Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation

Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive therapy response and outcome differences. Histologic transformation to castration-resistant neuroendocrine prostate cancer (CRPC-NE) is associated with distinct epigenetic alterations, including changes in DNA methylation. The current diagnosis of CRPC-NE is challenging and relies on metastatic biopsy. We developed a targeted DNA methylation assay to detect CRPC-NE using plasma cell-free DNA (cfDNA). The assay quantifies tumor content and provides a phenotype evidence score that captures diverse CRPC phenotypes, leveraging regions to inform transcriptional state. We tested the design in independent clinical cohorts (n = 222 plasma samples) and qualified it achieving an AUC > 0.93 for detecting pathology-confirmed CRPC-NE (n = 136). Methylation-defined cfDNA tumor content was associated with clinical outcomes in two prospective phase II clinical trials geared towards aggressive variant CRPC and CRPC-NE. These data support the application of targeted DNA methylation for CRPC-NE detection and patient stratification.

SIGNIFICANCE

Neuroendocrine prostate cancer is an aggressive subtype of treatment-resistant prostate cancer. Early detection is important, but the diagnosis currently relies on metastatic biopsy. We describe the development and validation of a plasma cell-free DNA targeted methylation panel that can quantify tumor fraction and identify patients with neuroendocrine prostate cancer noninvasively. This article is featured in Selected Articles from This Issue, p. 384.

Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients

Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell-free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining EV-associated RNA (EV-RNA) and cfDNA signals on n = 64 healthy donors (HD) and non-metastatic BrCa patients. Specifically, we isolated EV-enriched samples by a charge-based (CB) method and investigated EV-RNA and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV-RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi-analytes liquid biopsies' clinical implementation.

Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay

Sequencing of cell-free DNA (cfDNA) in cancer patients' plasma offers a minimally-invasive solution to detect tumor cell genomic alterations to aid real-time clinical decision-making. The reliability of copy number detection decreases at lower cfDNA tumor fractions, limiting utility at earlier stages of the disease. To test a novel strategy for detection of allelic imbalance, we developed a prostate cancer bespoke assay, PCF_SELECT, that includes an innovative sequencing panel covering ∼25 000 high minor allele frequency SNPs and tailored analytical solutions to enable allele-informed evaluation. First, we assessed it on plasma samples from 50 advanced prostate cancer patients. We then confirmed improved detection of genomic alterations in samples with <10% tumor fractions when compared against an independent assay. Finally, we applied PCF_SELECT to serial plasma samples intensively collected from three patients previously characterized as harboring alterations involving DNA repair genes and consequently offered PARP inhibition. We identified more extensive pan-genome allelic imbalance than previously recognized in prostate cancer. We confirmed high sensitivity detection of BRCA2 allelic imbalance with decreasing tumor fractions resultant from treatment and identified complex ATM genomic states that may be incongruent with protein losses. Overall, we present a framework for sensitive detection of allele-specific copy number changes in cfDNA.

Abstract B60: Isolation of cfDNA and circulating extracellular vesicles allows for biomarker detection in a single aliquot of breast cancer patients’ plasma

The last few years have witnessed exceptional advances in liquid biopsies based on the isolation and analysis of diverse tumor-derived material circulating in the blood, such as cell-free DNA (cfDNA) and extracellular vesicles (EVs). However, the isolation of different tumor-derived circulating components from a single aliquot of patients’ plasma and the consequent accurate detection of cancer biomarkers is still challenging. By taking advantage of a recently published nickel-based EVs isolation (NBI) protocol (1) that allows for recovery of cfDNA after EVs isolation, we generated a high-sensitivity molecular assay to accurately detect ERBB2 amplification and consequent HER2 overexpression on a limited volume of plasma collected from 20 breast cancer patients (stage I, II, and III) at diagnosis. The amplification of ERBB2 gene and the overexpression of the relevant encoded protein HER2 are currently used in the clinic for breast cancer classification at diagnosis and subsequent treatment decision with the anti-HER2 monoclonal antibody trastuzumab. By performing droplet digital PCR (ddPCR), we were able to detect ERBB2 amplifications in plasma cfDNA from 20 patients selected based on in situ evaluation of tissue biopsies (IHC and FISH). Moreover, we set up an antibody-based affinity reaction to detect HER2 protein on the surface of the isolated EVs that confirmed HER2 overexpression on a subset of patients. Most importantly, we also succeeded in absolute quantification of HER2 transcripts enclosed within EVs by performing ddPCR in samples of patients showing a range of circulating tumor-derived material. The yields and detection performance of this novel methodologic assay were tested on a cohort of healthy individuals (n=20) and on a cohort of triple-negative (and therefore HER2-negative) breast cancer patients (TNBC; n=20; stage: I, II, III). Overall, here we report a pilot study on a novel multimodal noninvasive method for breast cancer-specific biomarker detection from a minimal amount of plasma (1,5mL) integrating cfDNA-derived information with EVs-derived RNA and proteins analysis. This proof of concept may ultimately translate into relevant clinical applications for disease diagnosis as well as for therapy selection and monitoring of disease progression.

Reference: 1. Notarangelo M et al. Ultrasensitive detection of cancer biomarkers by nickel-based isolation of polydisperse extracellular vesicles from blood. EBioMedicine 2019;43:114–26.

Citation Format: Vera Mugoni, Caterina Nardella, Orsetta Quaini, Yari Ciani, Michela Notarangelo, Antonella Ferro, Orazio Caffo, Vito D'Agostino, Francesca Demichelis. Isolation of cfDNA and circulating extracellular vesicles allows for biomarker detection in a single aliquot of breast cancer patients’ plasma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B60.