Abstract A009: Integrative multiomic analysis of extracellular vesicle transcriptomics profiling combined with cfDNA methylation reveals improved stratification of low-risk and high- risk prostate cancer patients in urine-based liquid biopsy
Authors: Sudipto K Chakrabortty, Dulaney Miller, Kyle Manning, Rikky Xing, Jeff Cole, Christopher Benway, Sinead Nguyen, Allan George, Yiyuan Yao, Elena M Cortizas, Christian Ray, Siva Gowrisankar, Seth Yu, Allan Pollack, Sandra M Gaston, Sanoj Punnen, Johan Skog
Journal: Clinical Cancer Research (2024)

Abstract Introduction: Prostate cancer (PCa) ranks as the second most frequently diagnosed cancer and the sixth most prevalent cause of cancer-related mortality in men globally. In this study, we employ a multiomic approach that utilizes both urine cfDNA and extracellular vesicle (EV) RNA-derived analytes to improve the risk stratification of individuals with prostate cancer and compare this to multi-parametric MRI performance as well as risk calculators in the same cohort. Materials and Methods: Urine was collected from 95 individuals comprising 51 benign or low-risk (Grade Group (GG) &amp;lt;=1), 10 intermediate-risk (GG2) and 44 high-risk PCa patients (GG 3-5). EV-RNA and cfDNA were concurrently isolated from each urine specimen to exploit complementary information. We developed an EV-RNA sequencing platform targeting mRNAs and lncRNAs and targeted 50 million reads per sample; and cfDNA methylome profiling reached an equivalent sequencing depth. Expression of EV-RNA and splice variant Differential Transcript Usage (DTU) and cfDNA methylation patterns were analyzed using Bio-Techne’s multiomic platform. Machine learning-based feature selection algorithms identified biomarker signatures from each analyte. Receiver-operator characteristic curves (ROC) were generated utilizing leave-one-out cross-validation of naïve Bayes classifier models to compute the area under the curve (AUC). Individual signatures were integrated to create a multiomic classifier. Results: Differential gene expression (DEx) analysis identified 18 DEx genes between low and high-risk patients with both known and novel implications in PCa. Splice variant analysis unveiled 60 genes previously implicated in PCa with DTU. Over 18,000 differentially methylated bases were detected between high and low-risk PCa patients. Feature selection analysis identified the top ten features of EV-RNA expression, splice variants, and cfDNA methylation, resulting in an integrative multi-analyte signature. The multiomic signature demonstrated an AUC of 0.92, surpassing any individual analyte’s performance, as well as the performance achieved by PSA (AUC = 0.52) and MRI PI RADS(AUC=0.65). Conclusions: While biomarker signatures obtained from each analyte in this study resulted in effective stratification of PCa risk, the multiomic signature further improved the discriminatory power—underscoring the complementary nature of the signals. Thus, a multiomic biomarker discovery strategy leveraging cfDNA and EV cargo exhibits significant potential as a risk assessment tool for high-grade prostate cancer. This approach can facilitate more informed decision-making in the context of biopsy procedures. Citation Format: Sudipto K Chakrabortty, Dulaney Miller, Kyle Manning, Rikky Xing, Jeff Cole, Christopher Benway, Sinead Nguyen, Allan George, Yiyuan Yao, Elena M Cortizas, Christian Ray, Siva Gowrisankar, Seth Yu, Allan Pollack, Sandra M Gaston, Sanoj Punnen, Johan Skog. Integrative multiomic analysis of extracellular vesicle transcriptomics profiling combined with cfDNA methylation reveals improved stratification of low-risk and high- risk prostate cancer patients in urine-based liquid biopsy [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A009.