Researchers have developed two novel methods to detect a brain tumour (glioma) using cell-free DNA in the blood plasma and urine of patients, creating an opportunity for early diagnosis and improved patient care.
Liquid biopsy has recently been under the limelight given its potential to revolutionise cancer detection, diagnosis and monitoring. It involves detecting tumour cells and fragmented cell-free DNA (cfDNA) in body fluids, most commonly blood. These fragments are comprised of both germline DNA and tumour DNA. They are released from cells that haven undergo apoptosis or necrosis. Compared to traditional tissue biopsies, liquid biopsies are non-invasive and more accurately represent tumour heterogeneity.
However, detecting cfDNA from brain tumours has been challenging due to the low levels of these fragments within the blood plasma. This is because the blood-brain barrier inhibits the movement of cells and other molecules between the brains’ cerebrospinal fluid (CSF) and the blood. Until recently, no test has been sensitive enough to detect tumour-specific mutations for glioma-derived cfDNA.
Previous studies have used CSF as an alternative for analysing brain tumour cfDNA, but the detection sensitivity is poor. Furthermore, CSF sampling is invasive and painful for patients and requires the expertise of highly trained medical professionals.
Tumour-guided sequencing assay
Recently, researchers at the Cancer Research UK Cambridge Institute developed two novel analysis methods using plasma and urine cfDNA as a liquid biopsy for glioma, a type of brain tumour. Their work has been published in EMBO Molecular Medicine.
The first method is a tumour-guided sequencing assay which detects cfDNA in the body fluid of glioma patients. This is based on tracking many known glioma-specific mutations in cfDNA.
The team analysed each tumour specimen with whole-exome sequencing to identify mutations found in glioma-derived cfDNA. Multiple regions of each tumour were sequenced to increase the confidence in identifying tumour-specific mutations. Hybrid-capture sequencing panels were then designed by merging the variants and the 52 most frequently mutated genes in glioma. The capture panels were used to sequence the patients’ body fluids with high coverage.
Across all the samples taken from 8 glioma patients, the assay detected cfDNA in 7 of the 8 CSF samples, 10 of the 12 plasma samples and 10 of the 16 urine samples with high sensitivity.
Shallow whole-genome sequencing
The second method, shallow whole-genome sequencing (sWGS), identifies the presence of gliomas based on cfDNA fragmentation patterns. Unlike the tumour-guided sequencing assay, sWGS does not require tissue biopsies to obtain knowledge of tumour-specific mutations.
With low-coverage WGS, the researchers sequenced cfDNA in the urine samples of 35 glioma patients, 27 individuals with non-malignant brain disorders, and 26 healthy individuals. The results showed that cfDNA fragments in patients with gliomas were significantly different to those without gliomas.
sWGS data was then inputted into 4 machine-learning algorithms. Using size differences in the cfDNA, the algorithms successfully differentiated the urine samples from individuals with and without glioma. While this test is cheaper and easier than the tumour-guided sequencing assay, it is not as sensitive and is also less specific.
Implications for glioma patients
Although the researchers only analysed a small number of patients, their findings demonstrate the promise of using plasma and urine testing for glioma detection to improve patient care.
Typically, glioma patients are subject to constant monitoring as there is a high likelihood of tumour recurrence after tumour removal. This involves MRI scans and tumour biopsies every three months. For many patients, the period in between checks becomes a regular source of anxiety.
The simple tests proposed would ensure that cancer patients are monitored more regularly, without needing frequent trips to the hospital. Not only would this allow for tumour recurrence to be detected earlier, but it would also boost patients’ mental health. While this work is still in its early stages, it has demonstrated the potential of liquid biopsy in transforming the lives of cancer patients.
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