Induction of interferon response in two types of breast cancer cell lines

MDA-MB231 cells were incubated in conditioned media from CCL-171 monoculture, MDA-MB231 monoculture, T47D monoculture, CCL-171/MDA-MB231 co-culture and CCL-171/T47D co-culture. gene expression was determined by quantitative RT-PCR. The gene expression level of GAPDH was used for normalization between the samples. A strong induction of by the supernatant from the CCL-171/MDA-MB231 co-culture can be seen in MDA-MB231. Incubation of T47D cells with conditioned media from CCL-171 monoculture, MDA-MB231 monoculture, T47D monoculture, CCL-171/MDA-MB231 co-culture and CCL-171/T47D co-culture showed that only the CCL-171/MDA-MB231 co-culture supernatant induced gene expression, although to a much lesser extent than in MDA-MB231 cells. Gene expression levels of were determined by quantitative RT-PCR. CCL-171 cells show much higher expression levels when isolated by FACS after co-culture with MDA-MB231 than with T47D cells. Expression levels in tumor cells are shown as controls. The error bars show the standard deviation from the normalized mean.<p><b>Copyright information:</b></p><p>Taken from "Characterization of heterotypic interaction effects to deconvolute global gene expression profiles in cancer"</p><p>http://genomebiology.com/2007/8/9/R191</p><p>Genome Biology 2007;8(9):R191-R191.</p><p>Published online 14 Sep 2007</p><p>PMCID:PMC2375029.</p><p></p

Correlation of the 70 genes signature 38, the wound signature 24, the hypoxia signature 25 and the interferon response score in the NKI dataset

Pairwise scatterplot-matrix of four gene signatures. Pearson correlations are shown in the lower part of each plot.<p><b>Copyright information:</b></p><p>Taken from "Characterization of heterotypic interaction effects to deconvolute global gene expression profiles in cancer"</p><p>http://genomebiology.com/2007/8/9/R191</p><p>Genome Biology 2007;8(9):R191-R191.</p><p>Published online 14 Sep 2007</p><p>PMCID:PMC2375029.</p><p></p

Overview of gene expression changes over multiple co-cultures of breast cancer cell lines and normal breast epithelial cells with fibroblasts

Correlation of the measured co-culture gene expression levels and their estimated expression levels based on the proportional contribution of each cell type determined by a linear regression fit of the monoculture to the co-culture data. Fold change of each gene associated with co-culturing of MDA-MB231 and CCL-171. Genes of the interferon response gene set (Additional data file 1) as determined by SAM are indicated in red. Fold change in expression of the interferon response gene set (Additional data file 1) in co-culture of MCF-7, HMECs and MDA-MB-231 with either the CCL-171 lung fibroblast or the HTB-125 breast fibroblast, showing that CCL-171 and HTB-125 induce a distinct, but very similar response in co-culture with different epithelial cells. Overview of collapsed data from repeat co-culture experiments of eight benign and malignant epithelial cells with three different fibroblasts. Hierarchical clustering of the interaction effects of 3,000 genes in co-cultures of 7 breast cancer cell lines and normal breast epithelial cells with fibroblasts. Red and green denote relative changes in expression associated heterotypic interaction. The magnitude of the relative change is given by color intensity.<p><b>Copyright information:</b></p><p>Taken from "Characterization of heterotypic interaction effects to deconvolute global gene expression profiles in cancer"</p><p>http://genomebiology.com/2007/8/9/R191</p><p>Genome Biology 2007;8(9):R191-R191.</p><p>Published online 14 Sep 2007</p><p>PMCID:PMC2375029.</p><p></p

Immunohistochemical staining of STAT1 in a cohort of primary breast cancers: Kaplan-Meier disease-specific survival curve for 353 primary tumors assessed for STAT1

The red curve shows 102 patients bearing tumors with high STAT1 expression whereas the blue curve represents 251 patients with low or absent STAT1 expression. X = censored data.<p><b>Copyright information:</b></p><p>Taken from "Characterization of heterotypic interaction effects to deconvolute global gene expression profiles in cancer"</p><p>http://genomebiology.com/2007/8/9/R191</p><p>Genome Biology 2007;8(9):R191-R191.</p><p>Published online 14 Sep 2007</p><p>PMCID:PMC2375029.</p><p></p

Effect of heterotypic interaction between breast cancer cell line MDA-MB231 and CCL-171 fibroblasts

Biologically independent replicates of the monocultured fibroblast CCL-171, the breast cancer cell line MDA-MB231 and the mixed co-culture of CCL-171 and MDA-MB231 were grown for 48 h at low serum conditions and characterized by DNA microarray hybridization. Hierarchical clustering of a total of 4,333 elements that display a greater than 3-fold variance in expression in more than 3 different experimental samples. Data from individual elements or genes are represented as single rows, and different experiments are shown as columns. Red and green denote expression levels of the samples. The intensity of the color reflects the magnitude of the deviation from baseline. Unsupervised hierarchical clustering of the experiments grouped the biological replicates together. Gene expression varied considerably between fibroblast and MDA-MB231 cultures, as expected for cells of mesenchymal or epithelial origin, respectively. The co-culture profile showed mainly intermediate expression levels. However, the vertical black bar marks a cluster of genes induced in all co-cultures compared to both monocultures, indicating that they are induced by heterotypic interaction. Zooming in on the genes up-regulated in co-culture compared to monocultures reveals that they are associated with the response to interferon.<p><b>Copyright information:</b></p><p>Taken from "Characterization of heterotypic interaction effects to deconvolute global gene expression profiles in cancer"</p><p>http://genomebiology.com/2007/8/9/R191</p><p>Genome Biology 2007;8(9):R191-R191.</p><p>Published online 14 Sep 2007</p><p>PMCID:PMC2375029.</p><p></p

Additional file 1: of The Prosigna gene expression assay and responsiveness to adjuvant cyclophosphamide-based chemotherapy in premenopausal high-risk patients with breast cancer

Figure S1. Consort flow diagram. (PDF 234 kb

Intrinsic subtypes and benefit from postmastectomy radiotherapy in node-positive premenopausal breast cancer patients who received adjuvant chemotherapy – results from two independent randomized trials

<p><b>Background:</b> The study of the intrinsic molecular subtypes of breast cancer has revealed differences among them in terms of prognosis and response to chemotherapy and endocrine therapy. However, the ability of intrinsic subtypes to predict benefit from adjuvant radiotherapy has only been examined in few studies.</p> <p><b>Methods:</b> Gene expression-based intrinsic subtyping was performed in 228 breast tumors collected from two independent post-mastectomy clinical trials (British Columbia and the Danish Breast Cancer Cooperative Group 82b trials), where pre-menopausal patients with node-positive disease were randomized to adjuvant radiotherapy or not. All patients received adjuvant chemotherapy and a subgroup of patients underwent ovarian ablation. Tumors were classified into intrinsic subtypes: Luminal A, Luminal B, HER2-enriched, Basal-like and Normal-like using the research-based PAM50 classifier.</p> <p><b>Results:</b> In the British Columbia study, patients treated with radiation had an overall significant lower incidence of locoregional recurrence compared to the controls. For Luminal A tumors the risk of loco-regional recurrence was low and was further lowered by adjuvant radiation. These findings were validated in the DBCG 82b study. The individual data from the two cohorts were merged, the hazard ratio (HR) for loco-regional recurrence associated with giving radiation was 0.34 (0.19 to 0.61) overall and 0.12 (0.03 to 0.52) for Luminal A tumors.</p> <p><b>Conclusions:</b> In both postmastectomy trials, patients with Luminal A tumors turned out to have a significant lower incidence of loco-regional recurrence when randomized to adjuvant radiotherapy, leaving no indication to omit postmastectomy adjuvant radiation in pre-menopausal high-risk patients with Luminal A tumors. It was not possible to evaluate the effect of radiotherapy among the other subtypes because of limited sample sizes.</p

Additional file 10: Table S5. of Development and verification of the PAM50-based Prosigna breast cancer gene signature assay

Genes used to calculate the Prosigna proliferation score. (DOC 28 kb

Additional file 4: Table S3. of Development and verification of the PAM50-based Prosigna breast cancer gene signature assay

Accuracy estimates (ICC, Slopes, and R-squared) for all genes between nCounter and qRT-PCR. (DOC 57 kb

Additional file 2: Table S2. of Development and verification of the PAM50-based Prosigna breast cancer gene signature assay

Description of FFPE breast cancer patient samples used for training and verifying the Prosigna Algorithm. (DOCX 30 kb