer may offer promise to patients with advanced refractory disease. Biopsies of metastatic disease, genomic analysis in CLIA labs, establishment of molecular tumor boards, definition of “matched” versus “non-matched” therapies, capturing data in a registry to create a learning environment, and most importantly, availability of targeted therapies in clinical trials or commercially, are required for this individual patient strategy to inform current and future treatment options for much larger patient populations.
Funding from UC San Diego Moores Cancer Center MyAnswerToCancer philanthropic fund.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-15.
Abstract P4-05-02: Phospho-reactome measurements reveal heterogenic kinase signatures
Authors: Coppé J-P , Chen Z , Mori M , Boudreau A , van 't Veer L 
Published: August 2014

Abstract
Background: Treating cancer increasingly relies on targeting kinases, because their oncogenic activity drive tumorigenesis. Discovering which active mechanisms of disease progression can be efficiently targeted, and knowing whether kinase networks circumvent therapeutic interventions, are challenges researchers and clinicians face. Surprisingly however, measuring the phosphorylating activity of kinases, and potentially monitoring the functionality of the entire human phospho-reactome at once, remains largely unexplored. We developed a semi-high throughput assay to monitor the phospho-catalytic activity of kinase enzymes, using their biological targets as phospho-sensors. We successfully used this assay to identify oncogenic phospho-signatures prevalent in breast cancer, and can be used to establish drug-sensitivity profiles in models of kinase-targeted therapies.
Methods: We first defined how to computationally build a library of peptide sensors established from confirmed kinase substrates’ phosphorylation sites. Precisely, we used computational methods to create a unique phospho-repertoire cataloguing 3,408 peptide sequences established from validated human proteins’ phosphorylation sites, curated from 38 public databases. Second, we experimentally used these biologically relevant probes in multiplex assays to quantify the catalytic state of kinases. Specifically, a kinome-representative 242-peptide set was developed into an ATP-consumption screen to identify the activity signatures of EGFR, MAPK, AKT, ABL and SRC family kinases, and explore 642 kinase/substrate nodes. Next, we described analysis methods to derive phospho-signatures from semi-high throughput ATP-consumption measurements. We validated the assay using isogenic culture model of basal-like breast cancer (HMT-3522 S1 and T4-2), and cell lines harboring EGFR/HER2-oncogenic alterations such as MDA-MB-231, MCF7 or T47D.
Results: The differential phosphorylation activity of 25 recombinant, active kinase enzymes was successfully captured. In cancer cell extracts, hyper-activated EGFR, ERK, MEK, AKT, and SRC kinases originally identified by immuno-detection were reliably and specifically detectable using the peptide-based kinase-activity assay. The phospho-sensing assay revealed the heterogeneity of active kinase signaling circuits among different breast cancer cells.
Conclusion: This unique strategy and resources allow to comprehensively measure the catalytic activity of multitude kinases at once, representing a new molecular dimension to characterize biological samples. We will use such new phospho-reactome profiling system to determine the efficacy of new combinatorial therapies, and define how chemotherapeutic interventions lead to the reprogramming of phospho-circuits.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-02.
Abstract P4-05-08: Oncotype Dx assay in BRCA positive ER positive breast cancer patients
Authors: Halpern N , Sonnenblick A , Kaduori L , Uziely B , Goldberg Y , Katz D , Allweis T , Divinsky L , Merlet I , Maly B , Sagi M , Hamburger T , Carmon E , Peretz T 
Published: August 2014

Abstract
Background:
Oncotype DX is a 21-gene RT-PCR assay which quantifies the likelihood of breast cancer recurrence and the potential benefit of chemotherapy in patients with early stage, ER positive, Tamoxifen treated breast cancer. Breast cancer in BRCA carriers is considered more aggressive. The aim of our study was to evaluate whether Oncotype Dx recurrence score distribution is different in breast cancer patients with inherited BRCA mutation.
Methods:
The Oncotype DX assay has been used at Hadassah Medical Center since 2004 on specimens from over 450 patients. We analyzed and compared clinicopathological characteristics and Oncotype Dx recurrence scores of BRCA carriers versus non- BRCA or unknown status of BRCA patients.
Results:
Ten patients had validated inherited BRCA mutation, five of them are BRCA1 carriers and five BRCA2 carriers. There were no significant differences in the clinicopathological characteristics between the two groups. Oncotype Dx recurrence score distribution between low, intermediate and high risk groups was not significantly different. The mean recurrence score was 18.48 for the non- BRCA or unknown status of BRCA patients and 22.8 for the BRCA carriers patients. This difference was not statistically significant.
Conclusion:
Estrogen receptor positive breast cancer tumors from BRCA carriers does not display a significantly different Oncotype Dx recurrence score result distribution.
These preliminary data suggest Oncotype Dx assay might be used to help tailor treatment in this subset of patients, although further follow up is needed.
All patients evaluated for oncotype_DX All evaluated (except BRCA+) n = 456BRCA positiveP valueAgeMean57.4557.60.7 Median5857 Range56 (25-81)34 (42-76) T stageT167.7%70%0.9 T230.7%30% T31.6%0% Tumor sizeMean1.71.360.2 Median1.51.26 Range7.8 (0.2-8)1.3 (0.7-2) GradeGrade 1-278.8%60%0.15 Grade 321.2%40% RSLow50%40%0.57 Intermediate39.8%40% High10.2%20% RSMean18.4822.80.16 Median17.522.5 Range64 (0-64)27 (12-39)
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-08.