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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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE54002 | GEO | 2014/09/16

SECONDARY ACCESSION(S): PRJNA234318

REPOSITORIES: GEO

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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. 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.

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Expression data from LCM captured prostate cancer cells

Project description:The prostate represents a complex mix of cell types and there is a need to analyze distinct cell populations to better understand their potential interactions. This study of cell-type specific gene expression patterns will contribute to understanding of how tumor epithelial cells may be affected by adjacent interstitial stromal cells within the tumor microenvirnonment. LCM and microarray analysis were used to identify gene expression patterns in prostate cancer epithelial and interstitial stromal cell populations. More than 500 genes whose expression levels were significantly different in epithelial cells versus adjacent stromal tissue were identified. Several chemokines and growth factors were more highly expressed in prostate cancer stromal cells while several transcription factors and receptors were more highly expressed in epithelial cells. Five micron serial sections from three different intermediate grade prostate tumors were provided. One section from each had been stained by hematoxylin and eosin and the tumor areas marked for identification. To obtain RNA from 2 different tissue types (glandular epithelium and interstitial stroma) tumor areas observed to have abundant cells of interest were identified. Tumor epithelium and adjacent stromal tissue were collected separately from each slide. We sought to obtain similar populations of cells of each tissue type, so to that end, we examined each slide and and marked areas to direct the laser capture. Approximately 1,000 cells were captured per cap and RNA was extracted and hybridized to Affymetrix microarrays as recommended by manufacturer.

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