MDB-35. Elucidating YBX1 as a dependency in pediatric medulloblastoma

Abstract Current standard of care treatment for medulloblastoma (MB) consists of maximal resection surgery followed by craniospinal irradiation and chemotherapy, with survivors experiencing diminished quality of life from intensive treatment regimens. The identification of novel targets is an unmet need and critical to enhance patient survival. Using a batch-normalized bulk RNA-seq dataset comprised of 1350 MB samples and 291 normal cerebella, we reveal upregulation of the RNA/DNA binding protein Y-box binding protein 1 (YBX1) in MB compared to normal cerebellum. Further analysis of this dataset and others demonstrates G3 tumors with high MYC levels also have the highest YBX1 expression. Analysis of ChIP-seq data shows strong binding of MYC to the YBX1 promoter in G3 MB, and MYC expression in progenitor cells induces YBX1. Interestingly, knockout of YBX1 using CRISPR-Cas9 leads to decreased in vitro proliferation and a significant downregulation of MYC, the oncogenic factor required for tumor maintenance. Orthotopic implantation of YBX1KO tumor cells leads to a significant enhancement of animal survival in multiple G3 MB models. These findings support a proposed reciprocal MYC-YBX1 axis, which may regulate stem-like characteristics including tumorigenesis. We next tested the efficacy of a recently reported YBX1 antagonist (SU056), which exquisitely targets tumor cell proliferation, antagonizes MYC signaling, and leads to a rebalancing of stemness and differentiation genes. In vivo, single agent administration of SU056 extends survival of orthotopic G3 MB-tumor bearing animals. Using an anchor-probe approach we demonstrate that combining SU056 with chemotherapy or radiation exhibits significant synergy in primary tumor models. We also demonstrate retained sensitivity to SU056 in relapsed, refractory tumor models. In summary, our findings identify YBX1 as a dependency in MB, with a marked regulatory function on MYC, and suggest the clinical utility of YBX1 inhibition in both frontline and relapse settings in children with this deadly and aggressive disease.