Abstract 1977: Elucidating heterogeneity within cancer cell populations using single cell RNA detection

Abstract

Abstract As researchers continue to analyze the relationships between gene expression and biological processes involved in the development and progression of cancer, increasing importance is being placed on the study of genetic variation across single cells. However, traditional methods tend to measure RNA expression globally, with cell lysis and fixation steps resulting in a loss of key information about individual cells, making it challenging to properly assay the genetic heterogeneity within cell populations. We demonstrate the use of a single cell RNA detection technology that specifically measures gene expression in live cells without altering their viability or inherent biology. This enables researchers to not only detect heterogeneity within their samples, but also separate, enrich, and further characterize cell subpopulations based on RNA expression variation, when using techniques such as Fluorescent Activated Cell Sorting (FACS). Here, we describe live cell detection of cancer biomarkers within heterogeneous cell models. First, we co-cultured MCF-7 and SK-BR3 breast cancer cell lines in specific ratios to mimic heterogeneous breast cancer populations. Subsequent characterization of the populations was performed by both flow cytometry using fluorescent live-cell RNA detection probes, and quantitative real-time PCR. Next, we analyzed miR-221 expression in a mixture of T47D and MDA-MB-231 breast cancer cell lines, which allowed us to sort the two cell types based on differential expression of this microRNA and perform downstream immunohistochemical analysis of vimentin and E-cadherin, two protein markers known to be associated with the epithelial-to-mesenchymal transition during tumor progression. Use of a live cell RNA detection methodology in gene expression experiments allows scientists to formulate novel questions and design experiments that better address the importance of gene expression heterogeneity in normal and disease states, particularly in cancer, where individual cells within the tumor microenvironment may exhibit aberrant RNA expression profiles that render them invasive or metastatic. Note: This abstract was not presented at the meeting. Citation Format: Don Weldon, Yuko Williams, Victor Koong, Alex Ko. Elucidating heterogeneity within cancer cell populations using single cell RNA detection. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1977. doi:10.1158/1538-7445.AM2015-1977