Characterizing the Genomic Landscape of Brain Glioma With Circulating Tumor DNA From Tumor In Situ Fluid

Abstract

Tumor in situ fluid (TISF) refers to the fluid at the local surgical cavity. We evaluated the feasibility of TISF-derived circulating tumor DNA (ctDNA) characterizing the genomic landscape for glioma. This retrospective study included TISF and tumor samples from 10 patients with glioma, we extracted cell-free DNA (cfDNA) from the TISF and then performed deep sequencing on that. And we compared genomic alterations between TISF and tumor tissue. Results showed that the concentration of cfDNA fragments from the patients for TISF ranged from 7.2 to 1,397 ng/ml. At least one tumor-specific mutation was identified in all 10 patients (100%). Further analysis of TISF ctDNA revealed a broad spectrum of genetic mutations, which have been reported to have clinical relevance. The analysis of concordance between TISF and tumor tissue reflected the spatiotemporal heterogeneity of glioma. Collectively, TISF ctDNA was a powerfully potential source for characterizing the genomic landscape of glioma, which provided new possibilities for precision medicine in patients with glioma.

Keywords: circulating tumor DNA; glioma; liquid biopsy; precision medicine; tumor in situ fluid.

Figure 1

A diagram for the tumor in situ fluid (TISF) collection. A reservoir was implanted into the resection cavity during the resection surgery. The dome end was placed beneath the scalp attached to the catheter that was inserted within the brain leading to the tumor resection-created cavity. A small amount of fluid could be extracted with a disposable milliliter syringe from the resection cavity via this reservoir postoperatively.

Figure 2

Clinical courses of included patients. Each patient began from the primary surgery (Biopsy). TISF, tumor in situ fluid; CRT, concurrent chemoradiotherapy; TMZ, adjuvant temozolomide chemotherapy; BEV, bevacizumab.

Figure 3

Analysis of tumor DNA from TISF and tumor tissue. (A) the mutational landscape for both TISF and tumor tissue. For each patient, the left column represented TISF-derived ctDNA and the right column represented tumor tissue, patient 4 just had one column for the TISF. (B) Concordance of tumor DNA between TISF and tumor tissue. The percentage of shared mutations varied from 0% to 100% (median 30.0%). (C) Cell-free DNA (cfDNA) levels from TISF. The concentration of cfDNA from TISF ranged between 7.2 and 1397 ng/ml. For patient 9, the second time TISF cfDNA experienced a significant increase. (D) Survival curve for patients with different IDH status. In all 10 patients (including 6 IDH wild type and 4 IDH mutant gliomas), the IDH status was accordant between the TISF and tumor tissue (100%). Median overall survival after the primary surgery was 14.2 and 32.2 months (P = 0.0038) for TISF wild-type IDH and TISF mutant IDH glioma, respectively.

Figure 4

Follow-up MRI showed tumor progression. All patients received serial MRI as the standard of care. As presented in the images and the illustrative flowchart, A1–E1 stand for a postoperative representative timepoint, at which we could not notice an obvious sign of tumor progression on the MRI scans, but at which we suspected tumor progression according to the comprehensive conditions of patients, then TISF was collected, in which tumor-specific ctDNA mutations were detected. 2–4 months later, as shown in the images A2–E2, definite radiologic sign of tumor recurrence appeared. This is interesting but we still presume that the simple signature of ctDNA-positive in TISF could not be a biomarker for early predicting the recurrence of glioma, because of the special location of TISF, which is at the local site of the tumor. The tumor progression should be determined by a specific genetic analysis.