Serial H3K27M cell-free tumor DNA (cf-tDNA) tracking predicts ONC201 treatment response and progression in diffuse midline glioma

Abstract

Background: Diffuse Midline Glioma (DMG) with the H3K27M mutation is a lethal childhood brain cancer, with patients rarely surviving 2 years from diagnosis.

Methods: We conducted a multi-site Phase 1 trial of the imipridone ONC201 for children with H3K27M-mutant glioma (NCT03416530). Patients enrolled on Arm D of the trial (n = 24) underwent serial lumbar puncture for cell-free tumor DNA (cf-tDNA) analysis and patients on all arms at the University of Michigan underwent serial plasma collection. We performed digital droplet polymerase chain reaction (ddPCR) analysis of cf-tDNA samples and compared variant allele fraction (VAF) to radiographic change (maximal 2D tumor area on MRI).

Results: Change in H3.3K27M VAF over time ("VAF delta") correlated with prolonged PFS in both CSF and plasma samples. Nonrecurrent patients that had a decrease in CSF VAF displayed a longer progression free survival (P = .0042). Decrease in plasma VAF displayed a similar trend (P = .085). VAF "spikes" (increase of at least 25%) preceded tumor progression in 8/16 cases (50%) in plasma and 5/11 cases (45.4%) in CSF. In individual cases, early reduction in H3K27M VAF predicted long-term clinical response (>1 year) to ONC201, and did not increase in cases of later-defined pseudo-progression.

Conclusion: Our work demonstrates the feasibility and potential utility of serial cf-tDNA in both plasma and CSF of DMG patients to supplement radiographic monitoring. Patterns of change in H3K27M VAF over time demonstrate clinical utility in terms of predicting progression and sustained response and possible differentiation of pseudo-progression and pseudo-response.

Keywords: H3K27M; ONC201; circulating tumor DNA; diffuse midline glioma; liquid biopsy.

Fig. 1

Landscape of patient samples and H3K27M variant allele fraction (VAF) by time point.

Fig. 2

(A-B) Correlation of tumor area change from baseline with CSF and plasma VAF percentage change from baseline (P value by Pearson correlation.) (C-D) H3K27M VAF by location in CSF (all time points) (C) and plasma (D, t-test.).

Fig. 3

(A-B) Correlation of VAF change (delta: baseline-final time point VAF) to PFS (days of treatment) for CSF (A) and plasma (B, Pearson correlation) for nonrecurrent patients. (C-D) Progression free survival (PFS) (days of treatment) for nonrecurrent patients when patients are separated by VAF delta (increase or decrease from first to last value) for CSF (C) and plasma (D).

Fig. 4

(A) Patients with tDNA peak (25% increase) and relation to tumor progression on tumor imaging (B) and days prior to progression by sample type. (C) Increase in VAF predicts progression in CSF and correlates with progression in a 10-year-old female with DIPG treated with ONC201.

Fig. 5

(A) Pseudo-progression on tumor area by MRI (red dotted box) is not reflected in cf-tDNA H3K27M VAF reduction in a 6-year-old DMG patient with long-term response to ONC201. (B) A 13-year-old male with spinal H3K27M-mutant glioma demonstrates plasma VAF increase prior to radiologic progression. The drop in tumor area (gray plot) occurred during administration of bevacizumab, which caused reduction in tumor edema/area and contrast enhancement.