Optimization of a method for preserving nucleic acids in tissue lysates from archival formalin-fixed tissue samples

Abstract

Abstract Biomarker analysis of patient biopsies is essential for identifying biomarkers that have predictive or prognostic value. Such analyses not only have the potential for helping us understand the molecular mechanisms underlying response to therapy, but also in personalizing healthcare based on biomarker profiles in patient sub-populations. Patient biopsies are commonly preserved by formalin-fixing and paraffin-embedding (FFPE). Ability to evaluate nucleic-acid-based biomarkers in FFPE tissue is limited by the fact that formalin-fixing degrades the quality of nucleic acids. RNA and miRNA are further degraded in FFPE blocks as time passes. Hence, there is the basic need to find methods for stabilizing nucleic acids in FFPE tissues so that nucleic-acid-based biomarkers can be evaluated in archival tissue samples. We have evaluated various methods of tissue lysate preparation to identify ones that are optimal for stabilizing nucleic acids in storage, and for efficient recovery of DNA, RNA and miRNA. We also evaluated the quality and quantity of DNA and RNA recovered from these lysates across time. We will present a method that preserves quality of nucleic acids across time, and is compatible with protocols for DNA, RNA and miRNA isolation. This method is currently used in our laboratories to prepare tissue lysates from clinical trial samples and has enabled the development of molecular diagnostic assays.