Establishing A Pipeline For Individualized Treatment Options For Pediatric Brain Cancer

Abstract INTRODUCTION Despite being able to characterize pediatric brain tumors such as medulloblastoma and high-grade gliomas using detailed molecular analysis tools, this knowledge hasn’t been translated to better treatment methods. In this project, we aim to create a biobank of pediatric brain tumors (PBTs), characterize samples using next generation molecular diagnostics and identify patient specific drug-treatment options using high-throughput drug screening (HTDS). METHODS To establish tumor spheres from biopsies, we mechanically dissociated the tissue and digested it in trypsin. The cells isolated were cultured in serum free DMEM medium. Immunocytochemistry analysis was done to compare the spheres and original tumor. After the second passage, DNA was extracted and subjected to low-pass whole genome nanopore sequencing. HTDS with a library of FDA/EMA-approved anticancer drugs and investigational compounds was also performed. RESULTS We’ve established tumor sphere cultures that grew to passage two and onwards from five juvenile pilocytic astrocytomas, two gangliogliomas and two midline gliomas. The spheres expressed markers of stem cells (Nestin), neurons (β3-tubulin) and glial (GFAP), similar to the original tumor. Copy number profiling and methylation-based classification of the spheres showed the same alterations and classification as the biopsy. HTDS revealed significant differences in drug sensitivity including patient-specific vulnerabilities to anticancer drugs. CONCLUSION We’ve created a protocol to generate tumor spheres from PBTs. We are also building a biobank comprising high and low grade PBTs. Our tumor spheres maintain the characteristics of the original tumor and can be used for further downstream analysis including drug screening.