Abstract B015: CSF liquid biopsies reveal disease status and resistance mechanisms in children undergoing targeted therapy for malignant brain tumors
Authors: Han Katie , Smith Kyle S , Kostecka Anna , Dhanda Sandeep , Lin Hong , Mikkelsen Margit , Robinson Giles W , Northcott Paul A 
Published: November 2024

BACKGROUND: Patients with relapsed or refractory brain tumors face poor outcomes due to the aggressive nature of their disease. Recent studies suggest that administration of cell cycle inhibitors may help slow tumor progression. In the Phase I trial SJDAWN (NCT03434262) conducted at St. Jude Children’s Research Hospital, CDK4/6 inhibitor therapy (ribociclib) was assessed for safety and efficacy in such patients. To understand how tumors evolve in response to this treatment, longitudinal CSF liquid biopsies from SJDAWN were retrospectively analyzed by cell-free DNA (cfDNA) sequencing. METHODS: CSF samples (n=143) were collected by lumbar puncture from 34 of 68 (50%) patients before and during treatment. cfDNA was extracted and analyzed using an innovative DNA methylation-based platform that concurrently detects tumor-associated copy number alterations, classifies tumor subtypes, and distinguishes malignant from non-malignant methylation signatures. cfDNA inputs ranged from 50 to 500 pg. CSF profiles were compared to patient-matched tumor tissue DNA methylation arrays and subsequently correlated with MRI findings at corresponding timepoints. RESULTS: Circulating tumor DNA (ctDNA) was detected in 29 of 34 (85%) patients, yielding accurate tumor classification even in the setting of diploid genomes. CNV profiles from CSF liquid biopsies strongly correlated with patient-matched tumor tissue methylation arrays and often revealed genetic events not previously captured in the tumor tissue. Resistance to CDK4/6 inhibition was characterized by focal amplification of positive cell cycle regulators, including CDK6, CCND2, MYCN, and RRM2 that were detectable in CSF ∼6 months prior to radiographic progression. Remarkably, three high-risk Group 3/4-MB patients were progression-free for &gt;1.5 years. The trend of their longitudinal cfDNA profiles varied: one had persistent ctDNA detected throughout therapy with resistance emerging at ∼1.5 years; another had undetectable ctDNA for ∼2 years before reemergence of tumor; and the third remained MRD-negative, potentially owing to reduced ctDNA release resulting from CDK4/6 inhibition. Methylation changes in response to treatment were also observed, providing unprecedented insights into epigenetic landscapes associated with tumor evolution concurrent with targeted therapy. CONCLUSIONS: Methylation-based analysis of CSF liquid biopsies provides an ultra-sensitive and comprehensive method for serial disease monitoring. Even with sub-nanogram cfDNA inputs, tumor reemergence and resistance mechanisms were detectable months before MRI changes, enabling timely clinical intervention. Resistance to CDK4/6 inhibition is mediated by focal amplification of cell cycle regulators, suggesting alternative approaches will be required to overcome this path of resistance. CDK4/6 inhibitor therapy offers clinical benefit to a specific subset of high-risk Group 3/4-MB patients, motivating expanded evaluation of this population in future trials.

Citation Format: Katie Han, Kyle S Smith, Anna Kostecka, Sandeep Dhanda, Hong Lin, Margit Mikkelsen, Giles W Robinson, Paul A Northcott. CSF liquid biopsies reveal disease status and resistance mechanisms in children undergoing targeted therapy for malignant brain tumors [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B015.