Gene expression profiles of tumor epithelium and tumor-associated stroma of HER2+ breast tumors, plus normal epithelium and stroma from HER2+ and HER2- breast tumors

Breast cancer is a heterogeneous disease. This heterogeneity can be observed at multiple levels, including gene expression, chromosomal aberrations, and disease pathology. A clear understanding of these differences is important since they impact upon treatment efficacy and clinical outcome. Many studies have shown that the tumor microenvironment also plays a critical role in cancer initiation and progression. Although genomic technologies have been used to gain a better understanding of the impact of gene expression heterogeneity on breast cancer outcome by identifying gene expression signatures associated with clinical outcome, histopathological breast cancer subtypes, and a variety of cancer-related pathways and processes, relatively little is known about the spectrum of heterogeneity in the tumor microenvironment. 107 samples isolated by laser capture microdissection; in total, 40 samples of tumor epithelium, 39 samples of tumor stroma, 14 samples of normal epithelium and 14 samples of normal stroma; 2 samples possess biological replicates; each subjected to gene expression profiling in a common reference design using Agilent whole human genome oligonucleotide arrays.