Targeting ecDNA in High-Risk Medulloblastoma: A High-Throughput Assay to Discover Novel Therapeutic Probes

Novel Approaches, Targets, and Therapeutics; Childhood Cancers

Lukas Chavez, PhD (Sanford Burnham Prebys)

Megan Paul, MD (Rady Children’s Hospital)

Susanne Heyen-Genel, PhD (Sanford Burnham Prebys)

Extrachromosomal DNA (ecDNA) drives oncogene amplification and therapy resistance in aggressive cancers, such as Group 3 medulloblastoma (G3 MB), a lethal pediatric brain tumor. We hypothesize that small molecules capable of selectively reducing or eliminating ecDNA in G3 MB cells will disrupt oncogene-driven tumor growth and uncover novel therapeutic vulnerabilities. Our aims are: (1) to optimize and validate a high-throughput, image-based assay for ecDNA quantification, and (2) to screen a custom library of ~1,000 bioactive compounds to find ecDNA-targeting hits. Using high-content confocal imaging and machine learning-based analysis, we will quantify ecDNA in metaphase cells and assess compound effects across multiple concentrations and timepoints. Expected outcomes include identification of potent, ecDNA-suppressive compounds and insights into ecDNA biology, with potential for translation into therapies for aggressive tumors driven by ecDNA oncogene amplifications.