Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics

Abstract

Metaplastic breast cancers (MBC) are aggressive, chemoresistant tumors characterized by lineage plasticity. To advance understanding of their pathogenesis and relatedness to other breast cancer subtypes, 28 MBCs were compared with common breast cancers using comparative genomic hybridization, transcriptional profiling, and reverse-phase protein arrays and by sequencing for common breast cancer mutations. MBCs showed unique DNA copy number aberrations compared with common breast cancers. PIK3CA mutations were detected in 9 of 19 MBCs (47.4%) versus 80 of 232 hormone receptor-positive cancers (34.5%; P = 0.32), 17 of 75 HER-2-positive samples (22.7%; P = 0.04), 20 of 240 basal-like cancers (8.3%; P < 0.0001), and 0 of 14 claudin-low tumors (P = 0.004). Of 7 phosphatidylinositol 3-kinase/AKT pathway phosphorylation sites, 6 were more highly phosphorylated in MBCs than in other breast tumor subtypes. The majority of MBCs displayed mRNA profiles different from those of the most common, including basal-like cancers. By transcriptional profiling, MBCs and the recently identified claudin-low breast cancer subset constitute related receptor-negative subgroups characterized by low expression of GATA3-regulated genes and of genes responsible for cell-cell adhesion with enrichment for markers linked to stem cell function and epithelial-to-mesenchymal transition (EMT). In contrast to other breast cancers, claudin-low tumors and most MBCs showed a significant similarity to a "tumorigenic" signature defined using CD44(+)/CD24(-) breast tumor-initiating stem cell-like cells. MBCs and claudin-low tumors are thus enriched in EMT and stem cell-like features, and may arise from an earlier, more chemoresistant breast epithelial precursor than basal-like or luminal cancers. PIK3CA mutations, EMT, and stem cell-like characteristics likely contribute to the poor outcomes of MBC and suggest novel therapeutic targets.

Conflict of interest statement

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Figures

Figure 1

Gene copy number changes. Gains and losses in all common breast cancers (including luminal, HER-2–amplified, and basal-like cancers) and basal-like cancers alone versus metaplastic breast tumors were determined. Chromosomes are subdivided into arms and ordered from left to right, beginning with 1p, 1q and ending with X.

Figure 2

Functional proteomics of MBC. Comparative expression of seven core PI3K/AKT pathway phosphoproteins in 383 hormone receptor–positive (HR), 142 HER-2–positive (HER), and 168 triple-negative (TN) breast tumors and 16 MBCs was determined. GSK3, glycogen synthase kinase 3; XpY, phosphorylation of protein X at amino acid(s) Y.

Figure 3

Expression of claudin-low and stem cell markers in breast cancer subgroups. Using data from transcriptional profiling, metaplastic (Metap) and claudin-low tumors express low levels of claudins CLDN3, CLDN4, and CLDN7 of CDH1 (E-cadherin) and high CD44/CD24 and CD29/CD24 ratios. P values (ANOVA). P values for the metaplastic-basal comparison of stem cell markers were 0.41 (BMI1), 0.19 (CD44), 0.004 (CD29), 0.00009 (CD24), 0.00006 (CD44/CD24 ratio), and 0.00007 (CD29/CD24 ratio).

Figure 4

A CD44+/CD24−/low “tumorigenic” gene signature is enriched in human breast tumors of the “claudin-low” and metaplastic (MBC) subtypes. The correlation shown is between the “tumorigenic” signature pattern (Creighton and colleagues, submitted for publication; using “1” and “−1,” for up and down genes, respectively) and each MBC as well an each tumor in the gene expression profile dataset by Herschkowitz and colleagues (9). R values above red dotted line are significant (P < 0.00001).