Abstract LB-147: Simultaneous profiling of mRNA and protein in single human induced pluripotent stem cells

The cancer stem cell theory proposes that a discrete, small number of “stem-cell-like” cancer cells are primarily responsible for driving cancer. Thus, future cancer treatments are likely to be developed by targeting these cancer stem cells. One approach to modeling cancer therapy utilizes induced pluripotent stem cell (iPSC) technology. While gene expression studies have measured differentiation propensities between different iPSC clones and compared protein coding gene profiles between iPSCs and embryonic stem cells (ESCs), relatively little is known about the expression characteristics of individual RNA transcripts and their corresponding protein within each single iPSC. In addition, studies of the dynamic interaction between RNA and protein during the cell differentiation stage remains rare. Here we present an integrated assay that simultaneously quantifies mRNAs and proteins of interest within single iPSCs. The C1™ system was utilized for individual cell capture, cell lysis, DNA template generation for protein detection and cDNA synthesis. Final products from each iPSC were quantified on the 96.96 Dynamic Array™ IFC on the Biomark™ HD system. PCR data were analyzed using the Singular™ Analysis Toolset. For each run, up to 5,000 data points for 52 protein targets and 2,880 data points for 30 RNA targets, in addition to control and reference assays, were simultaneously generated and analyzed in less than two days. Combined RNA and protein signatures of each iPSC were identified. By comparing these results to those obtained from non-induced fibroblast cells, we demonstrate that this method is capable of obtaining expression levels of both RNA and protein associated with pluripotency marker genes at a single-cell level. More interestingly, the profiling data also indicates changes of some key members (EGFR, TGFB1, EPCAM, etc.) of cancer related common signaling pathways. The current system significantly controls lab-specific differences in reprogramming processes, progenitor cells or cell culture and handling conditions. We believe this powerful method makes it a suitable approach of choice for providing new insights into cell differentiation, reprogramming and tumor progression, as well as cancer therapeutic targets research. Citation Format: Benjamin Liu, Gajalakshmi Dakshinamoorthy, Haibiao Gong, Aik Ooi, Nianzhen Li, Marc Unger, Ilona Holcomb, Ramesh Ramakrishnan. Simultaneous profiling of mRNA and protein in single human induced pluripotent stem cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-147.