Gene expression analysis of pancreatic intraepithelial neoplasia (PanINs), the pancreatic ductal adenocarcinoma precursor, has been challenging because extracting and purifying RNA from pancreatic tissue is difficult. Since the pancreas is rich in ribonucleases and PanINs are typically very small lesions, attempts to purify RNA of sufficient quality and quantity for microarray or RNAseq are usually unsuccessful. This is especially true if the starting material is formalin fixed paraffin embedded tissue, where the fixation process introduces further degradation of the RNA. We sought to solve this problem of PanIN gene expression profiling by using the HTG Edgeseq instrument platform. This instrument is designed to work with small FFPE specimens and perform RNA profiling even when RNA is partially degraded by employing a novel extraction free hybridization approach. In our pilot study, we show that the HTG Edgeseq can be used to profile ~2500 genes from a cohort of microdissected low and high grade PanIN from FFPE of human pancreatic adenocarcinoma resections. We speculate that most of these PanIN lesions would not have been amenable to other gene expression methodologies and that the PanIN data from the HTG Edgeseq will contribute to our understanding of the molecular pathways that underlie pancreatic cancer.

Citation Format: Sheila Smiley, Celia Marginean, Bryan Lo.{Authors}. Gene expression profiling of pancreatic cancer precursors directly from formalin fixed paraffin embedded (FFPE) tissue without nucleic acid extraction. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A40.