Longitudinal glioma monitoring via cerebrospinal fluid cell-free DNA

Abstract

PURPOSE: Current methods for glioma response assessment are limited. This study aimed to assess the technical and clinical feasibility of molecular profiling using longitudinal intracranial CSF from patients with gliomas. EXPERIMENTAL DESIGN: Adults with gliomas underwent longitudinal intracranial CSF collection via Ommaya reservoirs or ventriculoperitoneal shunts. cfDNA was extracted and analyzed using PredicineCARE for cancer variant profiling and/or PredicineSCORE for low-pass whole genome sequencing (LP-WGS). RESULTS: Five patients (2 females, 3 males; median age: 40 years, range 32-64 years) underwent longitudinal intracranial CSF collection via Ommaya reservoirs (n=4) or ventriculoperitoneal shunts (n=1). In total, forty-seven CSF samples were obtained (median volume: 4.00 mL; 0.5-5 mL). Forty-one samples (87.2%) yielded sufficient cfDNA for testing. Patient-specific tumor-associated variant allelic frequencies (VAFs), and thus tumor fraction, decreased in pre-versus-post chemoradiation samples, including through pseudoprogression. These also increased with radiographic progression in three patients, although identifying the time of definitive disease progression from MRIs was a significant limitation. In two patients with isocitrate dehydrogenase (IDH) mutant gliomas, decreasing IDH1 VAF after resection and chemoradiation correlated with decreased CSF D-2-hydroxyglutarate (D-2-HG) levels (0.64x and 0.62x, respectively, for the first patient, and 0.01x and 0.07x for the other patient), although D-2-HG and IDH1 VAF were not concordant in one patient thereafter. Moreover, CNB decreased below the limit of quantification during treatment and increased above the limit at progression. CONCLUSION: Longitudinal intracranial CSF cfDNA can feasibly be obtained in patients with gliomas during their disease course. Numerous questions and challenges should be answered before deploying this technique.