Using Cerebrospinal Fluid to Track Glioma Tumor Evolution

Diffuse gliomas, the most common primary brain tumors, are often highly aggressive and are associated with poor outcomes and limited effective treatment options. The location of these tumors makes genetic profiling difficult and requires invasive brain surgery for tissue collection. Furthermore, because these tumors undergo several genomic alterations throughout their development, repeat biopsies are often necessary. In recent years, “liquid biopsy” technology that utilizes circulating tumor DNA (ctDNA) has emerged as an effective, less invasive method of tumor profiling for many tumor types. This technology utilizes tumor DNA found in the blood, but detection of ctDNA in glioma is much lower than in other solid tumors due to the blood-brain barrier.However, tumor ctDNA from brain tumors may be enriched in cerebrospinal fluid (CSF), which could be obtained by a lumbar puncture and provide an alternate route for liquid biopsy and tumor profiling.

A recent study evaluated CSF from 85 patients with diffuse gliomas to determine if CSF could be used as a source of ctDNA for glioma tumor characterization. All patients had tumor tissue available from biopsy or resection at diagnosis and had since received at least one treatment for glioma.

ctDNA was identified in 49.4% of patients analyzed. Shedding of tumor DNA in CSF was associated with tumor progression, tumor burden, and tumor spread toward the ventricular or subarachnoid space. In contrast, glioma grade, disease duration, and prior therapy did not impact presence of ctDNA in CSF. Importantly, presence of ctDNA in CSF was associated with shorter survival. Patients with ctDNA in CSF had fourfold higher risk of death than patients without (P = .00023315). Genetic analysis of ctDNA from CSF identified several genetic mutations that are known to occur early in glioma tumorigenesis, including 1p/19q codeletion and IDH1/2 mutations. There was 100% concordance between ctDNA and tissue biopsies for mutations considered definitive of the disease subtype. Additionally, in 5 patients who underwent tumor resection within 3 weeks of CSF collection, the genetic profile of resected tumor tissue was highly similar to that seen in CSF ctDNA, confirming that CSF ctDNA provides an accurate representation of tumor tissue.

There were a number of mutations and alterations present in ctDNA that were not found in tissue biopsy, including protein-coding mutations, copy number alterations, promoter mutations, and structural rearrangements. Many of the genomic alterations present in CSF but not in tissue from diagnosis could be linked to tumor treatment. Among 5 patients (12%), all of whom had previously received temozolomide, presence of a higher mutation rate and increased G:C to A:T transitions indicated exposure to an alkylating agent. Given that only 33% to 73% of genetic alterations are typically shared between initial and recurrent tumors, the presence of these additional mutations in CSF indicate evolution of the tumor genome during the course of the disease.

Of interest, in 84% of patients with positive CSF ctDNA, no mutations were found in blood, despite use of a highly sensitive next-generation sequencing assay (average raw sequence coverage >18,000x). This indicates that ctDNA from brain tumors is shed directly into CSF and not blood.

This study demonstrates that ctDNA in CSF of patients with diffuse glioma provides an accurate representation of the tumor’s genetic profile and may provide a less invasive method for tracking tumor evolution. This has applications for diagnosis and tumor staging as well as development of targeted, genotype-directed treatments.

Nature. 2019 Jan 23. [Epub ahead of print].

CSF-liquid-biopsy

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