Cell-free DNA from cerebrospinal fluid cytology specimens as a novel liquid biopsy approach for pediatric patients with primary central nervous system tumors

Abstract

BACKGROUND: Assessing circulating cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) has been proposed as a promising alternative to tissue biopsy. Advances in cfDNA sequencing have further underscored the potential of CSF liquid biopsies in the clinical setting. CSF is routinely collected for cytologic evaluation at diagnosis and at recurrence in both pediatric and adult central nervous system (CNS) tumors. Preliminary studies have shown that CSF cfDNA analysis may be more sensitive than CSF cytology for detecting the presence of tumor. METHODS: CSF specimens were prospectively collected from seven pediatric patients with primary CNS malignant tumors. When possible, CSF was collected fresh and from processed cytology specimens. Low-pass whole genome sequencing (LP-WGS) and next-generation sequencing (NGS) using a custom targeted sequencing panel were performed on the specimens to identify copy number alterations (CNAs), detect mutations, and estimate circulating tumor DNA (ctDNA) fractions. Results were compared with matched tumor tissue molecular profiles and corresponding imaging findings. RESULTS: Abnormalities in cfDNA were detected in four patients. Sequencing of CSF cytology supernatants demonstrated the presence of circulating tumor DNA with characteristic CNAs and mutations that matched what was seen the tumor tissue as well as the fresh CSF specimens. These studies also revealed tumor heterogeneity and genomic evolution over time. CONCLUSION: This study demonstrates the feasibility of utilizing routinely discarded supernatants from CSF cytology specimens for LP-WGS and targeted NGS. Our approach optimizes the use of CSF that may be limited in pediatric patients as a source for liquid biopsy-based genomic studies. Future research will be necessary to optimize and validate the methodology to enable clinical implementation.