Target Discovery and Validation Reviews and Protocols

Molecular Profiling of Breast Cancer 107
distinguished luminal subtype B from subtype A, such as GGH, LAPTMB4, and
MYBL2, were highly expressed in TP53-mutated tumors. Among the genes
highly expressed in tumors with a wild-type TP53 gene, most of the genes in
the luminal/ER+ cluster (ER, GATA-3, RERG, and so on) were found, which
recapitulates the low mutation rate of the luminal subtype A. Further studies are
needed to determine which of the genes are direct targets of TP53 and which
are present only by association with a particular expression phenotype.
6. Genome-Wide Copy Number Changes
The power of microarrays also is illustrated in their broad range of utility; the
same types of DNA microarrays can be used to investigate both the structural
and the expressed genome (68). Variations in gene expression measured by analyzing
the tumor RNA may be caused by underlying genomic DNA copy
number alterations, which are key genetic events in the development and progression
of human cancers. A genome-wide aCGH analysis of a subset of the
tumors described here was carried out using similar cDNA microarrays
as for the gene expression studies. In total, a profile was generated across
6691 mapped genes in 45 primary breast tumors and 10 breast cancer cell lines
(69). Numerous DNA copy number alterations were detected in the tumors
despite the presence of euploid nontumor cell types; the magnitudes of the
observed changes were generally lower in the tumor samples than the cell lines.
DNA copy number alterations were identified in all cancer cell lines and nearly
all (40/45) tumors, and on every human chromosome in at least one sample.
Recurrent regions of DNA copy number gain and loss were readily identifiable;
gains within 1q, 8q 17q, and 20q were observed in all breast cancer cell lines,
and a large proportion of tumor samples (75, 48, 50, and 34%, respectively),
consistent with published cytogenetic studies (70–72). The parallel measurements
of mRNA levels and copy number alterations revealed a global impact of
widespread DNA copy number alteration on gene expression in tumor cells.
The overall patterns of gene amplification and elevated gene expression are
concordant, i.e., a significant fraction of highly amplified genes seem to be correspondingly
highly expressed (69,73). The concordance between high-level
amplification and increased gene expression is best illustrated for genes on
chromosome 17 (Fig. 6), where the amplicon containing the oncogene ERBB2
is located. A comprehensive analysis of nearly 150 breast tumors by using
aCGH is underway with a specific emphasis on the distribution of genomic
alterations across the subtypes. Preliminary data indicate specific genomic
aberrations to be present in the different tumor subtypes, further supporting our
results that these molecular subtypes of breast cancer represent biologically
distinct disease entities.