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Background: Cervical cancer (CC) is the 4th most commonly diagnosed cancer among women, with approximately 528,000 new cases annually. Current screening approaches for this disease have certain limitations; Pap tests require dedicated cytopathology infrastructure, while human papillomavirus (HPV) DNA testing may lead to invasive procedures in patients with transient infection. Liquid biopsy has emerged as a minimally invasive approach to detect and monitor disease progression and treatment response. We and others have previously demonstrated the clinical utility of circulating tumor (ct)DNA to monitor HPV+ cancers. Moreover, cell free (cf)DNA fragmentation patterns have been found to be a biomarker of disease burden. This cfDNA is thought to originate largely as a result of cell death, where small fragments of ~167 bp are associated with apoptosis and larger fragments (>1000 bp) are associated with necrosis. Despite advances in liquid biopsy techniques, little is known about the composition of cfDNA from different analytes in CC patients. Methods: The aim of this study was to compare the presence and composition of cfDNA from different liquid biopsy analytes in patients with CC and high grade cervical intraepithelial neoplasia or dysplasia (CIN/CD). Blood, urine, and vaginal swabs were collected from 20 patients with CC and 9 patients with CIN/CD at the McGill University Health Centre. All samples were centrifuged twice to isolate supernatant. Samples were tested for HPV ctDNA by ddPCR. Analysis of fragment length was performed using the Agilent Bioanalyzer 2100. Dominant fragment was determined as the DNA fragment with the highest concentration, while overall fragment was calculated as the average fragment across all bioanalyzer peaks. Results: HPV16/18 ctDNA was detectable 14/20 CC patients and 2/6 CIN patients, and 0/3 CD patients in plasma, urine, and vaginal swab. Concordance for all sample types tested was seen in 90% of cases. On average, fragment analysis demonstrated 174, 195, and 183 bp dominant small fragments in plasma, urine and vaginal swab, respectively. Plasma samples showed only smaller fragments (range: 168-187 bp). Other analytes displayed a predominance of larger cfDNA, with an overall fragment size of 3996 and 5194 bp in urine and vaginal swab, respectively. Conclusions: HPV-DNA was detectable in all analytes sampled in patients with CC and CIN, with a trend of higher detection in CC samples. The fragmentation patterns of cfDNA varied between patients and within patients across analytes, with larger fragments - likely of necrotic origin - seen only in urine and vaginal swab cfDNA. Smaller fragments - likely related to apoptosis - were seen across all sample types studied. Overall, analysis of fragmentation may provide valuable insight into cfDNA origins in different sample types and provide a novel biomarker for diagnosis and surveillance. Citation Format: Sarah Tadhg Ferrier, Erica Mandato, Alexandra Bartolomucci, Thupten Tsering, Shuk On Annie Leung, Julia Valdemarin Burnier. Cell free DNA levels and fragmentation patterns in different liquid biopsy analytes (blood, urine and vaginal fluid) in cervical cancer patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5596.

Background: While the incidence of esophageal adenocarcinoma (EAC) is rapidly increasing, the 5-year survival rate of this disease remains poor at less than 25%, with a substantial number of patients exhibiting inherent or acquired resistance to chemotherapy. Circulating tumor DNA (ctDNA) isolated from liquid biopsies of EAC patients holds clinical biomarker potential in this disease, but our understanding of how chemotherapy affects ctDNA release remains limited. Methods: In order to study the impact of cancer treatment on ctDNA emission in vitro, we first sought to establish a chemo-resistant model of EAC. As such, the EAC cell line OE19 was exposed to discontinuous cisplatin treatments for three months in order to establish drug resistance. Following this, established chemo-resistant OE19 cells and parental (chemo-sensitive) OE19 cells were exposed to five daily cisplatin treatments, and cell culture supernatant was collected every day throughout treatment. ctDNA was subsequently isolated from cell culture supernatant and quantified by Qubit fluorometer dsDNA HS assay. ctDNA quantities were additionally assessed by droplet digital PCR (ddPCR) assay using primers and probes targeting the TP53 N310K mutation in the OE19 cell line. Finally, ctDNA fragment lengths were analyzed using the Agilent Bioanalyzer 2100. Results: A chemo-resistant model of the OE19 cell line was established, as exemplified by marked morphological changes in the cells and significantly increased cell viability determined by CCK8 assay after 48-hour treatments of various doses of cisplatin (p Conclusion: This study reveals that in vitro cancer models can be used to successfully study ctDNA emission during pre-clinical drug analyses. ctDNA release was found to be correlated to cytotoxicity and cell death, providing us with valuable insight into how clinical liquid biopsy data should be interpreted. Finally, fragment size analysis of ctDNA reveals a potential novel biomarker for treatment response in cancer patients. Citation Format: Alexandra Bartolomucci, Sarah Tadhg Ferrier, Thupten Tsering, Xin Su, Jonathan Cools-Lartigue, Julia V. Burnier. Characterizing circulating tumor DNA release kinetics and fragment length in a chemotherapy resistant model of esophageal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6700.