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. 2025 Mar 3;31(5):881-889.
doi: 10.1158/1078-0432.CCR-24-1814.

Longitudinal Glioma Monitoring via Cerebrospinal Fluid Cell-Free DNA

Cecile Riviere-Cazaux  1 , Xiaoxi Dong  2 , Wei Mo  2 , Rahul Kumar  1 , Chao Dai  2 , Lucas P Carlstrom  1   3 , Amanda Munoz-Casabella  1 , Keyvan Ghadimi  1   4 , Cody L Nesvick  1 , Katherine M Andersen  1 , Matthew D Hoplin  1 , Nicholas Canaday  1 , Ignacio Jusue-Torres  1 , Noor Malik  1 , Jian L Campian  5 , Michael W Ruff  6 , Joon H Uhm  6 , Jeanette E Eckel Passow  7 , Timothy J Kaufmann  8 , David M Routman  9 , Sani H Kizilbash  5 , Ugur Sener  6 , Arthur E Warrington  1   6 , Robert B Jenkins  10 , Pan Du  2 , Shidong Jia  2 , Terry C Burns  1
Affiliations

Longitudinal Glioma Monitoring via Cerebrospinal Fluid Cell-Free DNA

Cecile Riviere-Cazaux et al. Clin Cancer Res. .

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 cerebrospinal fluid (CSF) from patients with gliomas.

Experimental design: Adults with gliomas underwent longitudinal intracranial CSF collection via Ommaya reservoirs or ventriculoperitoneal shunts. Cell-free DNA (cfDNA) was extracted and analyzed using PredicineCARE for cancer variant profiling and/or PredicineSCORE for low-pass whole-genome sequencing.

Results: Five patients (two females and three 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, 47 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 (VAF), and thus tumor fraction, decreased in pre- versus postchemoradiation 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 levels (0.64× and 0.62×, respectively, for the first patient and 0.01× and 0.07× for the other patient), although D-2-hydroxyglutarate and IDH1 VAF were not concordant in one patient thereafter. Moreover, the copy-number burden decreased below the limit of quantification during treatment and increased above the limit at progression.

Conclusions: Longitudinal intracranial CSF cfDNA can be obtained in patients with gliomas during their disease course. However, before deploying this technique, numerous questions and challenges should be answered.

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Conflict of interest statement

I. Jusue-Torres reports unrelated potential conflicts of interest [International Society for Hydrocephalus and CSF Disorders (board of directors, nonfinancial)]. J.E. Eckel Passow reports grants from the NIH during the conduct of the study. D.M. Routman reports grants from the NCI Paul Calabresi Program in Clinical/Translational Research at the Mayo Clinic Comprehensive Cancer Center (K12CA090628) during the conduct of the study; other support from Adela outside the submitted work; and intellectual property for DNA Methylation licensed to Exact Sciences. S.H. Kizilbash reports grants from Orbus Therapeutics, Apollomics, Wayshine Biopharm, Celgene, Incyte, Loxo Oncology, Nerviano Medical Sciences, CNS Pharmaceuticals, SonALAsense, and Aminex Therapeutics outside the submitted work. U. Sener reports personal fees from Servier Pharmaceuticals and grants from UL1 TR002377 outside the submitted work. S. Jia reports employment with Predicine, Inc. and ownership of Predicine, Inc. stock. T.C. Burns reports nonfinancial support from Predicine during the conduct of the study, as well as nonfinancial support from Predicine outside the submitted work. No disclosures were reported by the other authors.

Figures

Figure 1.
Figure 1.
Longitudinal CSF cfDNA from patient 24 (recurrent GBM). A, The timeline of the clinical course of patient 24 is depicted starting from POD 0, the day of resection for her recurrent GBM. Black X indicates when CSF samples were obtained and sequenced; red X indicates when CSF was sampled but had insufficient cfDNA for analysis. Correlative MRIs are shown for each time point. B, (i) Total cfDNA abundance, (ii) tumor fraction, and (iii) CNB were calculated from each CSF sample. CNB <7.5 (gray box) is below the limit of quantification. Red X, CSF obtained but had insufficient cfDNA for testing. C, Copy-number plots were generated for each CSF sample; POD 118 is shown. D, The VAF were calculated for the two samples in which sufficient cfDNA was obtained for NGS, at POD 26 and POD 118. E, Observations and questions that arose from patient 24’s data. *All other variants, unknown significance or benign. AMP, amplification; HETD, heterozygous genes; HOMD, homozygous genes; NEUT, neutral.
Figure 2.
Figure 2.
Longitudinal CSF cfDNA from patient 78 (GBM). A, The timeline of the clinical course of patient 78 is depicted starting from POD 0, the day of resection for his primary GBM. On POD 0, both CSF (solid circle) and cyst fluid (hollow circle) were analyzed. The patient underwent treatment with pembrolizumab (pembro) in addition to standard chemoradiation (chemorad). Black X indicates when CSF samples were obtained and sequenced; red X indicates when CSF was sampled but had insufficient cfDNA for analysis. Correlative MRIs are shown for each time point. B, (i) Total cfDNA abundance, (ii) tumor fraction, and (iii) CNB were calculated from each CSF sample. C, (i and ii) Copy-number plots were generated for each sample; POD 0 from the cyst fluid and POD 296 are shown. D, Fish plot depicting the VAF of five detected mutations from POD 0 to POD 650. E, Observations and questions that arose from patient 78’s data. Red X, CSF obtained but had insufficient cfDNA for testing. AMP, amplification; HETD, heterozygous genes; HOMD, homozygous genes.
Figure 3.
Figure 3.
Longitudinal CSF cfDNA from patient 79 (GBM, mismatch repair deficient). A, The timeline of the clinical course of patient 79 is depicted starting from POD 0, the day of resection for her GBM that was mismatch repair deficient. She also underwent treatment with pembrolizumab (pembro) in addition to standard chemoradiation (chemorad). Black X indicates when CSF samples were obtained and sequenced; red X indicates when CSF was sampled but had insufficient cfDNA for analysis. Correlative MRIs are shown for each time point. Dashed lines, missing data between two points. B, (i) Total cfDNA abundance, (ii) tumor fraction, and (iii) CNB were calculated from each CSF sample. C, Copy-number plots were generated for each CSF sample; (i) POD 0, (ii) POD 36, and (iii) POD 310 are shown. D, Fish plot depicting the VAF of numerous detected mutations from POD 0 to POD 699. E, Observations and questions that arose from patient 79’s data. Red X, CSF obtained but had insufficient cfDNA for testing. AMP, amplification; HETD, heterozygous genes; HOMD, homozygous genes.
Figure 4.
Figure 4.
Longitudinal CSF cfDNA from patient 98 (astrocytoma, IDH mutant, CNS WHO grade 4). A, The timeline of the clinical course of patient 98 is depicted starting from POD 0, the day of resection for his astrocytoma, IDH mutant, CNS WHO grade 4. Black X indicates when CSF samples were obtained and sequenced; red X indicates when CSF was sampled but had insufficient cfDNA for analysis. B, (i) Total cfDNA abundance, (ii) tumor fraction, and (iii) CNB were calculated from each CSF sample. Additionally, (iv) volumetrics was performed to calculate the enhancing tumor volume (cm3) from each time point. The VAF for the IDH1 mutation and the levels of D-2-HG (in µmol/L) were also quantified at each time point. Hollow triangle: no IDH1 VAF detected. C, (i and ii) Copy-number plots were generated for each CSF sample; POD 0 and POD 305 are shown. D, Fish plot depicting the VAF of six detected mutations from POD 0 to POD 626. E, Observations and questions that arose from patient 98’s data. AMP, amplification; chemorad, chemoradiation; HETD, heterozygous genes; HOMD, homozygous genes; PARPi, PARP inhibitor.
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