Abstract 1618: Highly populated phylogenetic reconstruction in patients with hormone receptor positive - HER2 non-amplified metastatic breast cancer
Authors: Richard Francois , Geukens Tatjana , De Schepper Maxim , Mahdami Amena , Van Baelen Karen , Maetens Marion , Zels Gitte , Nguyen Ha-Linh , Pabba Anirudh , Leduc Sophoa , Isnaldi Edoardo , Van Cauwenberge Josephine , Borremans Kristien , Izci Hava , Bachir Imane , Hatse Sigrid , Vermeulen Peter , Vanderheyden Evy , Boeckx Bram , Lambrechts Diether , Smeets Ann , Nevelsteen Ines , Punie Kevin , Neven Patrick , Wildiers Hans , Bogaert Wouter Van Den , Demeulemeester Jonas , Biganzoli Elia , Floris Giuseppe , Desmedt Christine 
Published: March 2024

Abstract
Background: Tumor progression still needs to be further elucidated in hormone receptor positive (HR+) breast cancer, the most common subtype of breast cancer. Here, leveraging the extensive sampling approach of our postmortem rapid tissue donation program UPTIDER (NCT04531696), we used phylogenic reconstruction to analyze disease progression.
Patients and Methods: Thirteen patients with HR+/HER2 non-amplified primary breast cancer, recruited in UPTIDER between 12/2020 and 05/2022, were considered. Shallow whole-genome sequencing was performed on 495 solid samples including a matched germline DNA and archived primary tumor sample for each patient. Log2 coverage ratios were computed with CNVkit and profiles with median absolute pairwise deviation &lt; 0.35 were co-segmented per patient using the copynumber R package. Purity and ploidy were assessed by ABSOLUTE and manually reviewed. Samples with purity &gt; 30% were kept for downstream analysis. Phylogenetic reconstruction was performed using MEDICC2 for each patient. Metrics derived from the trees were: (i) tree length, (ii) trunk length, (iii) trunk ratio as trunk length/tree length*100. Overall survival (OS) was defined as time between primary diagnosis and death. Comparison was done using Wilcoxon test, time to event analysis using cox regression. Endocrine resistance was defined as per the ESMO guidelines (PMID:34678411).
Results: 81% (399/495) of the samples passed QC. Phylogenies included a median of 28 samples per patient (range: 9-59) and 10/13 phylogenies included primary samples at diagnosis. Multi-seeding from the primary tumor was observed in 7 patients, suspected in 1, and a single seeding was observed in 2 patients. Median OS was 8.0 years. Higher trunk ratios tended to associate with poorer OS (Hazard ratio: 1.08 per 1% increase, 95% confidence interval: 0.99-1.16, p=0.06). In organs where multiple metastatic lesions were sampled (n= 73 organs, median of 3 samples/organ, range: 2-18 and median of 5 organs per patient, range: 1-10) seeding from at least 2 organs was detected in 48% (35/73) of the organs. Phylogenies from patients with secondary endocrine resistance (7 patients) tended to have a shorter trunk compared to patients with primary endocrine resistance (5 patients, median of 18 and 48 alterations respectively, p=0.15).
Conclusion: Branching evolution from the primary tumor was more frequently observed than linear evolution. Phylogenies revealed extensive tumor heterogeneity, questioning treatment decisions based on a single biopsy. Additionally, evaluation of multiple metastatic samples per organ showed seeding from multiple organs in 48% of organs evaluated, indicating greater disease heterogeneity than previously thought. Phylogenetic differences were also noted according to the type of endocrine resistance (primary versus secondary).
Citation Format: Francois Richard, Tatjana Geukens, Maxim De Schepper, Amena Mahdami, Karen Van Baelen, Marion Maetens, Gitte Zels, Ha-Linh Nguyen, Anirudh Pabba, Sophoa Leduc, Edoardo Isnaldi, Josephine Van Cauwenberge, Kristien Borremans, Hava Izci, 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. Highly populated phylogenetic reconstruction in patients with hormone receptor positive - HER2 non-amplified metastatic breast cancer [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 1618.