Abstract 5042: Urine as a non-invasive proxy for plasma in prostate cancer-related liquid biopsy applications
Authors: Nafiseh Jafari, Jason Saenz, Lauren Lee, Carlos Hernandez, Andrew Dunnigan, Amit Arora, Rafal Iwasiow, Mayer Saidian
Journal: Cancer Research (2024)

Abstract Introduction: The non-invasive collection of urine renders it an attractive and pragmatic substitute for plasma in liquid biopsy applications, fostering the creation of diagnostic methods that are more patient-friendly and less cumbersome for clinicians. This study investigates the feasibility of urine-derived cfDNA as a non-invasive option for acquiring vital diagnostic insights, further enhancing the liquid biopsy field. Methods: Paired male first void urine (FVU) and venous blood samples were collected from healthy donors (n=40) using Colli-Pee UAS devices (Novosanis) and BD K2EDTA Vacutainer tubes, respectively. Out of these, 20 paired urine and blood samples were spiked with 10 ng of cfDNA reference standard containing the KRAS p.G12V mutation. ~35 ml of urinary cell-free supernatant and ~3.5 ml of plasma were obtained after centrifugation of FVU and blood sample, respectively, and used as input material for cell-free nucleic acids extraction using the nRichDX Revolution Max20 cfDNA Isolation Kit. The extracted cfDNAs profile was assessed on 4200 TapeStation System, Agilent, using cfDNA ScreenTape. Extracted nucleic acids from urine samples were subjected to a qPCR assay to quantify endogenous human cfDNA content using 2X iTaq Universal SYBR Mastermix (Bio-Rad). Human cfDNA quantity was assessed using Ct values obtained from the qPCR assay. The actionable cfDNA molecules recovery was determined by qPCR mutation detection assay using TaqMan Genotyping. Results: Male FVU collected in Colli-Pee UAS device showed the presence of 100-250 bp cell-free DNA fragments similar to plasma obtained from whole blood collected in 10 ml vacutainer tubes as demonstrated by the Agilent cfDNA ScreenTape analysis. The cfDNA yield was similar when comparing one tube of blood (~3.5 mL of plasma) to one Colli-Pee of urine (~35 mL) shown by endogenous cfDNA qPCR assay. Additionally, the amplifiability of the KRAS G12V mutation was consistent in both plasma and urine samples, with comparable Ct values. Conclusion: The nRichDX Revolution Sample Prep System demonstrates the ability to extract cfDNA from both plasma and urine samples, with comparable extraction efficiency observed between matched samples from the same donor. This study provides evidence supporting the viability of first void urine samples as a non-invasive alternative for prostate cancer-related liquid biopsy applications. It indicates that cfDNA can be recovered from a sample collected with a single BCT or Colli-Pee UAS urine collection device. Future investigations will be required to assess clinical samples and biomarkers to establish a robust correlation between cfDNA levels and various cancer types and stages. This study reinforces the utility of first void urine samples as a reliable proxy for blood-based liquid biopsy applications. Citation Format: Nafiseh Jafari, Jason Saenz, Lauren Lee, Carlos Hernandez, Andrew Dunnigan, Amit Arora, Rafal Iwasiow, Mayer Saidian. Urine as a non-invasive proxy for plasma in prostate cancer-related liquid biopsy applications [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 5042.