Abstract 4199: Regulation of microRNA-29c expression in different subtypes of breast cancer.
Authors: Poli Elizabeth , Han Yoo-Jeong , Gomez Maria , Zhang Jing , Olopade Olufunmilayo 
Published: August 2014

Abstract
Introduction: The basal-like subtype of breast cancer is associated with an aggressive phenotype and worse prognosis compared to other subtypes. Cancers of this subtype often do not express the ER, PR, or HER-2 receptor, and lack targets for molecular therapy. Research to identify pathways responsible for driving the malignant phenotype in basal-like breast cancer is critical to help develop more targeted therapies. Our lab has previously identified miR-29c as a significantly down-regulated miRNA in basal-like breast tumors and demonstrated an association with cell invasion and drug sensitivity. However, little is known about the genetic and regulatory factors contributing to the down-regulation of miR-29c in the basal-like subtype.
Materials and Methods: To characterize the expression of miR-29c, qRT-PCR was used to measure levels in four basal-like, four luminal, and five claudin-low breast cancer cell lines. We used CAGE-tag analysis and ChIP assays to determine transcription start sites of miR-29c and RNA polymerase II binding sites, respectively. Flouresecent In-Situ Hybridization (FISH) and qPCR were used to assess copy number variation (CNV) of the gene. Luciferase assays were used to measure the promoter activity in the cell lines.
Results: MiR-29c has lower expression in basal-like cell lines and higher expression in claudin-low cell lines compared to luminal cell lines. To determine if the changes in expression are driven by the changes in promoter activity, we first identified the promoter of miR-29c at the region 20kb upstream of the gene on Chromosome 1q32. Initial results from promoter activity assays support a trend of promoter activity that correlates with miR-29c expression in cell lines of the different subtypes. Sequencing of the promoter region revealed no significant mutations or SNPs to explain the expression pattern representing the basal, luminal, and claudin-low subtypes in tumors and cell lines. CNV assays using qPCR suggested lower copy numbers of miR-29c in basal-like cell lines with a large variation of copy numbers in tumors. FISH analysis yielded several abnormalities in the number and structure of 1q32 in cell lines. We are currently determining the correlation of CNV with expression pattern of mir-29c seen in the different subtypes as well as identifying a transcriptional factor contributing to differential expression of miR-29c in breast cancer subtypes.
Conclusions: Our results suggest that miR-29c has lower expression and promoter activity in basal-like breast cancer, which is most likely due to regulation of promoter activity rather than mutations or CNV in the promoter. More work is required to discover the regulatory factors or epigenetic changes that may be involved in the aberrant expression of mir-29c in breast cancer.
Citation Format: Elizabeth Poli, Yoo-Jeong Han, Maria Gomez, Jing Zhang, Olufunmilayo Olopade. Regulation of microRNA-29c expression in different subtypes of 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 4199. doi:10.1158/1538-7445.AM2013-4199