Abstract 5039: Preanalytical workflow enabling cfDNA analysis from urine samples

Abstract

Abstract Introduction: Urine has become an important source of information in the liquid biopsy field. In contrast to blood, specifications for the collection, storage, transport and processing of urine intended for molecular examination are not widely established. Preanalytical specifications were published for urine cell-free DNA (cfDNA) only recently (CEN/TS 17811:2022). In this study, we investigated post-collection changes to cfDNA profiles in urine samples and present the performance of an optimized preanalytical workflow for cfDNA analysis. Methods: Urine from apparently healthy, consented female individuals was spiked with processed cell-free male urine or with a cfDNA standard containing PIK3CA mutations (SensID). The urine was stabilized with a urine collection/stabilization solution under development at PreAnalytiX or was left unstabilized. Urine samples were stored for varying durations at different temperatures in a time course experiment to simulate different urine storage conditions. After storage, urine samples were centrifuged to remove cells and cfDNA was isolated from the supernatant via the QIAsymphony® platform (QIAGEN). Autosomal and male-specific targets were quantified using the Rotor-Gene® Q instrument and the therascreen® PIK3CA qPCR Kit (both QIAGEN) or the QIAcuity® Digital PCR System and a dPCR LNA PIK3CA Mutation Assay (both QIAGEN). Fragment size distribution was determined by TapeStation® Cell-free DNA ScreenTape® (Agilent Technologies). Results: Analysis of cfDNA profiles in unstabilized urine stored for varying durations and temperatures highlighted changes which create artificial cfDNA profiles. The yield of cfDNA drastically decreased over time. Furthermore, the size distribution of cfDNA isolated from unstabilized urine was impacted by release of gDNA as well as DNA degradation. Urine stabilization minimized cfDNA degradation and gDNA release and allowed isolation of cfDNA that was analyzed with qPCR and dPCR even after urine storage. Analysis of isolated cfDNA revealed positive detection of PIK3CA mutations in spiked urine samples. Conclusions: Changes in post-collection cfDNA profile can hinder downstream analysis, resulting in artificial or failed outcomes. Urine stabilization with a collection/stabilization solution under development at PreAnalytiX minimized DNA degradation and gDNA release. It enabled urine storage, allowed analysis of urine cfDNA and target detection by qPCR and dPCR. Citation Format: Daniela Mancarella, Julia Rutsch, Lisa Erkelenz, Moritz Meyer, Laura Sofie Witthaus, Moritz Rath, Thorsten Voss. Preanalytical workflow enabling cfDNA analysis from urine samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5039.