Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers

Abstract

Introduction: Basal-phenotype or basal-like breast cancers are characterized by basal epithelium cytokeratin (CK5/14/17) expression, negative estrogen receptor (ER) status and distinct gene expression signature. We studied the clinical and biological features of the basal-phenotype tumors determined by immunohistochemistry (IHC) and cDNA microarrays especially within the ER-negative subgroup.

Methods: IHC was used to evaluate the CK5/14 status of 445 stage II breast cancers. The gene expression signature of the CK5/14 immunopositive tumors was investigated within a subset (100) of the breast tumors (including 50 ER-negative tumors) with a cDNA microarray. Survival for basal-phenotype tumors as determined by CK5/14 IHC and gene expression signature was assessed.

Results: From the 375 analyzable tumor specimens, 48 (13%) were immunohistochemically positive for CK5/14. We found adverse distant disease-free survival for the CK5/14-positive tumors during the first years (3 years hazard ratio (HR) 2.23, 95% confidence interval (CI) 1.17 to 4.24, p = 0.01; 5 years HR 1.80, 95% CI 1.02 to 3.15, p = 0.04) but the significance was lost at the end of the follow-up period (10 years HR 1.43, 95% CI 0.84 to 2.43, p = 0.19). Gene expression profiles of immunohistochemically determined CK5/14-positive tumors within the ER-negative tumor group implicated 1,713 differently expressed genes (p < 0.05). Hierarchical clustering analysis with the top 500 of these genes formed one basal-like and a non-basal-like cluster also within the ER-negative tumor entity. A highly concordant classification could be constructed with a published gene set (Sorlie's intrinsic gene set, concordance 90%). Both gene sets identified a basal-like cluster that included most of the CK5/14-positive tumors, but also immunohistochemically CK5/14-negative tumors. Within the ER-negative tumor entity there was no survival difference between the non-basal and basal-like tumors as identified by immunohistochemical or gene-expression-based classification.

Conclusion: Basal cytokeratin-positive tumors have a biologically distinct gene expression signature from other ER-negative tumors. Even if basal cytokeratin expression predicts early relapse among non-selected tumors, the clinical outcome of basal tumors is similar to non-basal ER-negative tumors. Immunohistochemically basal cytokeratin-positive tumors almost always belong to the basal-like gene expression profile, but this cluster also includes few basal cytokeratin-negative tumors.

Figure 1

Hierarchical clustering of 50 ER-negative tumors based on the top 500 basal genes. The gene set was generated for the CK5/14-positive basal phenotype tumors. Yellow indicates the basal-like cluster and black the non-basal-like cluster. The boxes beneath indicate the immunohistochemically CK5/14-positive tumors and the HER-2 oncogene-amplified tumors (solid box, positive; open box, negative, crossed box, data missing).

Figure 2

Hierarchical clustering of 50 ER-negative tumors based on the intrinsic gene set [7]. Yellow indicates the basal-like cluster and black the non-basal-like cluster. The black boxes beneath indicate the basal-like cluster by the top 500 basal genes, immunohistochemically CK5/14-positive tumors, and HER-2 amplified tumors (solid box, positive; open box, negative, crossed box, data missing).

Figure 3

Distant disease-free survival of immunohistochemically CK5/14-negative and CK5/14-positive tumors in the whole data set. The basal cytokeratin-positive tumors show significantly shorter survival during the first years of the follow-up, but this difference is lost with time.

Figure 4

Distant disease-free survival of basal-like and non-basal-like tumors within the ER-negative tumor entity. The basal phenotype was defined by using immunohistochemistry (a), cDNA microarray and the top 500 gene set for the basal cytokeratin-immunopositive tumors (b) or cDNA microarray and the intrinsic gene set of Sorlie and colleagues [7] (c). There is no difference in survival between basal-like and non-basal-like tumors within the ER-negative tumor subgroup.