Abstract B016: Factors Driving Chemo-persistence in Atypical Teratoid Rhabdoid Tumors

Abstract Multi-modal chemotherapy, surgical resection, and radiation therapy (if applicable) make up the current standard of care for Atypical Teratoid Rhabdoid Tumors (ATRT), but they are insufficient. Up to 50% of patients experience relapse, but no standard treatment options have been established for ATRT recurrence. The malignant cells that persist after chemotherapy treatment may significantly contribute to this tumor rebound. Our principal goal is to track shifts in cell states and phenotypes under the selection of chemotherapy by combining CloneSifter barcoding technology with single cell RNA-seq. Patient derived ATRT cells, barcoded with sgRNA identifiers, are placed under the selection of a sub-lethal drug dose, and barcodes are tracked over 7 days. After treating the cells with the following chemotherapy agents - Cisplatin, Etoposide, Doxorubicin, Methotrexate, and Cyclophosphamide - barcode abundance profiles are compared between pre and post drug treated samples using hierarchical clustering. This analysis reveals that replicates subjected to the same drug treatment tend to show the most similar patterns of barcode abundance, suggesting that this drug persistence is intrinsic and pre-determined prior to treatment rather than stochastically acquired. Furthermore, a one-sided paired Wilcoxon test is leveraged to identify significant barcode enrichment in each of the drug treated replicates relative to their vehicle controls, differentiating between chemo-persistent versus chemo-sensitive barcodes. Competitive barcodes are identified under Etoposide, Cisplatin, and Methotrexate treatments and mapped to the single cell RNA-seq data, where a unique transcriptome profile can be generated for each barcode. Comparisons between transcriptome profiles of enriched versus depleted barcodes under drug treatment will reveal the underlying factors that provide a fitness advantage for chemo-persistent populations. Investigating the dynamics of chemotherapy-persistence in ATRT cell lines can help uncover vulnerabilities that may be exploited to begin overcoming chemotherapy-induced ATRT recurrence. Citation Format: Kelly Y Cai, Shriya Rangaswamy, April Apfelbaum, Jared Collins, Molina Das, Joelle Straehla, David Root, Tom Rosenberg, Susan Chi, Rameen Beroukhim, Pratiti Bandopadhayay. Factors Driving Chemo-persistence in Atypical Teratoid Rhabdoid Tumors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2):Abstract nr B016.