Cell-free DNA is abundant in ascites and represents a liquid biopsy of ovarian cancer

OBJECTIVE

Malignant ascites is a common clinical feature of ovarian cancer and represents a readily accessible sample of tumour cells and tumour DNA. This study aimed to characterise the cell-free DNA (cfDNA) in ascites in terms of its size profile, stability and cell-free tumour DNA (cftDNA) content.

METHODS

Cell spheroids, loose cells and cell-free fluid was collected from ascites from 18 patients with ovarian cancer. cfDNA was isolated and assessed for size by electrophoresis, concentration by fluorometry,cftDNA content by methylation specific qPCR of HOXA9 and IFFO1 promoter regions and by targeted sequencing. Stability was assessed after ascites fluid was stored at 4 °C for 24 and 72 h before fractionating.

RESULTS

The concentration of cfDNA in ascites ranged from 6.6 to 300 ng/mL. cfDNA size distribution resembled blood plasma-derived cfDNA, with major peaks corresponding to mono- and di-nucleosome DNA fragments. High molecular weight cfDNA was observed in 7 of 18 patients and appeared to be associated with extracellular vesicles. IFFO1 and HOXA9 methylation was proportionately higher in cfDNA than spheroid- and loose-cell fractions and was not observed in healthy primary cells. Variant allele frequency was highest in cfDNA compared to single cells and spheroids from ascites. Though cancer cell numbers in ascites declined to near zero in recurrent ascites from one patient undertaking chemotherapy, cftDNA could still be sampled. cfDNA size, concentration and tumour content was stable over 72 h.

CONCLUSION

cfDNA in ovarian cancer ascites demonstrates inter-patient variability, yet is consistently a rich source of cftDNA, which is a stable substrate. This supports the wider clinical use of ascites in the molecular analysis of ovarian cancer.

Abstract B28: Optimizing DNA processing and ovarian cancer methylation-specific PCR assays for the detection of early-stage ovarian cancer

Background: Ovarian cancer screening has the potential to greatly reduce mortality by shifting the time of diagnosis to an early stage when the tumor is confined to a single site and can be completely cured by surgical removal. Ovarian cancer DNA is present in blood and has a distinct methylation profile that distinguishes it from healthy blood cells, thus making it a target for ovarian cancer diagnosis via a blood test. However, while the presence of this DNA in the blood of cancer patients is well established, low abundance and DNA fragmentation present a barrier to developing clinical applications that target it.

Methods: We are systematically evaluating and optimizing each step of DNA extraction, processing, and analysis to increase the sensitivity of cancer DNA detection by PCR. At the same time, we are developing PCR assays to detect ovarian cancer specific methylation based on a previous tumor and blood screen that identified 73 methylated candidate biomarker regions.

Results: We have found that inhibitors of the PCR reaction introduced into the sample during DNA extraction and bisulphite treatment limit the total amount of DNA that can be analyzed, and thus the sensitivity of the test. Precipitation of the DNA samples prior to PCR analysis removes the inhibitors and increases useable sample volume and thus sensitivity. We have also developed methylation-specific PCR assays for DNA regions that are methylated in ovarian tumor tissue, and unmethylated in white blood cells.

Conclusions: We are progressing our candidate methylated DNA ovarian cancer biomarkers closer to testing in clinical samples. Our results on sample processing and DNA analysis methods to enable ovarian cancer DNA detection are relevant to all cancer types for which cell-free tumor DNA has clinical applications.

Citation Format: Kristina Warton, Nicole Yuwono, Claire Henry, Neville Hacker, Caroline Ford. Optimizing DNA processing and ovarian cancer methylation-specific PCR assays for the detection of early-stage ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B28.