Abstract B017: The evolution of doxorubicin resistance in <i>SMARCB1</i> -deficient cancers

Abstract SMARCB1 is a tumor suppressor gene and encodes a core subunit of the SWI-SNF chromatin remodeling complex. Loss of SMARCB1 leads to the development of highly aggressive pediatric malignancies, termed “SMARCB1-deficient cancers.” This includes malignant rhabdoid tumor, atypical teratoid rhabdoid tumor (ATRT), and renal medullary carcinoma (RMC). Survival rates in these patients remain low, and resistance to chemotherapeutic agents, including doxorubicin, are common. Therefore, this project aims to characterize the evolution of doxorubicin resistance in SMARCB1-deficient cancers. To address this question, we generated doxorubicin resistant (DR) cells from the ATRT cell line, BT16, and RMC cell line, PEDS005T, utilizing a dose escalation approach. This resulted in DR cell lines that are 10-to-30-fold resistant compared to the parental cell line. Furthermore, we generated two independent DR cell lines from each parental cell line, enabling the capture of distinct evolutionary trajectories leading to resistance. We profiled the transcriptomes by bulk RNA-sequencing and found an upregulation of the multidrug transporter ABCB1, also known as MDR1, in 3 of 4 models. To assess whether ABCB1 upregulation alone was sufficient for DR, we treated them with an ABCB1 pharmacological inhibitor and found that ABCB1-upregulated DR cells were re-sensitized to doxorubicin, whereas an ABCB1-negative BT16 DR cell line remained resistant. To determine a shared mechanism of resistance between these models, we profiled the methylomes by Oxford Nanopore Technologies long-read sequencing. We observed global hypermethylation when compared to the parental counterparts. Treatment with a hypomethylating agent reduced cell viability up to 75%. Future studies will focus on identifying and therapeutically targeting these commonalities to overcome resistance regardless of evolutionary trajectory. These preliminary findings suggest that despite a common genetic driver (loss of SMARCB1), there are different pathways to developing resistance to the DNA-damaging agent, doxorubicin. Furthermore, reduced cell viability resulting from treatment with a hypomethylating agent suggests there are common vulnerabilities despite differing evolutionary trajectories. Citation Format: Katie T. Skinner, Benjamin P. Lee, Jessica S. Yoon, Andrew L. Hong. The evolution of doxorubicin resistance in SMARCB1-deficient cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Cancer Evolution: The Dynamics of Progression and Persistence; 2025 Dec 4-6; Albuquerque, NM. Philadelphia (PA): AACR; Cancer Res 2025;85(23_Suppl):Abstract nr B017.