bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional profiling of patient-matched ER-positive breast cancer tissue from post-menopausal women treated with neoadjuvant RAD001.
Authors: Sabine VS , Sims AH , Macaskill EJ , Renshaw L , Thomas JS , Dixon JM , Bartlett JM 
Published: December 2010

Abstract
Abstract #2035
Background: RAD001 (everolimus) is a rapamycin derivative that inhibits mTOR and its downstream substrates and has shown promising results in Phase I clinical trials. This is the first clinical study of RAD001 administered alone in breast cancer. The aim of this study was to characterise the effects of RAD001 treatment on tumour gene expression and to assess whether we can predict which patients will respond to RAD001.&#x2028; Materials & Methods: 32 post-menopausal women with operable estrogen receptor positive early breast cancer received 5mg RAD001 pre-operative treatment daily for 14 days prior to primary surgery. 25 patients completed treatment, 6 withdrew and 1 did not start medication. Paired biopsies were taken at diagnosis and at surgery from each of the 31 patients who received RAD001. Half of the biopsy was immediately flash frozen in liquid nitrogen and RNA extracted, amplified in duplicate and analysed using Illumina Human Ref.8 chip v2, the other half of the biopsy was embedded in paraffin for the analysis of biological response markers, including changes in proliferation (Ki67) by immunohistochemistry (Macaskill et al., 2006: Breast Cancer Research & Treatment: 100: S1: S286). 15 patients were classified as responders to RAD001 and 10 patients non-responders (responders were defined by a fall in % Ki-67 positive cells). Gene expression changes were compared before and after treatment with RAD001 and between the responders and non-responders using Bioconductor programs implemented in the R statistical programming language.&#x2028; Results & Discussion: All pre- and post-treatment biopsies were available for microarray processing and assessment of biological response markers for patients completing RAD001 treatment. Analysing data from duplicate samples enabled us to vigorously evaluate the reproducibility of the Illumina beadarray platform and revealed some slight batch-to-batch variation which can be accounted for in the analysis. This dataset has enabled us to begin to identify genes and pathways associated with RAD001 treatment and to generate a gene expression classifier for predicting which patients will benefit from RAD001 treatment. Genes of interest will be validated by quantitative real time PCR and key pathways reported.&#x2028; Acknowledgements: This work was supported by a grant from Breast Cancer Research & Treatment, UK.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2035.
Role of KCNMA1 gene in breast cancer invasion and metastasis to brain.
Authors: Khaitan D , Sankpal UT , Ningaraj NS 
Published: December 2010

Abstract
Abstract #2043
Background: The prognosis for patients with brain metastasis from breast cancer is extremely poor. A significant number of breast tumor patients despite aggressive therapy develop metastatic disease in brain. The mechanism or the cause of breast cancer metastasis to brain is unknown. Therefore, it is critical to identify prognostic molecular markers of the metastatic process in order to design therapeutic modalities for reducing the occurrence of metastasis. In this study we investigated KCNMA1 gene, which encodes alpha subunit of calcium activated potassium (KCa) channels. Altered KCa channels, are described in a wide variety of tumor cell types and up-regulation of KCa channels was shown to be a novel mechanism for the malignant phenotype of human tumor cells.&#x2028; Material and Methods: We performed Global GeneChip exon arrays to study the expression of KCNMA1 gene in metastatic breast cancer in brain and compared it with primary breast cancer and breast cancers metastatic to other organs, and validated the findings by RT-PCR. Immuno-histochemistry was performed to study the expression and localization of alpha subunit of KCa channel protein in primary and metastatic breast tumor tissues and breast cancer cell lines. We performed Matrigel invasion, transendothelial migration and membrane potential assays in normal breast cells (MCF-10A), non-metastatic breast cancer (MCF-7), non-brain metastatic breast cancer cells (MDA-MB-231), and brain-specific metastatic breast cancer cells (MDA-MB-361) to study whether KCa channel inhibition attenuates breast tumor invasion and metastasis to brain.&#x2028; Results: The Global GeneChip exon array and RT-PCR showed higher KCNMA1 gene expression in metastatic breast cancer in brain compared to metastatic breast cancers in other organs. Our results clearly show that metastatic breast cancer cells exhibit increased KCa channel activity, leading to greater invasion and trans-endothelial migration, which could be attenuated by blocking the KCNMA1 gene with siRNA and biochemical inhibition with IBTX.&#x2028; Discussion: Recent investigations in patients with metastatic lung and breast cancers reported alarming rates of brain metastases. Unraveling the genetic aberrations that drive the metastatic events in these cancer cells offer insights into how to limit or prevent this lethal process. For instance, determining the relative abundance of KCNMA1 gene in breast cancer metastasis to brain and understanding the mechanism of brain metastasis provides a unique opportunity to identify specific genetic markers that could differentiate between low grade breast tumors that are at high risk for metastasis from those at low risk for metastasis. This would in turn allow for the appropriate and efficient application of treatments to obtain the greatest benefit while sparing low risk patients for metastasis from the toxic side effects of chemotherapy.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2043.
CXCR4 alters ID family and ITF2B/E2-2/TCF-4 dynamics to confer invasive phenotype to breast cancer cells.
Authors: Appaiah HN , Bhat-Nakshatri P , Nakshatri H , Badve S 
Published: December 2010

Abstract
Abstract #2045
Introduction: Breast cancer is characterized by a distinct metastatic pattern involving lymph nodes, bone marrow, lung, liver and brain. The chemokine CXCL12 and its receptor CXCR4 are suggested to play a role in invasion and organ-specific metastasis. Signaling pathways downstream of CXCL12:CXCR4 involved in invasion and/or metastasis are not known.&#x2028; Methods: MDA-MB-231 breast cancer cells were sorted for CXCR4-positive and CXCR4-negative subpopulation by FACS and subjected to microarray gene expression analysis. Differentially expressed genes were further verified by RT-PCR or qRT-PCR. siRNA or shRNA expression studies were used to evaluate the role of genes overexpressed in CXCR4-positive cells in invasion through Matrigel. Orthotopic xenograft model is being used to evaluate primary tumor growth and metastasis pattern of CXCR4-positive and CXCR4-negative subpopulation with various manipulations.&#x2028; Results: ITF2B, a class I bHLH transcription factor, is expressed at ∼4-fold higher level in CXCR4-positive cells. ITF2B mRNA level was lower in CXCR4 siRNA treated or CXCR4shRNA expressing CXCR4-positive cells suggesting that ITF2B is the direct target of CXCL12:CXCR4. ITF2B siRNA reduced invasion of CXCR4-positive cells whereas ITF2B overexpression increased invasive capacity of CXCR4-negative cells. ITF2B is a Wnt β-catenin regulated gene with transforming ability and controls the function of Inhibitor of DNA binding family of transcription factors (ID1 to ID4). ID1 is essential for lung metastasis whereas ID2 induces differentiation of breast cancer cells and higher levels of ID2 correlates with favorable prognosis in breast cancer. ID2 expression was higher in CXCR4-negative cells and its overexpression in CXCR4-positive cells reduced invasion. Both CXCR4 and ITF2B are involved in reducing ID2 expression as siRNA against both of these genes increased ID2 mRNA in CXCR4-positive cells. Interestingly, CXCR4-negative cells appear to have adapted to alternative mode of invasion/metastasis as these cells express higher levels of metastasis-associated genes such as TWIST and MT1-MMP. Xenograft studies with cells overexpressing ITF2B and ID2 are currently underway.&#x2028; Conclusions: CXCL12:CXCR4 activated signaling pathways target ID family/bHLH transcription factor network to promote invasion of breast cancer cells. Inducers of ID2 may help to overcome CXCR4- mediated invasion and/or metastasis of cancer cells.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2045.
Expression levels of histone deacetylases and acetylation of histone H4 and tubulin associated with breast cancer progression.
Authors: Suzuki J , Chen Y , DeVries S , Chan L , Baehner FL , Benz CC , Waldman FM , Hwang E 
Published: December 2010

Abstract
Abstract #2051
Background: Excess histone deacetylase (HDAC) activity can induce global hypoacetylation of histone and non-histone protein substrates, altering gene expression patterns and cell behavior potentially associated with malignant transformation. However, HDAC expression and protein acetylation have not previously been studied in the context of breast cancer progression.&#x2028; Materials and Methods: We performed immunohistochemistry (IHC) to assess expression levels of acetylated histone H4 (acH4), acH4K12, acTubulin, HDAC1, HDAC2 and HDAC6 in formalin fixed paraffin embedded sections with synchronous normal epithelium (N), ductal carcinoma in situ (DCIS), and invasive ductal carcinoma (IDC) components from 58 archived samples at UCSF. Staining was assessed on the basis of H-score, defined as the sum of the intensity of staining (0-3) multiplied by % of stained cells for each intensity (score range 0-300). H-score differences between groups were tested for significance using either the Mann-Whitney test or the Wilcoxon signed rank test for paired samples.&#x2028; Results: From N to DCIS, there was a marked reduction in histone acetylation (acH4, acH4K12). Tubulin acetylation, a marker of non-histone protein acetylation, showed a smaller reduction. Expression of all three HDACs was also reduced, but to a lesser extent than histone acetylation. Moreover, from DCIS to IDC, the same pattern of changes in acetylation and HDAC expression was seen, although these differences were of smaller magnitude than between N and DCIS. All markers were significantly different between N and DCIS (all p&lt;0.0001) and between DCIS and IDC (all p&lt;0.03). ER-negative tumors exhibited greater changes from N to DCIS than did ER-positive tumors, particularly for acH4 and HDAC1 (p=0.05 and 0.0001 respectively). High-grade invasive tumors showed more significant changes from N to DCIS than low/intermediate grade tumors for acH4, acH4K12, acTubulin, and HDAC1 (p=0.0009, 0.006, 0.05, and &lt;0.0001 respectively). The change in protein acetylation and HDAC expression with cancer progression did not differ by HER2 status or age (≤50 or &gt;50).&#x2028; &#x2028; Conclusions: Overall there was a pattern of hypoacetylation associated with malignant progression, with normal epithelium exhibiting the highest acH4, acH4K12, and acTubulin levels and IDC exhibiting the lowest levels. Paradoxically, expression of HDAC 1, 2 and 6 was not increased; thus, our data support that histone hypoacetylation is not regulated by HDAC expression but rather by modulation of HDAC activity. Outcome studies and clinical trials are needed to assess the prognostic significance of these findings and to determine how effectively HDAC inhibitors could reverse the hypoacetylation observed in progression from N to DCIS and IDC.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2051.
RANKL plays a role in migration and invasion of the bone-seeking cell line MDA-MB-231-BO2 through human type I collagen by up-regulating MMP1.
Authors: Casimiro S , Alho I , Fernandes A , Lipton A , Guise T , Costa L 
Published: December 2010

Abstract
Abstract #2052
Background: Cancer-induced bone destruction is associated with increased osteoclastogenic activity induced by tumor cells, and an unbalanced bone remodelling cycle that favours bone osteolysis. In this proccess the RANK-RANKL signaling is crucial for both osteoclastogenesis and osteoclastic activity. Furthermore, breast cancer cells have been shown to also express the RANK receptor and to increase migration towards RANKL stimuli, however it is not known if RANK - RANKL interaction stimulates breast cancer cell to invade and degrade bone collagen. Objective: To determine if RANKL increases the ability of breast cancer cells to invade a type I collagen matrix and degrade bone collagen. Material and Methods: The influence of sRANKL on MDA-MB-231-BO2 cell migration or cell invasion (type I collagen) were assessed by Boyden-chamber chemotaxis assay. Binding of RANKL to BO2 cells, levels of RANK expression and levels of matrix metalloproteinases secreted during invasion were determined by RT-PCR and WB analysis. The activation of AKT signaling pathway was determined by WB against the phosphorylated form pAKT1/2/3(Ser473). Results: sRANKL influences the migration and invasion of RANK-expressing BO2 cells in a dose-dependent manner (dose range 0.75-2.5 ug/mL), while the neutralization of sRANKL with a specific antibody abrogated this effect. sRANKL stimuli activates AKT pathway downstream of RANK, while the pre-treatment of cells with 100 nM of wortmannin (a PI(3)K inhibitor) blocked this effect and impaired invasion. During invasion of type I collagen the levels MMP1 expression and of secreted MMP1 increase and are positively correlated with the increase in sRANKL concentration. Conclusions: Our data suggest that RANKL can trigger an increase in expression of MMP1 by breast cancer cells expressing RANK, contributing to invasion via degradation of matrix proteins directly by the cancer cells.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2052.
Receptor activator of NF-kB (RANK) and RANK ligand protein expression in invasive ductal carcinoma.
Authors: Roudier-Meyer M , Jacob A , Tometsko M , Erwert R , Woody L , Soriano R , Huang L , Hawkins J , Branstetter D , Dougall W 
Published: December 2010

Abstract
Abstract #2057
Purpose: Bone metastases are commonly observed in patients with advanced breast cancer. Tumor cells interact with the bone microenvironment to induce osteoclastogenesis via local bone stromal expression of receptor activator of NF-kB ligand (RANKL), leading to bone destruction and release of growth factors. In addition to its critical role in tumor-induced osteolysis, RANKL has been demonstrated to enhance the invasive behavior of epithelial tumor cells that express RANK, and RANK over-expression in transgenic mice using the breast-specific MMTV promoter results in increased mammary carcinoma. This study assessed the expression of human RANK and its ligand (RANKL) in invasive ductal carcinoma (IDC).&#x2028; Methods: We studied a total of 57 IDC specimens. Antibodies against human RANK (AF683) and human RANKL (M366; Amgen) were used for immunohistochemistry (IHC) cell staining along with an isotype control. The specificity of the 2 antibodies was substantiated by IHC, flow cytometry and Western blot analysis of positive and negative control cells. In addition, for RANK, mass spectrometry/protein sequencing of immunoprecipitated proteins was performed. The intensity of IHC staining was scored on a semiquantitative scale (1=weak, 2=moderate, 3=intense) or a complex scale (sum of percentages of stained tumor cells x staining intensity (0-3)).&#x2028; Results: Using a complex score with a threshold of 10, 20/57 IDC (35%) expressed minimal level of RANK (range 0 to &lt;10, median 1) while 37/57 IDC (65%) expressed RANK protein with a score ranging from 10 to 100 (median 50). The expression in the tumor was heterogeneous, with cells having no expression and cells having intense expression. In addition, RANK was intensely expressed in the basal layer of all normal ducts and lobules. RANKL was observed in rare tumors (7/57; 11%), in rare lymphocytes of most tumor stroma (42/62; 68%), and in rare fibroblast-like cells in the stroma of rare tumors (3/62; 4.8%).&#x2028; Conclusion: In this study, RANK expression was observed by IHC in the majority (65%) of IDC. RANKL expression was observed in the epithelial carcinoma element of some tumors (11%) and was detected in 68% of tumors in rare lymphocytes infiltrating the tumor stroma. Correlation studies between prognosis markers ER, PR, Her2, and CK5/6 expression and RANK or RANKL expression in those IDC have been initiated.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2057.
Upregulation of Fra-1 and Fra-2 in breast cancer cells results in changes in adhesion, migration, invasion and stem cell markers.
Authors: Schroeder C , Janke S , Krenkel S , Streichert T , Jaenicke F , Milde-Langosch K 
Published: December 2010

Abstract
Abstract #2058
Background: Fra-1 and Fra-2 (Fos-related antigen1 and 2) are members of the Fos family of AP-1 transcription factors which are often up-regulated in human mammary carcinomas. The results of previous studies with clinical tumor tissues and experimental studies of breast cancer cell-lines suggested that they might be involved in the regulation of tumor invasion and metastasis in breast cancer.&#x2028; Materials and Methods: In order to analyze the impact of Fra-1 and Fra-2 on the aggressive behavior of breast cancer cells, we established stable transfectants of the weakly invasive MCF-7 cells and as well in the highly invasive MDA-MB231 breast cancer cells with Fra-1 and Fra-2 overexpression. Additionally we generated MCF-7 stable transfectants with inducible Fra-2 transcription controlled by the tetracycline-inducible tetON-system. The consequences of Fra-1 and Fra-2 upregulation on the biology of the breast cancer cells were analysed by MTT assays (proliferation) and Matrigel invasion assays (invasion and motility). In addition, possible target genes which were differentially regulated in stable transfectants with Fra-1 and Fra-2 overexpression were identified by microarray analysis and, partly Western blots.&#x2028; Results: Cell proliferation was not influenced by Fra-1 and Fra-2. In contrast, the invasive potential of the cells was increased by Fra-1 and Fra-2 in MDA-MB231 and MCF7 cells. In addition, there was a similar effect on cell motility. By using the GeneChip Human Genome U133A 2.0 array (Affymetrix), we identified several genes which are known to be involved in cell adhesion, migration or invasion and which were up- or downregulated in stable transfectants, i.e. ICAM, L1CAM, ALCAM, CX43 etc. Moreover, Fra-2 overexpression in MDA-MB231 cells resulted in CD44 upregulation and CD24 downregulation, which is characteristic of breast cancer stem cells.&#x2028; Discussion: In clinical breast cancer tissues, up-regulation of Fra-2 and Fra1 protein expression has been observed and was shown to be associated with a more aggressive phenotype. Our data of the experimental studies with breast cancer cell-lines indicates that Fra-2 as well as Fra-1 may play an important role in tumor progression by transcriptional regulation of genes which are involved in cell adhesion, invasion and motility.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2058.
Do isolated cells (pN0i+) in the sentinel lymph node change the post-operative management in breast cancer?.
Authors: Charles C , Alran S , De Rycke Y , Malka I , Fourchotte V , Falcou M , Berry M , Benamor M , Kirova Y , Pierga J , Sastre X , Sigal-Zafrani B , Salmon RJ 
Published: December 2010

Abstract
Abstract #206
Background: immunohistochemical (IHC) analysis of the sentinel lymph node (SLN) allows detection of occult metastases not routinely diagnosed by conventional techniques. There is, however, no consensus concerning the post-operative management of those patients with IHC-positive (pN0i+) nodes: should one re-operate, change the medical treatment or alter the irradiation fields?&#x2028; Patients and methods: 2692 patients with early invasive breast cancer underwent conservative treatment with SLN biopsy between 2000 and 2006. SLN were evaluated with frozen section followed by serial-section HES and IHC if HES showed no tumour cells. Lymph node staging followed the accepted pTNM classification: pN0, pN0i+ (≤ 0.2mm, IHC+), pNmi (0.2-2mm) and pN1a (&gt; 2mm). In 1506 patients with T1pN0 tumours : 143 were pN0i+, that is 10%. We compared the post-operative management of pN0 patients, who had no completion axillary dissection (CAD), to those pN0i+ who did. All positive SLNs underwent CAD according to our institutional protocol.&#x2028; Results: 15 of 143 (10.5%) pN0i+ patients showed metastases in their CAD; a single node in 10 cases, 2-3 in 4 and &gt; 3 in one patient. Univariate analysis showed chemo- and hormono-therapy to be more frequently administered in pN0i+ (24.5% vs. 77.6%) compared to pN0 (9.1% vs. 55.8%) patients; p &lt; 0.0001. Irrespective of the result of CAD, pN0i+ patients had significant modifications in their fields of lymphatic irradiation at the internal mammary (43.6% vs. 23.5%), supra-clavicular (40.9% vs. 21.5%) and sub-clavicular (13.5% vs. 3.7%) areas; p &lt; 0.0001. Other predictive factors showed a similar pattern including age &lt; 50 years (31.5% vs. 18.6%), tumour size bigger (1.51cm vs. 1.16 cm) and lymphovascular invasion (27.5% vs. 11.6%); p &lt; 0,0001. After multivariate analysis, the sole decisive factor for chemotherapy between the two groups was the presence of nodal metastasis in CAD. The duration of this study is, however, insufficient to comment on the long-term implications for pN0i+ patients.&#x2028; Discussion: immunohistochemistry alone plays a decisive role in favour of chemotherapy in N+ supplementary AD in only 10% of pN0i+ (15/143) patients. However, this concerns only 1% (15/1506) of those undergoing IHC so may have significant resource implications and other factors were found to be more influential. Moreover, pN0i+ patients underwent additional lymphatic irradiation, to all 3 fields, more frequently.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 206.