Abstract A004: Comparison of ctDNA detection in seven different types of body liquids from patients with metastatic breast cancer
Authors: Richard François , Geukens Tatjana , De Schepper Maxim , Mahdami Amena , Van Baelen Karen , Maetens Marion , Nguyen Ha-Linh , Pabba Anirudh , Leduc Sophia , Isnaldi Edoardo , Hajipirloo Maysam Mohammadzadeh , Berghe Emily Vanden , Bachir Imane , Hatse Sigrid , Vermeulen Peter , Vanderheyden Evy , Boeckx Bram , Lambrechts Diether , Smeets Ann , Nevelsteen Ines , Punie Kevin , Neven Patrick , Wildiers Hans , Van Den Bogaert Wouter , Demeulemeester Jonas , Biganzoli Elia , Floris Giuseppe , Desmedt Christine 
Published: February 2024

Abstract
Background. Liquid biopsies represent a less invasive alternative to tissue biopsy to characterize the disease in patients with metastatic cancer. Blood remains the most frequently investigated body liquid with regards to detection, quantification and characterization of the circulating tumor DNA (ctDNA). However, it might not capture the full disease profile, and other sources of body liquids may be complementary. The aim of the present study is to compare ctDNA detection in different types of body liquids. Patients and methods. Sixteen patients from the post-mortem tissue donation program UPTIDER (NCT04531696) were included in this study. The receptor status of their primary tumor was: estrogen receptor positive, Human Epidermal Growth Factor Receptor 2 non-amplified (ER+/HER2-) (n=12), ER-/HER2- (n=3) and ER+/HER2+ (n=1). Seven types of liquids were collected: blood, saliva, ascites, pleural fluid (PFL), cerebrospinal fluid (CSF), pericardial fluid and urine. Fluids were collected at study inclusion (blood, saliva, urine, and ascites whenever possible) and at autopsy (except for saliva). In total, 281 liquid samples were collected and processed according to standard protocols. All extracted cfDNA (supernatant), and the 16 matched germline DNA (buffy coat) samples underwent shallow whole genome sequencing. Log2 coverage ratios were computed with CNVkit, and good quality profiles were co-segmented per patient using the copynumber R package. Purity and ploidy were assessed by ABSOLUTE and manually reviewed. Associations between organ involvement and ctDNA yield were assessed by Wilcoxon rank-sum tests. Results. At the patient level, the proportion of liquid types in which ctDNA was detected was highly variable (median: 62%, IQR: 25-89%). ctDNA was detected in ascites of all patients where investigation was possible, in 92% of PFL, 77% of CSF, 69% of blood, 30% of pericardial fluid and in 10% of urine samples. No ctDNA was detected in the saliva samples. At autopsy, ctDNA could not be identified in blood in 4 out of the 16 patients but was detected in at least one of the other fluids for 3 of these patients. ctDNA levels tended to be higher in PFL and CSF in case of pleural and central nervous system (CNS) metastases, respectively. 3 patients had CSF ctDNA detected with no documented involvement of the CNS. In ascites, ctDNA levels were independent of peritoneal invasion. Conclusion. ctDNA was detected in 6 out of the 7 investigated body liquids and its level was partially associated with metastases in surrounding organs, except for ascites. In 3 patients, blood was not contributive but other liquids were, encouraging the evaluation of additional body fluids, when possible, in patients with metastatic breast cancer. These results open new avenues for the clinical monitoring and characterization of the disease.
Citation Format: François Richard, Tatjana Geukens, Maxim De Schepper, Amena Mahdami, Karen Van Baelen, Marion Maetens, Ha-Linh Nguyen, Anirudh Pabba, Sophia Leduc, Edoardo Isnaldi, Maysam Mohammadzadeh Hajipirloo, Emily Vanden Berghe, Imane Bachir, Sigrid Hatse, Peter Vermeulen, Evy Vanderheyden, Bram Boeckx, Diether Lambrechts, Ann Smeets, Ines Nevelsteen, Kevin Punie, Patrick Neven, Hans Wildiers, Wouter Van Den Bogaert, Jonas Demeulemeester, Elia Biganzoli, Giuseppe Floris, Christine Desmedt. Comparison of ctDNA detection in seven different types of body liquids from patients with metastatic breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A004.