ID #851 Multi-dimensional liquid biopsy approach for monitoring treatment response and tumor progression in pediatric CNS tumors.

Introduction

Medulloblastoma is a rapidly growing embryonal-CNS tumor with a 5-year survival-rate of nearly 0% in recurrent-cases. Current non-invasive monitoring relies primarily on imaging, which lacks the necessary sensitivity and fails to capture molecular features associated with tumor progression. Liquid-biopsies have emerged as a less invasive alternative that studies serially collectible sources of tumor-derived biomolecules. Relapsed Group 4 medulloblastomas are particularly challenging due to their poor prognosis and lack-of-molecular-biomarkers to predict relapse. This study aims to establish robust-assays for monitoring tumor progression, recurrence, and treatment response using liquid-biopsies to guide rational therapeutic interventions.

Methods

We used patient-derived cerebrospinal fluid (CSF; n = 7 patients) and plasma (n = 14 timepoints from n = 5 patients) to analyze longitudinal genetic, and immunological profiles with nanopore-sequencing and Mesoscale-Discovery (MSD) assay.

Results

Nanopore-sequencing assay detected copy-number-variation (CNVs) and distinct methylation patterns in group 4 medulloblastoma. Optimized protocols yielded high-purity cfDNA (64-97%; 20-376 ng) from just 500µL CSF, enabling consistent detection of tumor-derived-CNVs and methylation profiles, even at shallow-sequencing depths. Comparison against the gold-standard Illumina-EPICarray validated the effectiveness of nanopore-sequencing in generating similar CNV profiles using only 1/10th of cfDNA input. Matched-tumor-tissue vs CSF-CNV analysis highlighted the assay’s sensitivity in capturing further tumor heterogeneity. Additionally, we optimized a multianalyte ELISA (MSD) assay for monitoring treatment response and progression in patients undergoing immunotherapy in various clinical trials. The standardized MSD assay demonstrated a low pg/mL detection-limit and a 7-fold-dynamic detection-range, using only 50µL plasma. Longitudinal-immune- profiling in five medulloblastoma patients demonstrated an expected elevation in proinflammatory cytokines in Group 3/4 patients undergoing immunotherapy.

Impact

This multi-dimensional approach highlights the utility of such assays for monitoring progression and treatment-response using serial-liquid-biopsies, paving-the-way for precision-oncology in medulloblastoma-care. However, further investigation on a larger cohort will help toestablishstatistical significance.

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