Methods for rapid extraction of high‐quality RNA from FFPE cancer tissue (1048.14)

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer‐related deaths. Because there are virtually no biomarkers to aid in early detection or predicting therapy response, newly diagnosed patients have a dismal prognosis. Substantial archives of formalin‐fixed, paraffin‐embedded (FFPE) samples from PDAC tissue have been established and linked to clinical data. However, identifying biomarkers from these tumors is severely hindered because extracting high‐quality nucleic acid material from FFPE samples is time‐consuming and inefficient. Thus, developing improved methods for extracting high‐quality RNA/DNA from FFPE samples represents an unmet need in the fields of cancer biology and Next‐Generation Sequencing (NGS). We have tested Claremont BioSolutions’ microhomogenization (mH) tools in combination with commercial FFPE RNA extraction kits for their ability to improve high‐quality RNA recovery from PDAC xenograft samples. Our results demonstrate that the addition of brief (< 5min) mH steps improves total RNA yield up to 3‐fold over current methods, as well as RNA purity and length, as characterized by 260/280 ratios (2.03 +/‐ 0.02 w/ mH step) and chip‐based electrophoresis (RNA Quality Index = 7.3 w/ mH step). These results have important implications for streamlining the FFPE‐RNA‐NGS workflow as a realistic approach for cancer biomarker identification.Grant Funding Source: n/a