Dataset Information

Transcription profiling by array of human breast epithelium and stroma in normal reduction mammoplasty and invasive breast cancer patients

ABSTRACT: The molecular basis of breast cancer invasion and metastasis is not well understood. Our objective was to analyze transcriptome differences between stromal and epithelial cells in normal breast tissue and invasive breast cancer to define the role stroma plays in invasion. Total RNA was isolated from epithelial and stromal cells that were laser captured from normal breast tissue (n=5) and invasive breast cancer (n=28). Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Differential gene expression was evaluated and compared within a model that accounted for cell type (epithelial [E] versus stromal [S]), diagnosis (cancer [C] versus normal [N]) as well as cell type-diagnosis interactions. Compared to NE, the CE transcriptome was highly enriched with genes in proliferative, motility and ECM ontologies. Differences in CS and NS transcriptomes suggested that the ECM was being remodeled in invasive breast cancer, as genes were over-represented in ECM and proteolysis ontologies. Genes more highly expressed in CS compared to CE were primarily ECM components or were involved in the remodeling of ECM, suggesting that ECM biosynthesis and remodeling were initiated in the tumor stromal compartment. Experiment Overall Design: Breast tissue was collected at surgery from patients undergoing surgical resection for invasive breast cancer (n=28) and reduction mammoplasty (n=5). Tissue was cryopreserved in OCT and serial sections were cut using a cryostat. Sections were stained and epithelial and stromal cells were isolated by laser capture microdissection. Total RNA was isolated and target was prepared using NuGen Ribo-SPIA Ovation Technology. Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Gene expression differences were evaluated using a linear model of the Robust Multichip Average gene expression statistic, a model that accounted for cell type (E and S), patient diagnosis (C and N), as well as cell type-diagnosis interactions. Data were examined to determine false discovery rate and were filtered for fold changes in gene expression and p-value.

ORGANISM(S): Homo sapiens

SUBMITTER: Casey T

PROVIDER: S-ECPF-GEOD-10797 | biostudies-other | 2009 Mar

REPOSITORIES: biostudies-other

ACCESS DATA

Similar Datasets

Project description:The molecular basis of breast cancer invasion and metastasis is not well understood. Our objective was to analyze transcriptome differences between stromal and epithelial cells in normal breast tissue and invasive breast cancer to define the role stroma plays in invasion. Total RNA was isolated from epithelial and stromal cells that were laser captured from normal breast tissue (n=5) and invasive breast cancer (n=28). Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Differential gene expression was evaluated and compared within a model that accounted for cell type (epithelial [E] versus stromal [S]), diagnosis (cancer [C] versus normal [N]) as well as cell type-diagnosis interactions. Compared to NE, the CE transcriptome was highly enriched with genes in proliferative, motility and ECM ontologies. Differences in CS and NS transcriptomes suggested that the ECM was being remodeled in invasive breast cancer, as genes were over-represented in ECM and proteolysis ontologies. Genes more highly expressed in CS compared to CE were primarily ECM components or were involved in the remodeling of ECM, suggesting that ECM biosynthesis and remodeling were initiated in the tumor stromal compartment. Experiment Overall Design: Breast tissue was collected at surgery from patients undergoing surgical resection for invasive breast cancer (n=28) and reduction mammoplasty (n=5). Tissue was cryopreserved in OCT and serial sections were cut using a cryostat. Sections were stained and epithelial and stromal cells were isolated by laser capture microdissection. Total RNA was isolated and target was prepared using NuGen Ribo-SPIA Ovation Technology. Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Gene expression differences were evaluated using a linear model of the Robust Multichip Average gene expression statistic, a model that accounted for cell type (E and S), patient diagnosis (C and N), as well as cell type-diagnosis interactions. Data were examined to determine false discovery rate and were filtered for fold changes in gene expression and p-value.

Project description:Normal-appearing epithelium of cancer patients can harbor occult genetic abnormalities. Data comprehensively comparing gene expression between histologically normal breast epithelium of breast cancer patients and cancer-free controls are limited. The present study compares global gene expression between these groups. We performed microarrays using RNA from microdissected histologically normal terminal ductal-lobular units (TDLU) from 2 groups: (i) cancer normal (CN) (TDLUs adjacent to untreated ER1 breast cancers (n = 14)) and (ii) reduction mammoplasty (RM) (TDLUs of age-matched women without breast disease (n = 15)). Cyber-T identi?ed differentially expressed genes. Quantitative RT-PCR (qRT-PCR), immunohistochemistry (IHC), and comparison to independent microarray data including 6 carcinomas in situ (CIS), validated the results. Gene ontology (GO), UniProt and published literature evaluated gene function. About 127 probesets, corresponding to 105 genes, were differentially expressed between CN and RM (p < 0.0009, corresponding to FDR <0.10). 104/127 (82%) probesets were also differentially expressed between CIS and RM, nearly always (102/104 (98%)) in the same direction as in CN vs. RM. Two-thirds of the 105 genes were implicated previously in carcinogenesis. Overrepresented functional groups included transcription, G-protein coupled and chemokine receptor activity, the MAPK cascade and immediate early genes. Most genes in these categories were under-expressed in CN vs. RM. We conclude that global gene expression abnormalities exist in normal epithelium of breast cancer patients and are also present in early cancers. Thus, cancer-related pathways may be perturbed in normal epithelium. These abnormalities could be markers of disease risk, occult disease, or the tissue’s response to an existing tumor. Experiment Overall Design: 29 samples from histologically normal microdissected breast epithelium are included in this series. 14 samples are from epithelium adjacent to a breast tumor, 15 samples were obtained from patients undergoing reduction mammoplasty without apparent breast cancer

Dataset Information

Transcription profiling by array of human breast epithelium and stroma in normal reduction mammoplasty and invasive breast cancer patients

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure