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Gene expression profiling of LCM captured breast cancer cells

ABSTRACT: The purpose of this study is to obtain comprehensive gene expression profiles in breast cancer. Mammary gland cells were specifically isolated from 433 clinical tissue samples by laser capture microdissection (LCM). Total RNAs were extracted from LCM captured samples. We investigated gene expression profiles in 417 patients with breast cancer and 16 non-tumor tissues as a normal control using an Affymetrix GeneChip. Mammary gland cells were captured from clinical tissues of breast cancer patient by LCM. Gene expression profilings for 417 tumor and 16 non-tumor samples were acquired using GeneChip Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA). Microarray datasets were normalized and transformed to log2 values using robust multi-array average (RMA) method with R statistical software and BioConductor package.

ORGANISM(S): Homo sapiens

SUBMITTER: Tuan Zea Tan

PROVIDER: E-GEOD-54002 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients.

Tan Tuan Zea TZ Miow Qing Hao QH Miki Yoshio Y Noda Tetsuo T Mori Seiichi S Huang Ruby Yun-Ju RY Thiery Jean Paul JP

EMBO molecular medicine 20141001 10

Epithelial-mesenchymal transition (EMT) is a reversible and dynamic process hypothesized to be co-opted by carcinoma during invasion and metastasis. Yet, there is still no quantitative measure to assess the interplay between EMT and cancer progression. Here, we derived a method for universal EMT scoring from cancer-specific transcriptomic EMT signatures of ovarian, breast, bladder, lung, colorectal and gastric cancers. We show that EMT scoring exhibits good correlation with previously published, ...[more]

PMID: 25214461

Similar Datasets

Gene expression profiling of LCM captured breast cancer cells

Project description:The purpose of this study is to obtain comprehensive gene expression profiles in breast cancer. Mammary gland cells were specifically isolated from 433 clinical tissue samples by laser capture microdissection (LCM). Total RNAs were extracted from LCM captured samples. We investigated gene expression profiles in 417 patients with breast cancer and 16 non-tumor tissues as a normal control using an Affymetrix GeneChip.

2014-09-16 | GSE54002 | GEO

Tumor and stroma from breast by LCM

2007-09-30 | GSE5847 | GEO

wnt1-induced mammary tumor from Rarb KO mice vs. those from Rarb wt (control)

Project description:Previously we have demonstrated that inactivation of retinoic acid receptor beta (Rarb) in the mouse results in a protective effect against ErbB2-induced mammary gland tumorigenesis although Rarb has been reported as a tumor suppressor before. In the current study, we further confirmed that ablation of Rarb has a very similar impact on Wnt1-induced mammary gland tumorigenesis as those on ErbB2-induced mammary gland tumorigenesis. Nevertheless, the mechanisms by which Rarb confers its effects on tumor progression is quite different although both involving in tumor microenvironment (TME) remodeling. In the Wnt1 tumors, ectopic wnt1 produced by malignant luminal cells activates nearby stromal cells by a paracrine manner. In return, the stromal cells secreted IGF1 to regulate the growth of tumor cells. There is a need of Rarb expression in this interaction. Deletion of Rarb inhibits both wnt1/β-catenin signaling and IGF1/Akt axis in the myoepithelial tumor cells which results in the suppression of epithelial-mesenchymal transition (EMT) in these tumors. Since wnt1 tumors resemble basal-like breast cancer with a poor clinical prognosis in which EMT is one of the most important way for tumor cells to survive against standard treatment and to go to metastasis, we propose that (1) the stromal gene expression signature of Rarb ablation in wnt1 tumors could have some clinical value in predicting the breast cancer outcome; and (2) Rarb antagonist might be a potential therapeutic strategy in EMT-driven aggressive cancers such as basal-like breast cancer. Laser capture microdissection (LCM) was performed to separate the mammary tumor samples into epithelial cell compartment and stromal cell compartment. Transcriptional profiling of the two compartments were investigated by microarray analysis.

2014-10-23 | E-GEOD-56391 | biostudies-arrayexpress

Gene expression anlaysis of laser-capture microdissected tumor and stroma from triple negative breast cancer

Project description:LCM was perfomed on adjacent tumor and stromal cells to identify differentially expressed genes in triple negative breast cancer. To determine differences in tumor and adjacent stromal tissue, laser-capture microdissction was perfomed on 10 triple negative breast cancer specimans to isolate tumor and stromal cells for gene expression analysis. RNA was isolated from captured cells and hybridized to affymetrix gene expression microarrays.

2016-07-01 | E-GEOD-81838 | biostudies-arrayexpress

The differences in miRNA expression with miRNA microarrays of two-dimensional (2D)- and three-dimensional (3D)-SNP cells

Project description:Canine mammary gland tumors can be used as predictive models for human breast cancer. There are several types of microRNAs common in human breast cancer and canine mammary gland tumors. The functions of microRNAs in canine mammary gland tumors are not well understood. In the present study, we compared the characterization of microRNA expression in two-dimensional and three-dimensional canine mammary gland tumor cell models. The expression of microRNA-210 in the three-dimensional-SNP cells was 10.19 times higher than that in the two-dimensional-SNP cells.

2022-07-07 | GSE203410 | GEO

Rat mammary normal - tumor

Project description:Rat mammary tumors induced by N-methyl-N-nitrosurea (NMU) and normal mammary gland Keywords = breast cancer Keywords = rat mammary tumor Keywords = NMU Keywords = animal model. Keywords: other

2005-04-30 | GSE1872 | GEO

Transcription profiling of human tumor and stroma from breast catured by LCM of inflammatory and non inflammatory breast cancers

Project description:Tumor epithelium and surrounding stromal cells were isolated using laser capture microdissection of human breast cancer to examine differences in gene expression based on tissue types from inflammatory and non-inflammatory breast cancer Experiment Overall Design: We applied LCM to obtain samples enriched in tumor epithelium and stroma from 15 IBC and 35 non-IBC cases to study the relative contribution of each component to the IBC phenotype and to patient survival.

2008-06-14 | E-GEOD-5847 | biostudies-arrayexpress

Homo sapiens

Project description:Gene expression profiling of LCM captured breast cancer cells

| PRJNA234318 | ENA

Transcription profiling of human tumor microenvironment during breast cancer progression

Project description:To better understand the role of tumor microenvironment in breast cancer progression, we combined laser capture microdissection and microarray analysis to provide a comprehensive catalog of gene expression changes in both tumor and tumor-associated stroma. Experiment Overall Design: We used LCM to isolate the epithelial and stroma compartments separately from each of 14 fresh frozen primary breast cancer biopsies. In the epithelial compartment, we captured normal (N) and malignant (DCIS or IDC or both where available) epithelium from each tissue slide. In the stroma compartment, we captured both normal stroma away from the malignant lesion (NSS) and the DCIS-associated stroma (ISS) and/or IDC-associated stroma (INVS) whenever possible.

2009-02-26 | E-GEOD-14548 | biostudies-arrayexpress

Transcription profiling of mouse WAP-SVT/t transgenic animals during breast cancer formation

Project description:Microarray studies revealed that as a first hit, SV40 T/t-antigen causes deregulation of 462 genes in mammary gland cells (ME-cells) of WAP-SVT/t transgenic animals. The majority of deregulated genes are cell-proliferation specific and Rb-E2F dependent, causing ME-cell proliferation and gland hyperplasia but not breast cancer formation. In the breast tumor cells, a further 207 genes are differentially expressed, most of them belonging to the cell communication category. In tissue culture, breast tumor cells frequently switch off WAP-SVT/t transgene expression and regain the morphology and growth characteristics of normal-ME-cells, although the tumor-revertant cells are aneuploid and only 114 genes regain the expression level of normal-ME-cells. The profile of retransformants shows that only 38 deregulated genes appear to be tumor-relevant and that none of them is considered to be a typical breast cancer gene. Experiment Overall Design: We have analyzed nine mammary gland tissue segments from three normal NMRI, three WAP-SVT/t mice on the first day of lactation and from three WAP-SVT/t breast cancers (583-tumor 1, 585-tumor 2, 597-tumor 3) as well as three distinct breast cancer derived cell lines (ME-A cells, revertant-ME-B cells and ME-B-T/t cells).

2009-04-25 | E-GEOD-6246 | biostudies-arrayexpress

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