Abstract P6-04-12: Pathway Analysis of Primary Human Triple-Negative Breast Cancers
Authors: Ossovskaya V , Xu Q , Lituev A , Potapova O , Monforte J , Daraselia N. 
Published: April 2011

Abstract
BACKGROUND: Breast cancer is a complex, heterogeneous disease due to vast differences in cellular origin, genetic mutations, metastatic potential, and disease progression. Triple-negative breast cancer (TNBC) is a subtype defined by negative expression of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2. Because of its aggressive nature and poor prognosis, TNBC has gained recent attention within the oncology community. Tissue expression profiling with microarrays is a robust and straightforward method to study molecular features of TNBC at a systems level. The goal of this project was to further understand the pathogenesis of TNBC through comprehensive characterization of molecular and pathway signatures, based on analysis of freshly frozen and paraffin-embedded primary tumors from 20 TNBC patients, compared with syngeneic normal breast samples.
METHODS: Microarrary profiling of quadruplet sets of samples (freshly frozen and paraffin-embedded; 80 samples total) was conducted using the Affymetrix Human Gene 1.0 ST array. The differential expression profile of cancer vs. syngeneic normal tissue was calculated for each patient, as well as for combined samples, using the unpaired t-test. Pathway analyses based on gene expression profiling were performed using Pathway Studio (Ariadne Genomics, Inc). Functional enrichment was performed using Fisher's Exact test and Mann-Whitney test.
RESULTS: This analysis demonstrated that TNBC is characterized by a distinct molecular signature which includes genes and pathways of DNA repair, cell cycle, and energy production. Several DNA repair genes were upregulated by at least 2.3-fold, including CHEK1, BLM, NEIL3, PARP1, FANCI, FANCD2 and EXO1 (P &lt;.0001 for each). While several genes in excision-repair pathways (DDB2, RPA1, XAB2 and RAB23A) were downregulated, most genes involved in homologous recombination (BRCA1, BRCA2, RAD54B, RAD51, and RAD51L1), DNA repair synthesis (POLQ and PCNA), and DNA mismatch repair (MLH1, MSH3, PMS1 and PMS2) were upregulated. Analysis of the PARP1 pathway revealed that most upstream and downstream neighbors of PARP1 were significantly upregulated between 2- and 4.5-fold in TNBC. Consistent with previous observations, PARP1 was significantly upregulated by 2.5-fold (P &lt; .0001) in TNBC. Genes involved with cell cycle checkpoint control were also significantly altered, including 4.4-fold, 3.6-fold, and 6.8-fold upregulation of CCNB1, CDC2, and TOP2A, respectively (P &lt; .0001 for each). Of genes involved in metabolic pathways, those involved in purine, folate and pyrimidine metabolism demonstrated changes consistent with active proliferation of TNBC cells. In addition, expression patterns related to inflammation (leukocyte migration, lymphocyte activation, macrophage chemotaxis) and angiogenesis were observed. This finding is consistent with previously described activation of the NFkB pathway and suggestive of an inflammatory component in the pathogenesis of TNBC. CONCLUSIONS : TNBC appears to be characterized by distinct alterations in DNA repair, cell cycle regulation, and metabolism, thus providing a molecular basis for identifying novel therapeutic strategies for this disease.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-04-12.