PD03-03: Identification of Transcription Factors Critical for the Growth of Basal Breast Cancer.
Authors: Shepherd JH , Mazumdar A , Tsimelzon A , Hilsenbeck SG , Brown PH 
Published: June 2012

Background: Basal breast cancers are aggressive, poor prognosis tumors that occur commonly in young women and in African American women. Profiling of breast tumor mRNA has demonstrated that there are differences in gene expression between the basal and luminal subtypes of breast cancer. In this study, we identified response elements in the genes that define basal breast cancers, and identified transcription factors that are critical for the growth of basal breast cancer cells.

Materials and Methods: We performed promoter analysis using 4 published microarray studies (PMID: 12829800; PMID: 19435916; PMID: 17157792; PMID: 11562467) to select genes that are highly expressed in basal tumors compared to luminal tumors. For this analysis we selected 61 genes highly expressed in a set of basal tumors in any of the 4 microarray studies. We next used the online tool, CORE_TF, along with the MATCH algorithm minimizing for the sum of false positives and false negatives to identify binding motifs within the promoter (defined from −1 kb to the first exon) of each gene. The frequency of binding motif occurrence for these 61 basal genes was compared to the frequency within the promoters of 3000 randomly selected genes. Significance was tested using an exact binomial test with a cutoff of p&lt;0.05. RNA expression of motif-identified transcription factors was then analyzed in-silico using all 10 datasets in Oncomine™ that contained annotation for triple-negative status. Expression in triple negative samples was compared to expression in non-triple-negative samples with a cutoff of p &lt;0.05. We next performed siRNA knockdown studies to determine whether the identified TFs regulate basal breast cancer growth. Basal and luminal cells transfected with control and specific siRNAs were grown in triplicate and mean cell counts at day 6 were compared.

Results: Promoter analysis identified 24 binding motifs that were over-represented in basal breast tumor genes compared to a random set of 3000 genes. TransFac analysis indicated that 47 transcription factors bind the 24 identified motifs. Oncomine analysis showed that 8 of the 47 transcription factors were significantly more highly expressed in basal as compared to non-basal tumors. Identified transcription factors include FOXC1, FOXM1, CDC5L, E2F3, CEBP and NF-Y. siRNA to FOXM1 in 2 basal breast cell lines reduced growth by &gt;70% after 6 days, whereas, in the luminal cell line MCF7, growth was reduced by 15%.

Discussion: This study identified transcription factors that are highly expressed in basal breast tumors (as compared to non-basal breast tumors). siRNA knockdown studies showed that FOXM1 is critical for basal breast cancer cell growth. These results suggest that transcription factors highly expressed in basal breast cancers may be novel targets for the treatment of this disease.

These studies were supported by a Promise grant from the Susan G. Komen for the Cure (PB, SGH), and by the Norman E. Brinker Award for Research Excellence (PB).

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD03-03.