Abstract LB-135: The transcriptome of p300 loss in MCF-7 cells
Authors: Sil Sukanya M. , Yuan Huijun , Bishopric Nanette H. 
Published: February 2011

Abstract
Introduction: p300 is a transcriptional co-activator that promotes gene transcription by acetylating DNA-binding factors and bridging them to the basal transcription machinery. Recent studies have revealed decreased levels of p300 in breast cancer cells, suggesting that p300 may be involved in the control of breast cancer growth and progression. Preliminary data from our laboratory also indicates that decreased p300 function promotes MCF-7 breast cancer cell proliferation in vitro and tumorigenesis in vivo.
Methodology: In order to identify the effects of p300 loss on gene expression in breast cancer cells, microarray analysis was performed on total RNA from MCF-7 cells, stably transduced with lentiviruses expressing one of 3 p300 shRNAs or a non-silencing sequence. Silencing of p300 was &gt; 50% in response to each of the shRNAs. Endogenous RNA was converted to cDNA using random primers and then to biotinylated cRNA for hybridization to human exonic evidence-based oligonucleotide microarrays (Ocean Ridge Biosciences, Palm Beach Gardens, FL). 877 genes were found to be differentially expressed in p300 knockdown MCF-7 cells compared to non-silenced controls. Differentially regulated genes were ranked according to the significance of change (p value &lt; 0.0005) and compared to previously reported data in the Oncomine database, for both directionality (up versus down-regulation) and positive correlation with decreased p300 levels. As an additional strategy we ranked the differentially expressed genes from our microarray with good level of significance (p&lt;0.05) by fold change and repeated the comparative analysis with Oncomine as described above.
Results: In our analysis, 877 genes were found to be differentially expressed out of which 27 genes were either significantly up-regulated or down-regulated. The rest of the gene expression levels found in the microarray analysis were not as highly significant as the top 27 genes. Among those 27 genes, four (SPAG7, OAS2, RARRES3, SERPINA6) showed highly significant (p&lt;0.0005) increase in their expression and five genes (DHX9, EIF4G2, POLR2D, MCM6, CYP4F2) showed highly significant decrease. Among the genes with the largest fold changes, 10 (IFI27, IFI6, ATF-3, PIK3IP1, TNFAIP3, P8, RARRES3, FOS, IRF9, and RNF39) showed significantly increased expression and 8 were decreased (WNT3A, CAMK1, CENPH, DCTN1, CASC5, HSPA4, CDC25A, and CDKN2C). The second set of genes showed correlations with p300 levels as indicated in analyses of Oncomine data. Some of these genes may be contributing to epithelial to mesenchymal- transition (EMT) under p300 knock-down conditions.
Conclusions: Our microarray analysis in MCF-7 cells with partial p300 loss has identified several key genes that are related to breast cancer growth. These genes may be important in mediating the function of p300 loss in tumorigenicity, and future studies will focus on the use of p300 or its downstream signaling components as therapeutic targets in breast cancer treatment.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-135.