Abstract 2368: Differential gene expression in key oncolytic pathways between node-matched Caucasian-American, African-American and East African triple-negative breast cancer patients
Authors: Getz Julie , Ahearn Mary E. , Gomez Carmen , Pegram Mark , Bird Peter , Carpten John , Baumbach-Reardon Lisa L. 
Published: May 2015

African-American (AA) women have a 20% greater mortality rate from breast cancer (BC) than that observed in Caucasian-American women (CA). Additional BC disparities in AA women include later stage presentation with higher tumor grade, and increased occurrence of Triple-negative breast cancer (TNBC). In this study, we performed a series of gene expression array analyses on archived formalin fixed paraffin embedded (FFPE) blocks from a multi-ethnic U.S. cohort of node-negative (N0) TNBC samples, in addition to a cohort of (N0) TNBC samples from East African patients (Kijabe,Kenya). Using 10 μm scrolls from each FFPE block, total RNA was isolated, cDNA prepared, and hybridized to a breast-enriched gene expression array (Affymetrix, BC DSA Research Tool®). Expression analysis was conducted using GeneSpring 12.1® analytical software. After QC analyses, the final study cohort consisted of 10-AA, 13-CA and 21-Kenyan samples. PCA analysis revealed that the samples clustered well with respect to ethnicity. Unsupervised cluster analysis, based on ethnicity and genes (p value 2.5), was performed. The resulting dendogram clearly segregated into distinct subgroups based on ethnicity, revealing a pattern of differential gene expression between the cohorts. A list of differentially expressed genes from each cohort (DEG) were selected using ANOVA analysis (fold change &gt; 3.0, p value &lt;.05) followed by the Benjamin/Hochberg method for multiple-testing correction. Finally, the lists of DEG were uploaded into GeneGo MetaCore to identify functionally enriched pathways.

These analyses revealed differentially expressed genes pathways enriched for cytoskeletal remodeling, cell adhesion and EMT pathways. In particular, significantly deregulated genes associated with the Wnt/β-catenin pathway were observed in the AA cohort as compared to the CA, suggesting that this pathway may contribute to the more aggressive phenotype in AA women diagnosed with TNBC. Additionally, significantly deregulated genes associated with the Oncostatin M pathway were discovered in the Kenyan cohort, as compared to the AA and CA tumors. In particular, STAT1 was significantly downregulated in the Kenyan cohort compared to the CA and AA. Thus, our results indicate gene expression differences within several key oncolytic pathways across these ethnic groups. These results are being technically and biologically validated through several parallel approaches. Validation study results will be presented. In summary, this study represents the first direct comparison of gene expression in TNBC specimens across U.S. CA and AA BC patients and Kenyan East Africans. These studies have important implications for further understanding BC ethnic disparities, as well as future tailored approaches to prediction, prevention and therapeutic advances.

Citation Format: Julie Getz, Mary E. Ahearn, Carmen Gomez, Mark Pegram, Peter Bird, John Carpten, Lisa L. Baumbach-Reardon. Differential gene expression in key oncolytic pathways between node-matched Caucasian-American, African-American and East African triple-negative breast cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2368. doi:10.1158/1538-7445.AM2014-2368