Abstract 3124: Identification of transcription factors critical for the growth of basal-like breast cancer.
Authors: Shepherd Jonathan , Uray Ivan P. , Mazumdar Abhijit , Tsimelzon Anna , Hilsenbeck Susan G. , Brown Powel H. 
Published: August 2014

Abstract
Background: Intrinsic differences in gene expression between basal-like breast cancer (BLBC) and other breast cancer subtypes imply that transcriptional regulators are differentially activated in breast cancer subtypes and may be promising therapeutic targets. We hypothesized that genomic comparisons between BLBC and non-BLBC will identify transcription factors (TFs) critical for BLBC growth. We identified TFs using an integrative analysis comparing mRNA expression, frequency of TF response elements in differentially expressed genes, and DNA-binding activity of nuclear proteins in BLBC and non-BLBC. We then tested whether inhibition of these specific TFs suppresses the growth of BLBC.
Methods: We compared mRNA expression of 702 TFs in TNBC tumors compared to non-TNBC samples across 15 breast tumor datasets in Oncomine™ and identified TFs with a combined p-value &lt;0.05 and higher expression in TNBC.
We used the online tool, CORE_TF, to identify TF response elements occurring more frequently within promoters (-1kb through first exon) of 117 genes significantly more highly expressed in BLBC tumors compared to non-BLBC samples (p&lt;0.01 in 3 independent datasets) as compared to ∼1500 non-BLBC genes, with a p-value &lt;0.05 using Fisher's exact test.
Nuclear protein was collected from BLBC (BT20, HCC1143, HCC1937, MDA468) and non-BLBC cells (BT474, MCF7, T47D, ZR75-1) in triplicate and binding of DNA motifs by nuclear protein was measured by protein/DNA Arrays (Affymetrix, Santa Clara, CA). TF motifs with a fold change of &gt;1.2 and p &lt;0.05 in BLBC compared to non-BLBC nuclear lysates were identified.
BLBC and non-BLBC cells transfected with control or specific siRNAs to each TF identified in at least 2/3 of the assays were grown in quadruplicate and cell counts at day 6 were compared.
Results: mRNA analysis identified 132 TFs significantly more highly expressed in TNBC compared to non-TNBC. Analysis of TF response elements identified 94 motifs seen more frequently in genes more highly expressed in BLBC. Analysis of protein-bound DNA motifs identified 11 motifs significantly more highly bound using BLBC protein than non-BLBC protein. Integrative analysis of these results identified two TFs that were detected in all three analyses: STAT1 and PPARα, an additional 26 TFs identified in both mRNA expression and DNA element analyses, and 5 identified in the RNA expression and DNA-binding protein analyses. siRNA knockdown of the identified TFs showed that several of the TFs are critical for BLBC growth.
Conclusions: This study identified TFs with differential expression and activity in BLBC and non-BLBC using an integrative analysis of RNA, DNA and proteins. Inhibition of specific TFs demonstrates that several of these TFs are critical for the growth of BLBC. Further investigation of the TFs identified in this study will improve our understanding BLBC and will identify novel targets for the treatment and prevention of BLBC.
Citation Format: Jonathan Shepherd, Ivan P. Uray, Abhijit Mazumdar, Anna Tsimelzon, Susan G. Hilsenbeck, Powel H. Brown. Identification of transcription factors critical for the growth of basal-like breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3124. doi:10.1158/1538-7445.AM2013-3124