Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

Abstract

The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A total of 85 cDNA microarray experiments representing 78 cancers, three fibroadenomas, and four normal breast tissues were analyzed by hierarchical clustering. As reported previously, the cancers could be classified into a basal epithelial-like group, an ERBB2-overexpressing group and a normal breast-like group based on variations in gene expression. A novel finding was that the previously characterized luminal epithelial/estrogen receptor-positive group could be divided into at least two subgroups, each with a distinctive expression profile. These subtypes proved to be reasonably robust by clustering using two different gene sets: first, a set of 456 cDNA clones previously selected to reflect intrinsic properties of the tumors and, second, a gene set that highly correlated with patient outcome. Survival analyses on a subcohort of patients with locally advanced breast cancer uniformly treated in a prospective study showed significantly different outcomes for the patients belonging to the various groups, including a poor prognosis for the basal-like subtype and a significant difference in outcome for the two estrogen receptor-positive groups.

Figures

Figure 1

Gene expression patterns of 85 experimental samples representing 78 carcinomas, three benign tumors, and four normal tissues, analyzed by hierarchical clustering using the 476 cDNA intrinsic clone set. (A) The tumor specimens were divided into five (or six) subtypes based on differences in gene expression. The cluster dendrogram showing the five (six) subtypes of tumors are colored as: luminal subtype A, dark blue; luminal subtype B, yellow; luminal subtype C, light blue; normal breast-like, green; basal-like, red; and ERBB2+, pink. (B) The full cluster diagram scaled down (the complete 456-clone cluster diagram is available as Fig. 4). The colored bars on the right represent the inserts presented in C–G. (C) ERBB2 amplicon cluster. (D) Novel unknown cluster. (E) Basal epithelial cell-enriched cluster. (F) Normal breast-like cluster. (G) Luminal epithelial gene cluster containing ER.

Figure 2

Comparison of experimental sample-associated dendrograms from two different hierarchical clustering analyses. (Upper) Dendrogram is taken from Fig. 1 (85 samples) with the status of TP53 indicated by the color of the terminal dendrogram line. Red lines indicate tumors with mutated TP53 genes, green lines wild-type TP53, and black lines samples not tested. (Lower) The experimental dendrogram from the hierarchical-clustering analysis using the 51 Norway carcinomas, three benign tumors, and four normal breast tissues (58 samples). The subgroups are colored accordingly and show that the group of tumors highlighted in orange changed position compared with the dendrogram from Fig. 1A. Furthermore, the basal-like tumors shown in red are inserted in between luminal subtypes A and C. To the left are shown the correlation coefficients for the dendrogram branches.

Figure 3

Overall and relapse-free survival analysis of the 49 breast cancer patients, uniformly treated in a prospective study, based on different gene expression classification. (A) Overall survival and (B) relapse-free survival for the five expression-based tumor subtypes based on the classification presented in Fig. 1 (luminals B and C were considered one group). (C) Overall survival estimated for the six-subtype classification with the three different luminal subtypes presented in Fig. 1. (D) Overall survival based on the five-subtype classification presented in Figs. 2 Lower and 5.