Early Detection of Medulloblastoma Relapse by Genomic Profiling of CSF-Derived Circulating Tumor DNA

Abstract

Introduction: Medulloblastoma progression or recurrence occurs in 30% of patients and confers dismal prognosis. Despite incremental advances in multi-modal management and identification of relevant molecular subgroups, suboptimal outcomes in MB is partly due to the lack of sensitive biomarkers for relapse detection and response-adapted treatment personalization. Cell-free circulating tumor DNA (cf/ctDNA) has emerged as a robust platform for tumor detection and characterization through liquid biopsy of the cerebrospinal fluid (CSF). Methods: CSF from MB patients was collected by lumbar puncture prior to therapy, during therapy, and at 3-month interval follow-up as part of institutional clinical trials. cfDNA was isolated and quantified for yield and fragment size from approximately 1 mL of frozen CSF. After construction of next-generation sequencing libraries, low-pass whole-genome sequencing enabled detection of genome-wide chromosomal and focal copy number alterations (CNAs). CNAs detected in cfDNA were compared against known somatic changes in corresponding tumor-tissue. Detectability of tumor-specific CNAs in cfDNA was then correlated with tumor burden, disease course, and patient outcome. Results: In preliminary analysis, tumor-specific CNAs were identified in at least one post-resection timepoint in 22/23 (96%) relapsing patients. Of patients with CSF available at or 3 months prior to clinicoradiographic progression, tumor-specific CNAs were identifiable in 16/17 (94%). Presence of tumor-specific CNAs at the end of therapy alone predicted future relapse in 8/12 (67%). A subset of genomic alterations were divergent from tissue-derived primary tumor profiles, suggesting potential tumor evolution and oncogenic mechanisms underlying treatment failure and relapse. Conclusion: The feasibility and applicability of CSF liquid biopsy for detection and characterization of tumor-derived cfDNA in MB patients is established. With continued expansion of the clinical cohort, we anticipate the broad applicability of CSF-derived cfDNA as an adjunct to clinicoradiographic surveillance while enabling response-adapted treatment.