Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas

Abstract

Introduction: Breast cancer is a heterogeneous group of tumors, and can be subdivided on the basis of histopathological features, genetic alterations and gene-expression profiles. One well-defined subtype of breast cancer is characterized by a lack of HER2 gene amplification and estrogen and progesterone receptor expression ('triple-negative tumors'). We examined the histopathological and gene-expression profile of triple-negative tumors to define subgroups with specific characteristics, including risk of developing distant metastases.

Methods: 97 triple-negative tumors were selected from the fresh-frozen tissue bank of the Netherlands Cancer Institute, and gene-expression profiles were generated using 35K oligonucleotide microarrays. In addition, histopathological and immunohistochemical characterization was performed, and the findings were associated to clinical features.

Results: All triple-negative tumors were classified as basal-like tumors on the basis of their overall gene-expression profile. Hierarchical cluster analysis revealed five distinct subgroups of triple-negative breast cancers. Multivariable analysis showed that a large amount of lymphocytic infiltrate (HR = 0.30, 95% CI 0.09-0.96) and absence of central fibrosis in the tumors (HR = 0.14, 95% CI 0.03-0.62) were associated with distant metastasis-free survival.

Conclusion: Triple-negative tumors are synonymous with basal-like tumors, and can be identified by immunohistochemistry. Based on gene-expression profiling, basal-like tumors are still heterogeneous and can be subdivided into at least five distinct subgroups. The development of distant metastasis in basal-like tumors is associated with the presence of central fibrosis and a small amount of lymphocytic infiltrate.

Figure 1

Tumor dendogram of 199 samples. The dendogram depicts the hierarchical cluster analysis with 97 triple-negative tumors (red) combined with 102 invasive breast carcinomas, which were not selected based on their triple-negative status (green and blue), using the 293 intrinsic-gene list.

Figure 2

Overall gene expression profile of triple-negative tumors. Hierarchical cluster analysis of 97 triple-negative tumors and 7,770 genes.

Figure 3

Association of pathological and immunohistochemical characteristics with the overall gene-expression profile of triple-negative tumors. Distribution of tumor type and immunohistochemical staining for KRT5/6, epidermal growth factor receptor (EGFR) and KIT in the dendogram of the 97 triple-negative tumors after hierarchical clustering of these samples based on the expression of 7,770 genes.

Figure 4

Overall gene-expression profile of triple-negative tumors associated with disease outcome. (a) Hierarchical cluster analysis of the overall gene-expression profile of 71 triple-negative tumors with identifiable gene clusters indicated on the right hand side. (b) Metastasis-free survival of 71 patients with triple-negative breast carcinomas, comparing the left branch with the right branch of the overall gene-expression hierarchical cluster analysis.

Figure 5

Kaplan-Meier curves. Metastasis-free survival of 71 patients with triple-negative breast carcinomas comparing: (a) number of tumor-positive lymph nodes, (b) amount of lymphocytic infiltrate, (c) presence of a central fibrotic zone and (d) combination of the amount of lymphocytic infiltrate and presence of a central fibrotic zone.