Repeated observation of breast tumor subtypes in independent gene expression data sets

Abstract

Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be distinguished by their distinct patterns of gene expression. A total of 115 malignant breast tumors were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into one basal-like, one ERBB2-overexpressing, two luminal-like, and one normal breast tissue-like subgroup. The genes used for classification were selected based on their similar expression levels between pairs of consecutive samples taken from the same tumor separated by 15 weeks of neoadjuvant treatment. Similar cluster analyses of two published, independent data sets representing different patient cohorts from different laboratories, uncovered some of the same breast cancer subtypes. In the one data set that included information on time to development of distant metastasis, subtypes were associated with significant differences in this clinical feature. By including a group of tumors from BRCA1 carriers in the analysis, we found that this genotype predisposes to the basal tumor subtype. Our results strongly support the idea that many of these breast tumor subtypes represent biologically distinct disease entities.

Figures

Fig. 1.

Hierarchical clustering of 115 tumor tissues and 7 nonmalignant tissues using the “intrinsic” gene set. (A) A scaled-down representation of the entire cluster of 534 genes and 122 tissue samples based on similarities in gene expression. (B) Experimental dendrogram showing the clustering of the tumors into five subgroups. Branches corresponding to tumors with low correlation to any subtype are shown in gray. (C) Gene cluster showing the ERBB2 oncogene and other coexpressed genes. (D) Gene cluster associated with luminal subtype B. (E) Gene cluster associated with the basal subtype. (F) A gene cluster relevant for the normal breast-like group. (G) Cluster of genes including the estrogen receptor (ESR1) highly expressed in luminal subtype A tumors. Scale bar represents fold change for any given gene relative to the median level of expression across all samples. (See also Fig. 6.)

Fig. 2.

Hierarchical clustering of gene expression data from van't Veer et al. (A) The full cluster of 461 genes across 97 sporadic tumors. (B) Experimental dendrogram displaying similarities between the tumors. Branches are color-coded according to the subtype to which the corresponding tumor sample shows the highest correlation. Tumors with low correlation (<0.1) to a specific subtype are indicated by gray branches. (C) Gene cluster associated with the luminal subtype A. (D) Gene cluster containing the ERBB2 oncogene and coclustered genes. (E) Group of genes that tend to be highly expressed in luminal subtype B tumors. (F) Gene cluster characteristic of basal tumors. Scale bar represents fold change for any given gene relative to the median level of expression across all samples. (See also Fig. 7, which is published as supporting information on the PNAS web site.)

Fig. 3.

BRCA1 tumors associated with a basal tumor profile. (A) Dendrogram showing all tumors from van't Veer et al., including 18 tumors fromBRCA1 mutation carriers (black branches) and two tumors fromBRCA2 mutation carriers (yellow branches). BRCA1 tumors are indicated with longer arrows; BRCA2 tumors are indicated with shorter arrows. (B) Cluster of genes characteristic of basal tumors and highly expressed in tumors from BRCA1-carriers. (See also Fig. 8, which is published as supporting information on the PNAS web site.)

Fig. 4.

Hierarchical clustering of gene expression data from West et al. (A) Scaled-down representation of the full cluster of 242 intrinsic genes across 49 breast tumors. (B) Dendrogram displaying the relative organization of the tumor samples. Branches are colored according to which subtype the corresponding tumor showed the strongest correlation with. Gray branches indicate tumors with low correlation (<0.1) to any specific subtype. (C) Luminal epithelial/estrogen receptor gene cluster. (D) Basal gene cluster. (E) ERBB2+ gene cluster. (See also Fig. 9, which is published as supporting information on the PNAS web site.)

Fig. 5.

Kaplan–Meier analysis of disease outcome in two patient cohorts. (A) Time to development of distant metastasis in the 97 sporadic cases from van't Veer et al. Patients were stratified according to the subtypes as shown in Fig. 2B. (B) Overall survival for 72 patients with locally advanced breast cancer in the Norway cohort. The normal-like tumor subgroups were omitted from both data sets in this analysis.