Target Discovery and Validation Reviews and Protocols

104 Sørlie
this cluster of genes varied widely among the tumor samples analyzed in our
study and was generally well correlated with the mitotic index. Genes encoding
two generally used immunohistochemical markers of cell proliferation, Ki-67
and proliferating cell nuclear antigen, also were included in this cluster. The
proliferation cluster has been observed in virtually every tumor type examined,
including ovarian carcinomas (48), lymphomas (49), liver (50), and prostate
cancer (51). More than half of the genes in the proliferation cluster were shown
to be cell cycle regulated when the patterns of expression for these genes were
analyzed in synchronized HeLa cell cultures (17). To investigate the expression
of these genes in relation to the five subtypes, expression data were extracted,
and the genes were clustered using average-linkage clustering, but the samples
were ordered according to the subtypes as presented in ref. 22. What could be
learned from this analysis was that the basal-like and the luminal subtype B
both highly expressed these proliferation-associated genes, whereas luminal A,
the normal-like and to some extent, the ERBB2+ subtype, were mostly negative
for the expression of these genes. This finding may indicate large differences in
the amount of cycling cells among the tumors. That the ERBB2+ tumors were
less proliferative, despite being characterized by overexpression of an oncogene
and being a poor prognostic group, was somewhat surprising. However, this
characteristic underlines the very strong influence of the ERBB2 amplicon on
the expression patterns of these tumors; no other distinct molecular signature
protrudes at the transcriptional or at the genomic level (assessed by array comparative
genomic hybridization [aCGH]).
5.1.1. Effects of BRCA1 Mutations on Global Gene Expression
Germline mutations in the BRCA1 gene predispose carriers to early onset
breast and ovarian cancer (52). A previous microarray study reported significantly
different gene expression profiles of tumors from BRCA1 vs. BRCA2
carriers (53). In the data set produced by van’t Veer and colleagues (30), breast
tumors from 18 carriers of BRCA1 mutations and two carriers of BRCA2 mutations,
also were analyzed. When we included these 20 tumors along with the
97 sporadic tumor samples in the clustering analysis, we saw little difference in
the overall pattern, except for the striking result that all the tumors from patients
carrying BRCA1 mutations fell within the basal-like tumor subgroup (22). This
finding indicates that a mutation in the BRCA1 gene predisposes for the basal-like
tumor subtype, which is associated with lack of expression of the ER receptor and
poor prognosis. As also reported previously, BRCA1-associated breast cancers
are usually highly proliferative, TP53 mutated, and lack expression of ESR1
and ERBB2 (54,55). Recent studies have found that BRCA1 interacts with and
regulates the activity of the ER and the androgen receptor (56), thereby providing
a link between BRCA1 and hormone-related cancers. Furthermore, wild-type,