Abstract 4940: Unraveling ctDNA features in high-grade serous ovarian carcinoma and insights from genomic and transcriptomic integration
Authors: Mai TN Nguyen, Jaana Oikkonen, Yilin Li, Daria Afentave, Johanna Hynninen, Sampsa K. Hautaniemi
Journal: Cancer Research (2024)

Abstract High-grade serous carcinoma (HGSC) is often diagnosed at advanced stages with less than 40% of patients surviving for five years after diagnosis. Circulating tumor DNA (ctDNA) is a minimally invasive technology that can provide crucial insights into tumor biology. Unique features from ctDNA, fragment patterns and nucleosome footprints at transcription start sites (TSS), complement genomic variants. Our study explored ctDNA features in HGSC, integrating with tumor biopsies' genomic and transcriptomic profiles. We focus on two aspects in HGSC: understanding how ctDNA features assist genomic profiling and track dynamic changes during treatment and exploring the biological factors impacting ctDNA release. We used 500+ longitudinal plasma and 400+ pretreatment tissue samples from HGSC patients in the DECIDER study (NCT04846933). Shallow whole-genome sequencing (sWGS) with 0.4x average coverage was conducted on plasma. Integration of DNA and RNA pretreatment tissue data was performed for 98 and 91 patients with available plasma before treatment, respectively. Plasma samples underwent analysis for fragment patterns and TSS signals. Somatic mutations and mutational signatures were retrieved for patients with available WGS tissue data. Pathway enrichment analysis was applied to diverse gene expression profiles. WGS data from 29 healthy individuals (Zhu, G. et al. (2023)) served as controls. DNA fragment profiles and TSS signals distinguish ctDNA from healthy samples. The ability to cluster sample phases based on ctDNA features facilitates tracking longitudinal changes. Integrating tissue DNA and RNA data reveals a positive correlation between high ctDNA release and mutational burden, single-base substitution signature SBS1 as a marker for cell division/mitotic clock and doublet-base substitution signatures linked to late replication. These mechanisms help explain why high ctDNA release group (n=40) is associated with a shorter progression-free survival. Additionally, transcriptomics data indicates associations with proliferation pathways in cancer cells and ctDNA release. The concordance in results from DNA and RNA points to a higher proliferation rate in patients with high ctDNA release, suggesting the need for alternative treatment compared to those with low ctDNA release. In conclusion, our results provide a multifaceted perspective on ctDNA in HGSC. The identification of longitudinal ctDNA features signifies the capability to stratify sample states and show the potential findings through fragment profiles and the discernment of key TSS regions. The proposed aetiologies and enriched pathways associated with ctDNA release, mutation burden and proliferation, shed light on potential treatment avenues. These findings contribute to our understanding of ctDNA in HGSC and offer insights for personalized treatment strategies and monitoring approaches. Citation Format: Mai TN Nguyen, Jaana Oikkonen, Yilin Li, Daria Afentave, Johanna Hynninen, Sampsa K. Hautaniemi. Unraveling ctDNA features in high-grade serous ovarian carcinoma and insights from genomic and transcriptomic integration [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 4940.