Dormant SOX9-positive cells facilitate MYC-driven recurrence of medulloblastoma

Tumor recurrence is a slow biological process involving therapy resistance, immune escape and metastasis and is the leading cause of death in medulloblastoma, the most frequent malignant pediatric brain tumor. By studying paired primary-recurrent patient samples and patient-derived xenografts we identified significant accumulation of SOX9-positive cells in relapses and metastases. They exist as rare, quiescent cells in Group 3 and Group 4 patients that constitute two thirds of medulloblastoma. To follow relapse at the single cell level we developed an inducible dual Tet Off animal model of MYC-driven MB, where MYC can be directed from treatment-sensitive bulk cells to resistant, dormant SOX9-positive cells. SOX9 promoted immune escape, DNA repair suppression and was essential for recurrence. Tumor cell dormancy was non-hierarchical, migratory and depended on MYC suppression by SOX9 to promote relapse. By using computational modeling and treatment we further showed how doxorubicin and MGMT inhibitors are specifically targeting relapsing cells. We examined tumor recurrence using RNA-seq, single cell RNA-seq and ATAC-seq. In total 27 samples were sequenced by conventional RNA-seq, of which 12 samples (triple replicates) were part of a treatment study (DMSO, DOX). 16 samples were ATAC-sequenced, all in duplicates, and 8 were part of a treatment study (DMSO, DOX). The single cell RNA-seq rendered in 4498 and 4645 cells for each sample respectively.