Longitudinal glioma monitoring via cerebrospinal fluid cell-free DNA: one patient at a time
Authors: Riviere-Cazaux Cecile , Dong Xiaoxi , Mo Wei , Dai Chao , Carlstrom Lucas P. , Munoz-Casabella Amanda , Kumar Rahul , Ghadimi Keyvan , Nesvick Cody L. , Andersen Katherine M. , Hoplin Matthew D. , Canaday Nicholas , Jusue-Torres Ignacio , Malik Noor , Campian Jian L. , Ruff Michael W. , Uhm Joon H. , Eckel Passow Jeanette E. , Kaufmann Timothy J. , Routman David M. , Kizilbash Sani H. , Warrington Arthur E. , Jenkins Robert B. , Du Pan , Jia Shidong , Burns Terry C. 
Published: December 2024

ABSTRACTIMPORTANCECurrent methods for glioma treatment response assessment are limited. Intracranial cerebrospinal fluid (CSF) may provide a previously untapped source of longitudinal biomarkers, such as cell-free DNA (cfDNA), for disease monitoring.OBJECTIVETo assess the feasibility of obtaining longitudinal intracranial CSF cfDNA from patients with gliomas during their disease course.DESIGNThis case series was initiated in 2021, with patients followed until last clinical follow-up (death or present time).SETTINGThis single-center study was conducted at a large academic medical center.PARTICIPANTSAdults with gliomas were recruited for longitudinal intracranial CSF collection using 1) Ommaya reservoirs, from which CSF would be sampled on at least two separate occasions, or 2) CSF collection from other clinically indicated CSF access devices, such as ventriculoperitoneal (VP) shunts.INTERVENTIONSCSF was collected from Ommaya reservoirs in four patients and from an existing VP shunt in one patient.MAIN OUTCOMES AND MEASURESThe study aimed to collect CSF for biobanking and biomarker discovery, with the hypothesis that CSF could serve as a source of longitudinally acquirable biomarkers.RESULTSFive patients (2 females, 3 males; median: 40 years, range 32-64 years) underwent longitudinal intracranial CSF collection via Ommaya reservoirs (n=4/5 patients) or VP shunt (n=1/5). Three patients had glioblastoma and two had astrocytoma, IDH-mutant, grade 4. In total, thirty-five CSF samples were obtained (median: 3.80 mL; 0.5-5 mL), with 30 (85.7%) yielding sufficient cfDNA for Next-Generation Sequencing (n=28) or Low-Pass Whole Genome sequencing (all samples). Tumor fraction was found to increase with radiographic progression. Changes in variant allelic frequencies (VAFs) may be seen within individual patients after resection and chemoradiation. In two patients, changes in tumor-specific IDH1 VAF correlated with CSF D-2-hydroxyglutarate levels, the oncometabolite of IDH mutant tumors. Copy number burden (CNB) decreased below the limit of quantification during treatment.CONCLUSIONS AND RELEVANCELongitudinal CSF cfDNA can feasibly be obtained via CSF access devices in patients with gliomas during their disease course. Ongoing studies will evaluate hypotheses generated in this case series regarding how longitudinal CSF cfDNA could be utilized to sensitively detect changes in disease burden.Trial RegistrationNCT04692324https://clinicaltrials.gov/study/NCT04692324;NCT04692337https://clinicaltrials.gov/study/NCT04692337QUESTIONWhat is the feasibility of obtaining longitudinal intracranial cerebrospinal fluid cell-free DNA from patients with high-grade gliomas to evaluate changes during treatment?FINDINGIn this case series, we find that CSF cfDNA can feasibly be obtained throughout treatment via CSF access devices. We find that changes in tumor fraction or tumor-associated variant allele frequencies (VAFs) may correlate with disease trajectory, with VAFs positively correlating to other tumor-associated candidate biomarkers.MEANINGLongitudinal cerebrospinal cell-free DNA may inform the impact of treatment throughout a specific patient’s disease course, from the time of resection through radiographic progression.