bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract P3-02-05: Evaluation of Gene Transcripts in Primary Tumors at Time of Diagnosis and Circulating Tumor Cells (CTCs) at Time of Metastatic Disease
Authors: Sieuwerts AM , Mostert B , Bolt-de Vries J , Kraan J , Dirix LY , van Dam PA , van Galen A , van der Spoel P , Ramírez-Moreno R , Yu JX , Wang Y , Gratama JW , Sleijfer S , Foekens JA , Martens JWM. 
Published: April 2011

Abstract
Introduction: The enumeration of CTCs has already shown to bear clinical relevance as a prognostic and predictive factor in metastatic breast cancer. In addition to enumeration, isolation of CTCs enables their molecular characterization and thus holds great promise to establish association of their genetic profile with patient outcome and to identify potential drugable targets. In this study we established epithelial-specific mRNA and microRNA profiles in CTCs of patients with metastatic breast cancer, compared these profiles to the profiles measured in corresponding primary tumors, and determined their association with clinical parameters.
Study design:
For this study we included 50 breast cancer patients, of which 32 presented themselves with over 5 CTCs at the time of metastatic disease. From 14 of these patients with more than 5 CTCs at the time of metastatic disease also the primary tumor at time of breast cancer diagnosis was evaluated. Total RNA was extracted 1) from blood of the 50 patients with metastatic disease after EpCAM-based enrichment of 7.5 mL whole blood with the CellSearch™ Profile Kit [Veridex LCC], 2) from 14 unprocessed whole blood preparations from healthy blood donors, and 3) from 14 primary tumors. Gene transcript levels of CTC-specific and potentially clinically relevant mRNAs and microRNAs were compared in CTCs isolated at time of metastatic disease and the corresponding primary tumors. In addition, the association of these transcript levels with clinical data was assessed.
Results:
We identified 24 mRNA and 14 microRNAs more abundantly expressed in CellSearch-enriched fractions from patients with at least 5 CTCs compared with those without CTCs and/or compared with unprocessed whole blood prior to CellSearch enrichment (Mann-Whitney U-test P&lt;0.05). In addition, when comparing transcript levels present in CTCs during metastatic disease and those measured in the corresponding primary tumor, potentially clinically relevant discrepancies were observed. Findings of interest included changes in transcript levels of genes such as ESR1, ERBB2, TOP2A and MGB1, and in genes associated with proliferation and EMT. Finally, associations were observed between transcript levels measured in CTC preparations and clinical data like nodal status and size of the primary tumor.
Conclusion:
Our results show that molecular characterization of CTCs is feasible and has potential for a more tailored clinical approach above CTC enumeration in the treatment of metastatic breast cancer patients.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-02-05.
Abstract P3-03-01: Minimal Residual Disease Monitoring in Breast Cancer Patients
Authors: Mikulova V , Janatkova I , Cabinakova M , Tesarova P , Pavlista D , Kolostova K , Pinterova D , Romzova M , Rusnakova V , Kubista M , Zima T. 
Published: April 2011

Abstract
BACKGROUND: Breast cancer (BC) patients still harbor a considerable risk of metastatic relapse caused by minimal residual disease (MRD) despite of complete removal of primary tumor. The aim of this study was to identify single disseminated tumor cells (DTC) in the bone marrow and circulating tumor cells (CTC) in the peripheral blood as potential biomarkers for therapy response monitoring and metastatic relapse risk prediction. Finally, the gene expression profiles of CTCs have been analyzed.
METHODS: A total of 87 patients with diagnosed BC at stage I to III and 115 metastatic patients were enrolled into a prospective study between years 2008 - 2010. Peripheral blood (5ml) for CTC-detection was collected from primary BC patients before chemotherapy (CHT), after 2 cycles of CHT and after the CHT. Metastatic BC patients have been examined for CTCs before starting a new line of the treatment. Bone marrow aspirates from 16 premenopausal BC patients (mean age 31) with primary tumor were analyzed for the presence of DTC by immunocytochemistry using the pan-cytokeratin antibody A45-B/B3 (Epimet™, AS Diagnostik, Germany) before surgery. CTC detection in blood was performed by AdnaTest BreastCancerTM(AdnaGen AG, Germany), which is based on the detection of EpCAM, HER2 and MUC1 specific transcripts in enriched CTC-lysates. cDNA from isolated CTCs has been further pre-amplified and used for multimarker qPCR gene expression profiling using Biomark® microfluidic 48x48 GE Dynamic arrays (Fluidigm, USA). qPCR results have been analyzed by GENEX vs. 5.2 software (MultiD Analysis). RESULTS: 286 CTC samples have been analyzed in total. The analysis has shown that the expression profiles of CTCs from primary BC patients have been significantly different comparing them to the CTC-profiles from metastatic BC patients for several of tested genes (e.g., CK19, GA7332,
MLFIP1, SATB1, PTEN). Interestingly, before surgery of primary tumor DTCs were found in 5/16 patients (31 %) and CTCs in 7/16 (43 %). Both DTCs and CTCs together were found in 4/16 (25%) patients. In 18% of the primary BC patients no dissemination markers were found CONCLUSIONS: Information based on the CTCs-gene expression profiles could provide an additional support for therapy management. Metastatic potential of enriched CTCs will be further evaluated on the single cell level.
This work has been supported by Grant Agency of Ministry of Health, Czech Republic (IGA NS9976) and Grant Agency of Charles University in Prague, Czech Republic no. 7709 and 59410.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-03-01.
Abstract P3-04-02: Promoter CpG Island Hypermethylation along Multistep Carcinogenesis of Breast Cancer
Authors: Park SY , Kwon HJ , Lee HE , Kim S-W , Kim JH , Kim IA , Cho N-Y , Kang GH. 
Published: April 2011

Abstract
Background: In breast cancer, promoter CpG island hypermethylation has been described for various genes in all aspects of cellular function. However, most studies focused on the methylation status in tumor-related genes in invasive breast cancer, compared to normal breast tissue, and methylation studies of potential precursor lesions of breast cancer were sparse. We investigated the changes in promoter CpG islands hypermethylation during breast cancer progression from intraductal proliferative lesions [usual ductal hyperplasia (UDH), atypical ductal hyperplasia (ADH) and ductal carcinoma in situ (DCIS)] to invasive ductal carcinoma (IDC) of breast, and tried to find the specific changes in each step of tumorigenesis. Materials and Methods: We performed MethyLight analyses for methylation status of 57 CpG island loci in 20 IDCs and its paired normal breast tissues. After selecting 15 CpG island loci showing cancer-specific DNA methylation, another sets of normal breast tissue from non-cancer patients (n=10), UDH (n=10), ADH (n=20), DCIS (n=30) and IDC (n=30) were analyzed for these loci.
Results: By this approach, we found six new methylation markers of breast cancer including DLEC1, GRIN2B, HOXA1, MT1G, SFRP4 and TMEFF2, as well as APC, GSTP1, HOXAIO, IGF2, RARB, RASSF1A, RUNX3, SCGB3A1 (HIN-1) and SFRP1. The number of methylated genes showed stepwise increase from normal breast to ducal hyperplasia (DH) and
DCIS, while IDC showed no difference with DCIS (median, 1 for normal breast, 2 for DH, 5 for DCIS, 6 for IDC; P&lt;0.001). Of the 15 CpG island loci tested, nine loci already showed methylation in normal breast tissue. Methylation of RASSF1A, DLEC1 and SCGB3A1 (HIN-1) promoter CpG islands was significantly higher in DH than in normal breast tissues. Eight CpG island loci (APC, GRIN2B, GSTP1, HOXA1, RARB, RUNX3, SFRP1 and TMEFF2) showed higher methylation frequency and levels in DCIS compared to DH. DICS and IDC showed no difference in the methylation levels or frequency in the 14 CpG islands except HOXA10. Discussion: Our results indicated that CpG island methylation of tumor-related genes is an early event and accumulate with breast cancer progression. CpG island methylation was significantly changed during the progression of DH to DCIS, and DCIS showed similar CpG island methylation with IDC, suggesting that the transition of DH to DCIS is a critical step for breast cancer tumorigenesis associated with promoter CpG islands hypermethylation.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-04-02.
Abstract P3-04-05: Hypermethylation and Downregulation of Glutathione Peroxidase-3 in Inflammatory Breast Carcinogenesis
Authors: Sabet SF , Mostafa MM , El-Shinawi M , Peng D , Nouh MA , El-Rifai W. 
Published: April 2011

Abstract
Background: The breast tumor microenvironment is characterized by the release of endogenous reactive oxygen species (ROS), and has been suggested as being associated with disease aggressiveness. Normal cells have an antioxidant system that controls the balance between production and removal of oxygen radicals, thereby protecting against oxidative damage, such as the Glutathione peroxidases (GPXs) enzymes. Epigenetics and DNA methylation play important roles in several inflammatory disorders. We therefore, analyzed the promoter of GPX3 and found a dense CpG island closest to the transcription start-site. The aim of the present study is to 1) investigate GPX3 expression in breast carcinoma and normal breast tissues, 2) identify whether GPX3 is epigenetically regulated in breast carcinoma tissues versus normal tissue, and 3) compare the levels of expression of GPX3 in Inflammatory Breast Cancer (IBC) versus non-IBC tissues.
Material and Methods: We enrolled 40 breast cancer patients with tumor mass range from 1.8-9cm (with median size 4.77 ± 3.9). Patients were sub-grouped as IBC (n = 20) or non-IBC (n = 20), healthy breast tissues from the same patients were used as control. Using real-time PCR and immunohistochemistry, we assessed the level of expression of GPX3 at mRNA and protein levels in breast cancer tissues versus control. To identify whether the CpG island of the GPX3 gene was epigenetically regulated, we analyzed the methylation profile of GPX3 in breast carcinoma versus normal tissues using DNA bisulfate treatment and methylation-specific PCR (MSP).
Results: GPX3-mRNA expression was down regulated in breast cancer samples compared to control tissues. There was a significant decrease (P = 0.01) in the mRNA expression level of IBC compared to non-IBC carcinoma tissues. MSP showed that the GPX3 gene was hypermethylated in breast carcinoma tissues compared to control. Moreover, confirmatory semiquantitative immunohistochemical scoring revealed weak or negative immunostain of carcinoma tissues compared to healthy breast tissues. Conclusion: These preliminary data suggest that epigenetic inactivation of GPX3 is a frequent finding in inflammatory breast cancer. Silencing of GPX3 in IBC versus non-IBC carcinoma cells suggested that GPX3 may be critical in the development and progression of IBC. To our knowledge, this is first study to test the role of GPX3 in breast cancer.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-04-05.
Abstract P3-04-06: A Functional Investigation of MAL: A Frequently Hypermethylated Gene Marker in Breast Cancer
Authors: Hillocks YMN , Lo P-K , Teo WW , Fackler MJ , Sukumar S. 
Published: April 2011

Abstract
Hypermethylation of CpG islands in the promoter region of tumor suppressor genes is a common event in cancer, and is an important mechanism in inactivating tumor suppressor gene function in breast cancer. Computational searches of existing large databases for genes underexpressed in multiple cancers, combined with CpG island analysis of those genes, identified a novel potential methylation marker gene in breast cancer called MAL (Maturation-Associated protein for T-Lymphocyte). MAL encodes a 17kD protein that is found in mature T-cells and participates in T-cell differentiation and T-cell receptor signaling. Recent studies have reported gene promoter hypermethylation of MAL in breast tumors and breast cancer cell lines. Furthermore, MAL inactivation has been shown to be predictive of benefit from adjuvant chemotherapy. We proposed that alteration of MAL expression has functional implications in breast cancer. In addition, we proposed that MAL has the potential to serve as a methylation marker for early detection of breast cancer. MAL gene methylation as assessed in breast cancer cell lines and primary tumors by quantitative multiplex methylation specific PCR (QM-MSP) showed that it is frequently methylated in cell lines (40/48; 83%), in primary tumors (11/22; 50%) and in distant metastasis (16/32; 50%), but not in normal breast tissues or human mammary epithelial cells (HMECs). The high frequency of MAL methylation was common to all of the subtypes of breast cancer cells tested (Basal A, Basal B, and Luminal). Q-RT-PCR analysis of MAL expression and QM-MSP analysis of MAL methylation showed that 71% (20/28) of breast cancer cell lines show an inverse correlation between methylation and mRNA expression. This suggests that epigenetic alteration is the major mechanism of silencing since pharmacologic intervention with demethylating agents and histone deacetylase inhibitors resulted in re-expression of MAL in the breast cancer cell lines tested. MAL methylation is being assessed in a panel of 150 primary tumor samples with corresponding clinical data such as histological subtype, tumor grade and tumor specific survival. This will allow for correlations to be made between MAL methylation status and survival data etc. to see if MAL can serve as a predictive marker for breast cancer. This analysis will be useful in further validating MAL as a DNA methylation marker for breast cancer detection in tissue samples. The function of MAL is being deciphered at both the biological and biochemical level by performing overexpression and knockdown studies in breast cells using already constructed expression vectors. The characterization and validation of MAL, a lipid raft protein, as a potential DNA methylation marker in breast cancer could provide a valuable early detection tool for breast cancer.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-04-06.
Abstract P3-05-01: “VISA” Nanopaticles to Breast Cancer In Vitro and in Living Imaging Animal Models
Authors: Xie X , Wei W , Guo J , Xiao X , Xie X , Kong Y , Tang J , Liu P , Wang X , Lv N. 
Published: April 2011

Abstract
Development of cancer gene therapy has been hampered by the fact that there are no effective cancer-specific expression vectors available, which is critical for improving therapeutic efficacy and reducing toxicity in clinics. To overcome this problem, we recently developed a safe and effective strategy fro targeting a potent pro-apoptotic gene (BikDD) to the pancreatic tumors (Xie et al. Cancer Cell, 2007), lung cancer (Sher et al. Oncogene, 2009) and ovarian cancer (Xie et al. Molecular Cancer Therapeutics, 2009). A VISA system (VP16-Gal4-WPRE integrated systemic amplifier) was engineered by using the two-step transcriptional amplification (TSTA) system and the posttranscriptional regulatory element of the woodchuck hepatitis virus (WPRE). The VISA system can boost the activity of cancer-specific promoters by an average of 600-800-folds compared to their basal levels. C-VISA (CCKAR-VISA) nanoparticles transcriptionally targets transgene expression effectively to pancreatic tumors in vivo. C-VISA-BikDD nanoparticles was shown to be highly effective in reducing tumor burden and increasing animal survival rate in orthotopic pancreatic cancer models which is moving into clinical trials at University of Texas M.D. Anderson Cancer Center, USA. In the current study, we identified hTERT(human telomerase reverse transcriptase), survivin, β-cateinin, claudin-4, and FASN (fatty acid synthase) promoters as breast cancer-selective promoters, and amplified their activity to hundreds of folds greater by the “VISA” system(called x-VISA) without loss of their specificity. Very importantly, the x-VISA promoters were also robust in the primary cultured breast cancer cells, with 42.5 %-65% of the CMV promoter, while retaining stringent pancreatic cancer specificity. x-VISA was also shown to target expression of firefly luciferase to MDA-MB-468 xenografts in an orthotopic mouse model, confirmed by noninvasive imaging with an Xenogen IVIS™ imaging system and measuring with a luminometer. The cancer-specific index was 35-60 for x-VISA-Luc and 0.01 for CMV-Luc in vivo. We further demonstrated significant antitumor activity of targeted BikDD expression driven by nanoparticles of the hTERT-VISA-BikDD vectors in Her-2-negative and-positive and triple-negative breast cancer cell lines in vitro, and in multiple breast cancer models of living imaging by the Xenogen IVIS imaging system with limited toxicity. In addition, treatment with hTERT-VISA-BikDD nanoparticles plus lapatinib or produces evident combinational therapeutic efficacy, which is likely due to the ability of lapatinib to promote apoptosis of Her-2-overexpressing breast cancer cells. Thus, our newly developed hTERT-VISA-BikDD nanoparticles are an innovative strategy for targeted antitumor effects of Her-2-negative, Her-2-positive and triple-negative breast cancer.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-05-01.
Abstract P3-07-01: Clonal Relatedness between Lobular Carcinoma In Situ and Synchronous Malignant Lesions: Analysis of Fresh Frozen Tissue Using SNP Array
Authors: Andrade VP , Morrogh M , Giri D , Ostrovnaya I , Seshan V , Olvera N , Begg C , Morrow M , King TA. 
Published: April 2011

Abstract
INTRODUCTION: Lobular carcinoma in situ (LCIS) confers one of the greatest risks for subsequent development of invasive breast carcinoma yet historical data suggests that LCIS is not a precursor to invasive disease. Emerging evidence of shared molecular alterations between LCIS and co-existing invasive lesions in a small number of archival samples have reopened the debate regarding the true significance of LCIS and its malignant potential.
METHODS: We investigated clonality between LCIS and adjacent malignant lesions in 26 patients using fresh frozen samples harvested from mastectomy specimens. Laser Capture Microdissection was used to isolate pure cell populations and DNA was subject to Affymetrix SNP 6.0 array. Data were converted for copy number analysis and the closeness of identified paired copy number changes was measured to determine the probability of clonality.
RESULTS: After excluding cases with low DNA yield/quality and noise signals, 14 LCIS with seven patient matched invasive lobular carcinomas (ILC), 6 matched ductal carcinoma in situ (DCIS) and 3 matched invasive ductal carcinomas with lobular features (IDCLF) were considered adequate for statistical comparison. The immunohistochemical profile of invasive cancer showed: 10 cases ER+/PR+/Her-2(-), 2 cases ER-/PR-/Her-2(+), 1 ER-/PR-/Her2(-) and 1 case non-available for staining (microinvasive carcinoma). The results suggest that the tumor pairs are more likely to be of clonal than independent origin between LCIS and DCIS in 4/6 samples (66.6%), between LCIS and low-grade IDCLF in 3/3 (100%) samples and between LCIS and classic ILC in 5/7 (71.4%) samples. Independent LCIS/DCIS samples were seen in association with Her2+ cancers. In LCIS/DCIS samples favoring a clonal origin the DCIS were low-grade cribriform type associated with ER+ cancers.
CONCLUSION: Clonal relatedness was detected in the majority of LCIS and adjacent malignancies, including cases of low-grade DCIS and IDCLF. These results support a true precursor role for LCIS and provide additional evidence to the concept of a low-grade malignancy pathway as opposed to the classic lobular versus ductal dichotomy.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-07-01.
Abstract P3-08-01: The Influence of the BAD Apoptosis Pathway on Breast Cancer Progression and Relapse-Free Survival after Adjuvant Treatment
Authors: Ismail-Khan RR , Marichion DC , Xiong Y , Fulp WJ , Kamath SG , Eschrich SA , Chen D-T , Lancaster JM. 
Published: April 2011

Abstract
Objective. The phosphorylation status of the BCL2 Antagonist of Cell Death (BAD) protein influences cell survival and apoptosis. BAD phosphorylation is determined by the relative activity of a series of kinases and phosphatases within the BAD pathway. We therefore sought to evaluate the influence that expression of the BAD apoptosis pathway has on breast cancer progression and on clinical outcome in a series of breast cancer patients.
Methods. We used Principal components analysis to derive a BAD-pathway gene expression signature with a corresponding “pathway score” representing overall gene expression levels for BAD pathway genes. The BAD-pathway signature score was evaluated in clinical-genomic breast cancer datasets obtained from a total of 502 patients, including intra-ductal hyperplasia (n=8), ductal carcinoma in-situ (n=30), and three separate data sets of invasive ductal carcinoma patient samples (n=23, n=286, n=155). The influence of the BAD-pathway signature score on breast cancer progression and relapse-free survival was evaluated by student's t-test and Kaplan Meier/log-rank test, respectively.
Results. We developed a 48-gene BAD-pathway signature, the expression score of which decreased with progression from intra-ductal hyperplasia through ductal carcinoma in-situ and invasive ductal carcinoma (p=0.0004). Furthermore, BAD-pathway signature score was associated with relapse free survival from breast cancer in two independent clinical-genomic datasets (n=286, p=0.01; n=155, p=0.02). Conclusions.BAD pathway gene expression is associated with breast cancer progression and disease-free survival. The pathway represents an appealing human cancer prognostic biomarker and therapeutic target. Figures available in online version.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-08-01.