TITLE-Characterization of a naturally occurring breast cancer subset enriched in EMT and stem cell characteristics Running title-Metaplastic breast cancer characterization

Metaplastic breast cancers (MBCs) are aggressive, chemoresistant tumors characterized by lineage plasticity. To advance understanding of their pathogenesis and relatedness to other breast cancer subtypes, twenty-eight MBCs were compared with common breast cancers using comparative genomic hybridization, transcriptional profiling, reverse phase protein arrays and by sequencing for common breast cancer mutations. MBCs demonstrated unique DNA copy number aberrations compared with common breast cancers. PIK3CA mutations were detected in 9/19 MBCs (47.4%) versus 80/232 hormone receptor-positive cancers (34.5%; p=0.32), 17/75 HER2 -positive samples (22.7%; p=0.04), 20/240 basal-like cancers (8.3%; p<0.0001) and 0/14 claudin-low tumors (p=0.004). Of 7 PI3K/AKT pathway phosphorylation sites, six were more highly phosphorylated in MBCs than in other breast tumor subtypes. The majority of MBCs displayed mRNA profiles different from those of 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-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

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