The Molecular Anatomy of Breast Cancer Stroma; Independent Prognostic Role in ER-Positive and ER-Negative Cancers.
Authors: G. Bianchini, G. Bianchini, R. Alvarez, Y. Qi, C. Hatzis, T. Iwamoto, C. Shiang, C. Coutant, G. Hortobagyi, W. Symmans, L. Pusztai
Journal: Cancer Research (2009)

Abstract BackgroundIn this paper we examine the various molecular components of a breast cancer stromal gene signature and correlate these with clinical phenotype and outcome including prognosis and response to preoperative chemotherapy.MethodsWe compared Affymetrix HGU133A-based gene expression profiles of 37 matching core needle biopsies (CNB) and fine-needle aspirations (FNA) from the same cancers. Genes over-expressed in CNB relative to the FNA were defined as the “stromal signature”. Gene expression data from 56 breast cancer cell lines, two separate neoadjuvant data sets (n=233, n=103), 3 independent cohorts of node negative, untreated patients (n=286, n=198, n=200) and 259 estrogen receptor-positive (ER+) tamoxifen-treated patients were used to assess the prognostic and predictive values of these genes in ER+ and ER- cancers separately. Univariate and multivariate Cox analyses were performed. Metagenes were defined as average expression of co-clustered genes.Results293 probe sets (206 genes) were significantly over-expressed in the CNBs (false discovery rate ≤ 0.001, fold-change ≥ 3). These genes overlapped with previously reported stromal signatures and fell into several co-expression clusters including a B-cell/Plasma Cell (B-cell), Dendritic cell, extracellular matrix (ECM), and TGFb-receptor metagenes. Interestingly, ER+ and ER- cancers showed a significantly different stroma-gene expression pattern, and many stromal genes were also differentially expressed between ER+ and ER- breast cancer cell lines. The ECM and TGFb metagenes had modest and variable prognostic value across different datasets in both ER groups. The Dendritic and B cell metagenes were highly co-expressed, but the B-cell metagene had more robust and consistent prognostic value. The B-cell metagene was statistically significant prognostic in univariate and multivariate analysis in ER+/High proliferative and ER- tumors, but it was not prognostic in ER+/Low proliferative tumors. In the 3 different node negative, untreated patient cohorts, the ER+/High proliferative cancers in the lowest B-cell metagene tertile had 10-year distant metastasis free survival (DMFS) of 0.18 (0.07-0.46), 0.22 (0.06-0.75), and 0.44 (0.21-0.92) compared to 0.71 (0.54-0.94), 0.89 (0.71-1.00) and 0.89 (0.71-1.00) in the highest tertile. Among the ER- cancers, the lowest B cell metagene group had 10-year DMFS of 0.57 (0.44-0.75), 0.63 (0.48-0.83), and 0.44 (0.25-0.76) compared to 0.93 (0.81-1.00), 0.83 (0.64-1.00) and 0.83 (0.58-1.00) in the highest B-cell metagene group in each prognostic dataset, respectively. The B-cell metagene was also prognostic in univariate (HR 0.83 (0.71-0.98) p=0.03) and multivariate (HR 0.80 (0.68-0.94) p=0.007) analysis in the Tamoxifen-treated cohort. None of the above stromal metagenes showed reproducible association with response to chemotherapy.ConclusionsThe B-cell/Plasma cell metagene component of the “stroma-related genes” is a robust and reproducible prognostic marker in ER+/High proliferative and also in ER- cancers. Other stromal genes are variably expressed in ER+ and ER- tumors and many are also expressed by neoplastic cells in culture and by primary tumors and carry less reproducible prognostic value. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 105.