Clinical Utility of Plasma Cell-Free DNA in Adult Patients with Newly Diagnosed Glioblastoma: A Pilot Prospective Study

Abstract

Purpose: The clinical utility of plasma cell-free DNA (cfDNA) has not been assessed prospectively in patients with glioblastoma (GBM). We aimed to determine the prognostic impact of plasma cfDNA in GBM, as well as its role as a surrogate of tumor burden and substrate for next-generation sequencing (NGS).

Experimental design: We conducted a prospective cohort study of 42 patients with newly diagnosed GBM. Plasma cfDNA was quantified at baseline prior to initial tumor resection and longitudinally during chemoradiotherapy. Plasma cfDNA was assessed for its association with progression-free survival (PFS) and overall survival (OS), correlated with radiographic tumor burden, and subjected to a targeted NGS panel.

Results: Prior to initial surgery, GBM patients had higher plasma cfDNA concentration than age-matched healthy controls (mean 13.4 vs. 6.7 ng/mL, P < 0.001). Plasma cfDNA concentration was correlated with radiographic tumor burden on patients' first post-radiation magnetic resonance imaging scan (ρ = 0.77, P = 0.003) and tended to rise prior to or concurrently with radiographic tumor progression. Preoperative plasma cfDNA concentration above the mean (>13.4 ng/mL) was associated with inferior PFS (median 4.9 vs. 9.5 months, P = 0.038). Detection of ≥1 somatic mutation in plasma cfDNA occurred in 55% of patients and was associated with nonstatistically significant decreases in PFS (median 6.0 vs. 8.7 months, P = 0.093) and OS (median 5.5 vs. 9.2 months, P = 0.053).

Conclusions: Plasma cfDNA may be an effective prognostic tool and surrogate of tumor burden in newly diagnosed GBM. Detection of somatic alterations in plasma is feasible when samples are obtained prior to initial surgical resection.

Figure 1.

Plasma cell-free DNA (cfDNA) concentration in age-matched healthy donors (known cancers and/or inflammatory diseases excluded) versus patients with newly diagnosed GBM prior to surgical resection.

Figure 2.

Kaplan-Meier curves for progression-free and overall survival (months from initial surgery) of glioblastoma patients according to (A) and (B) baseline plasma cell-free DNA (cfDNA) concentration, and (C) and (D) detectability of ≥1 versus no somatic mutations in cfDNA.

Figure 3.

Mutational analysis for 20 patients for whom both plasma and tissue samples were obtained concurrently and sequenced. A detailed summary of all disease-associated somatic variants covered and called by both the tissue tumor DNA and circulating tumor DNA (ctDNA) platforms are included.

Figure 4.

cfDNA dynamics and radiographic tumor burden for subjects enrolled on the longitudinal portion of the study who had not yet experienced tumor progression by the time of the data cutoff for this analysis. Time points are the following: 1 (pre-operative), 2 (post-operative), 3 (radiation simulation), 4 (1-month post-radiation scan), 5 (1^st follow up scan), 6 (2^nd follow up scan), and 7 (3^rd follow up scan). All subjects had stable disease and were continued on maintenance temozolomide at all time points. cfDNA generally remained low and stable in these subjects, although there were minor increases (all less than 5ng/mL changes) at the most recent time point in subjects A014 (B), A042 (E), and A045 (F).

Figure 5.

cfDNA dynamics and radiographic tumor burden for subjects enrolled on the longitudinal portion of the study who had confirmed progressive disease prior to the data cutoff for this analysis. Time points are the following: 1 (pre-operative), 2 (post-operative), 3 (radiation simulation), 4 (1-month post-radiation scan), 5 (1^st follow up scan), 6 (2^nd follow up scan), and 7 (3^rd follow up scan). A, Subject A016 had increased tumor volume on the first post-radiation MRI, concerning for progressive tumor versus pseudoprogression. The subject was steroid-dependent, and bevacizumab was initiated with radiographic response (time point #5). However, cfDNA rose rapidly during this time, which was followed over the subsequent month (time point #6) by radiographic tumor progression, clinical decline, and death of the subject from disease progression. B, Subject A040 developed tumor progression after 3 cycles of temozolomide, accompanied by a modest rise in cfDNA. C, Subject A046 experienced early disease progression on the first post-radiation MRI, accompanied by a dramatic rise in cfDNA. The subject died from disease progression 2 months later. D, Subject A047 had a significant rise in cfDNA between the radiation planning and first post-radiation MRIs. Although this rise was initially accompanied by a decline in radiographic tumor volume, cfDNA concentration continued to increase and was followed by non-enhancing tumor progression and clinical decline, resulting in subject’s death from disease progression within 4 weeks. E, Subject A048 had radiographic increase in tumor volume 3 months after completion of radiation (time point #5). Steroids were initiated and an additional cycle of temozolomide was administered. One month later (time point # 6), there was only minimal continued increase in tumor size with no clinical decline, and cfDNA concentration decreased. Ongoing pseudoprogression was clinically suspected, and the subject completed another cycle of temozolomide. At the next time point (# 7), the tumor had grown considerably, accompanied by resumed increase in cfDNA. The subject underwent repeat craniotomy with histopathology demonstrating recurrent GBM and died 1 month later. F, Subject A057 had increased tumor volume on the first post-radiation MRI. A repeat MRI one month later showed continued increase in contrast-enhancing tumor, accompanied by dramatic rise in cfDNA. The subject underwent repeat craniotomy with histopathology confirming recurrent GBM.