Abstract B001: Timing the development of chemoresistance in relapsed pediatric cancer with mutational signatures
Authors: Blay Sasha , Layeghifard Mehdi , Davidson Scott , Chen David , Schwertschkow Astra , Ramaswamy Vijay , Taylor Michael , Papaemmanuil Elli , Villani Anita , Malkin David , Alexandrov Ludmil , Cowley Mark , Shlien Adam 
Published: September 2024

Abstract
Survivors of pediatric cancer face lifelong battles with severe morbidities, including a significant risk of recurrence. Pre-existing genetic variation within primary tumors give certain cell populations an evolutionary advantage, increasing the likelihood of treatment resistance and relapse. The rarity of pediatric cancer and limited clinical metadata have restricted comprehensive studies on chemoresistance development. I aim to characterize the timing of chemoresistance in common childhood cancers. I developed a pipeline combining clonal evolution reconstruction with mutational signature extraction at the subpopulation level to elucidate changes in mutational processes over time. Analyzing 1,886 tumor genomes from 10 pediatric cancer cohorts revealed a common pattern of parallel evolution in most pediatric cancers, regardless of tissue origin. After de novo signature extraction, mutational signatures linked to specific cancer treatments were detected in post-treatment tumor samples. In a subset of 611 samples with detailed clinical data, mutational signatures associated with alkylating agents like cisplatin were found in 37.8% of samples, accounting for a mean 30.6% of the mutation burden, whereas antimetabolite agents like fluorouracil were found in 14.9% of samples and contributed 13.8% of the mutation burden. The higher prevalence and burden of alkylating agent signatures suggested a mechanism of direct and continuous DNA damage, while antimetabolite agents depend on active cell cycling. The specific chemotherapy’s mechanism of action dictates its genomic presentation in treated tumors. When placed in the context of the phylogenetic tree, we identified specific subpopulations with therapy signatures, indicating subpopulation-level resistance. In cases with multiple tumor samples, resistant subpopulations in recurrences or metastases were traced to early ancestral clones already present at diagnosis, suggesting that early-stage chemotherapy-resistant subpopulations expanded post-treatment. Finally, the timing of resistance phenotype development varies between pediatric cancer types. In osteosarcoma, pulmonary metastases separate and expand independently before developing cisplatin-associated signatures. In contrast, gliomas show therapy effects earlier; shared subpopulations exhibit therapy-associated signatures before the bifurcation and expansion of progressive subpopulations. Thus, the mechanisms responsible for metastasis likely differ from those driving resistance in osteosarcoma, while in glioma, the effect of therapy coincides with transformation to high-grade subtypes. In summary, investigating mutational signatures at the subclonal level unveils new insights into the clonal dynamics and development of chemoresistance in pediatric cancers, contributing to our understanding of cancer evolution and advancing the field of personalized medicine.
Citation Format: Sasha Blay, Mehdi Layeghifard, Scott Davidson, David Chen, Astra Schwertschkow, Vijay Ramaswamy, Michael Taylor, Elli Papaemmanuil, Anita Villani, David Malkin, Ludmil Alexandrov, Mark Cowley, Adam Shlien. Timing the development of chemoresistance in relapsed pediatric cancer with mutational signatures [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr B001.