Abstract P5-01-09: Identification of Molecular Apocrine Triple Negative Breast Cancer Using a Novel 2-Gene Assay and Comparison with Androgen Receptor Protein Expression and Gene Expression Profiling by DASL
Authors: Alvarez J , Schaffer M , Karkera J , Martinez G , Gaffney D , Bell K , Sharp M , Wong J , Hertzog B , Ricci D , Platero S 
Published: August 2014

Abstract
Background: The molecular apocrine (MA) subtype of breast cancer is identified by gene expression profiling. MA tumors are estrogen receptor (ER) negative and progesterone receptor (PR) negative, but still express estrogen responsive genes. The androgen receptor (AR) pathway may be driving growth in these tumors because androgen responsive genes are expressed in tumors with the MA gene signature. The MA gene signature is identified in approximately 10% of triple negative breast cancer (TNBC) and may predict patients with tumors responsive to agents that inhibit the AR pathway. AR protein expression, measured by immunohistochemistry (IHC), may be a surrogate for the MA gene signature, but to date, a careful comparison of gene expression profiles and AR protein expression has not been conducted. In this study, cohorts of TNBCs were assessed for the MA gene signature and these results were compared with AR IHC expression and with a novel gene expression assay that may predict tumors with the MA gene signature.
Methods: Formalin fixed, paraffin-embedded (FFPE) TNBC samples were commercially obtained. ER, PR and HER2 status of these samples was confirmed by IHC. AR expression was detected by IHC using two different antibody clones. Both staining intensity and percent positive cells were recorded for each sample. Gene expression data was collected from a cohort of TNBC FFPE samples using cDNA-mediated Annealing, Selection, extension, and Ligation (DASL) technology. A 2-gene classifier of the MA gene expression signature was derived by interrogating publically available gene expression data from ER-negative breast cancers. A reverse-transcriptase polymerase chain reaction (RT-PCR) assay to detect the 2-gene classifier was developed. Cell lines predicted to have the MA gene signature by the 2-gene assay were tested for sensitivity to R-1881 in vitro.
Results: Using computational approaches and publically available datasets, we confirmed the validity of the MA gene signature and estimated the prevalence to be between 12% and 37% in ER-negative breast tumors. The 2-gene classifier was 100% specific in determining MA tumors in a training set using gene expression data as a standard. In a validation set, the 2-gene assay was 66% correlative with AR IHC positivity when the IHC cut-off was set at 10% positive tumor cells. Cell lines predicted to express the MA gene signature by the 2-gene classifier proliferated in response to androgen. This effect was blocked by Flutamide.
Conclusions: These results indicate that AR IHC using a 10% cut-off may not completely correlate with the MA gene signature. Further refinement of AR IHC scoring criteria may produce greater specificity. Cell proliferation data suggests the 2-gene assay can predict tumors that will proliferate in response to androgen. Work is ongoing to determine the correlation between the 2-gene assay results, AR IHC and DASL gene expression data to fully understand the predictability of this assay. Understanding this correlation may allow use of simple clinical assays to accurately select patients responsive to agents that block AR signaling.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-01-09.