Review Article

Gene Expression Analysis of In Vitro Cocultures to Study Interactions between Breast Epithelium and Stroma

Table 1

Whole genome microarray studies to investigate breast cancer microenvironments in human tissues.

Authors [citation]Type of specimen studiedProcessing of specimenType of microenvironmentMajor findings

Finak et. al. (2008) [13]Fresh, frozen tissue from primary cancers (53) and adjacent nonaffected tissue (31) from breast cancer patientsLaser capture microdissection
of tumor stroma
Intratumoral versus extratumoral Stromal derived prognostic Predictor (SDPP), a gene set that stratifies patients by disease outcome. Genes are involved in immune response, angiogenesis, and hypoxic response.

Ma et al. (2009) [14]Fresh frozen biopsies from disease-free tissue, DCIS, and invasive breast cancer (14).Laser capture microdissectionIntratumoralTumor microenvironment participates in tumorigensis before tumor cells invade. Invasiveness is dependent on the signals from myoepithelial cells, fibroblasts, and myfibroblosts.

Allinen et al. (2004) [15]Snap-frozen biopsies from reduction mammoplasties, DCIS, and invasive breast cancer.Isolation of pure cell populations by differential centrifugationIntratumoralWidespread genome changes in all stromal cell types. Genetic alterations only occur in epithelial cancer cells.

Troester et al. (2009) [11]Snap-frozen tissue from histologically normal tissue adjacent to breast cancer (47) and reduction mammoplasties (60).Whole genome profiles
of the tissue
ExtratumoralA wound response is activated in the tumor microenvironment. The wound response signature predicts cancer progression.

Chang et al. (2004) [12], Chang et al. (2005) [16]Isolated fibroblasts from 10 different anatomical sites and tissue from early breast cancer patients (295)In vitro response of the fibroblast populations
to serum
Intratumoral
normal tissue
Identification of an in vitro wound response, enriched in early stage tumors. High expression of this signature correlates with worse overall survival and increased distant metastasis.

Beck et al. (2008) [18]Desmoid fibromatosis and solitary fibrous tumors.IntratumoralDTF core gene set (derived mainly from fibroblasts) is a robust descriptor of stromal response that is associated with improved clinical outcome in public genomic data from breast cancer patients.

Beck et al. (2009) [17]Tenosynovial giant cell tumors and pigmented villonodular synovitisIntratumoralThe CSF1 gene expression signature (derived mainly from macrophages) is present in more aggressive cancers.

Luciani et al. (2011) [29]Tissue from primary breast tumors and reduction mammoplastiesIsolation of epithelial
and fibroblast cells.
IntratumoralA “fibroblast triggered gene expression” gene set generated by coculture of primary breast tumor cell lines and fibroblasts is enriched for inflammatory signaling, cell death, and cell proliferation genes. Predicts survival in independent datasets.