By Tim Aitman, Professor of Molecular Pathology and Genetics at University of Edinburgh
Transcribed by Tia Byer
The liquid biopsy market is a rapidly expanding area of the biomarkers field and is expected to increase at a CAGR of 13.5% to reach $19.35 billion by 2028. It is a pioneering technique which is anticipated to gain sizeable importance within oncology research and diagnostics. The rapid market growth is attributed to cutting-edge advancements in Next Generation Sequencing technology, the evolving pipeline of commercialised products such as circulating DNA-based liquid biopsy tests, and the increasing opportunities for personalised cancer management. Liquid biopsy testing also presents an opportunity for non-invasive testing for cancer detection and monitoring of response to treatment.
Liquid Biopsy Background and Applications:
Liquid biopsies are comprised of more than just cell-free DNA and contain an entire host of components, including circulating tumour cells, exosomes, RNA, red blood cells, and platelets. While these are interesting in the research scenario, cell-free DNA assays have shown far greater clinical applicability than other assays. Clinical applications of liquid biopsy in cancer management can pertain to all stages of the patients’ journey, from early cancer detection in healthy people and treatment selection in defined cases, to determining the level of minimal residual disease. Predicting the treatment outcome and early indications of disease recurrence and progression are additional benefits.
Opportunities for Easy and Difficult Cancers:
While research attests to the clinical applications of liquid biopsies, the varying complexity of cancer types remains a bottleneck for their wide-spread use. Within cancer management there are easy and difficult scenarios. Some cancers secrete a lot of DNA, such as bladder, colorectal, gastroesophageal, and ovarian and there are those that secrete very little, such as prostate, renal cell carcinoma, thyroid, and glioma. We do not know precisely why this is, but glioma is undoubtedly the most difficult to detect circulating tumour DNA. It is also recognised that early-stage cancer detection is more difficult than late-stage cancer as this is partly due to the multiple sites and partly due to the tumour burden in the individual. Screening for circulating tumour DNA in the aftermath of initial treatment can be highly predictive of the outcome 2 to 5 years later.
Easy and Difficult Cancers: Two Exemplar Projects
At the Genome Medicine Research Group our researchers discussed two projects to exemplify liquid biopsy for easy and difficult cancers. The first, and the easier scenario, was the use of human papillomavirus (HPV) as a biomarker for head and neck cancer. We report a novel method to tackle the more difficult cancers using cell-free DNA capture by apheresis, conducted by the institution’s spinout company, BioCaptiva.
1.) HPV Detection in Head and Neck Cancer: Researchers deemed HPV biomarker as the easier of the two because it detects the viral DNA that gets incorporated into the cancer cells. There are often multiple copies of the viral genome in the cell, and it is secreted at a relatively high proportion into the circulation. Approximately 70% of head and neck cancers are associated with HPV, and in 2020, the research group conducted an experiment with 104 patients with oropharyngeal squamous cell cancer. During this, plasma cell-free DNA was extracted from 10 ml blood, and then a follow-up was conducted with 48 patients for 20 months. Researchers established ddPCR assays for the five following HPV subtypes: 16, 18, 31, 33, and 35. Pre-treatment results were then compared to conventional p16 immunohistochemistry and qualitative PCR of tumour tissue.
70% of these cancers were HPV positive for one or more HPV subtypes. Overall results were 93% concordant with immunohistochemistry findings and the conventional PCR of solid tumour tissue, testifying to the assay’s accuracy. The longitudinal follow-up showed that 40 out of the 48 patients fell to zero and remained undetectable. In 8 out of 48, levels either never fell to zero or did fall to zero and then rose subsequently. A rise in HPV copy number in more than one blood sample was associated with or predicted disease progression with these patients. It was concluded that routine pre-and post-treatment measurement of cell-free DNA HPV copy numbers can assist with challenging management decisions and may improve patient outcomes.
2.) Cell-free DNA Capture by Apheresis (BioCaptiva): The second example comes from the university’s spinout company, where the team has developed a method to increase the sensitivity of liquid biopsies by apheresis-based capture of cell-free DNA. BioCaptiva aims to markedly increase assay sensitivity for liquid biopsy as a diagnostic tool with a novel blood-based biopsy device. Because of low circulating tumour DNA concentration, most cell-free DNA studies and assays have had the greatest success with high circulating tumour DNA-secreting cancers or late-stage cancers. However, BioCaptiva found themselves asking whether it would be possible to use apheresis to capture up to 500 ng of cell-free DNA, 50-100-fold greater than usually extracted from a blood draw. The solution was to devise and patent the DNA BioCaptor, a hemocompatible DNA-binding polymer device to transform liquid biopsy testing and enhance cancer detection.
Apheresis functions in a similar way to dialysis or plasmapheresis in that a needle is injected into a vein of one arm, and then the blood gets channelled through a cartridge, which filters and binds DNA from either whole-blood or separately from the plasma. After separating the desired component then you return the rest of the blood to the patient. Apheresis is helpful in procedures such as hemodialysis for removing toxic chemicals and in plasmapheresis for removing cholesterol or antibodies that are causing damage to the body. In an early experiment, a functional prototype of the DNA BioCaptor, 83cm3 capacity could bind upwards of 5,500 ng cell-free DNA, approximately 1000-fold more than what is usually obtained from a blood draw.
The DNA BioCaptor provides a biocompatible environment that can safely and effectively deliver high input levels of cell-free DNA for liquid biopsy analysis. The DNA binding technology will undergo clinical trials next year and is expected to drive significant commercial growth. Whilst, current cell-free DNA protocols have demonstrated efficacy for detecting minimal residual disease and have potential in population screening, low cell-free DNA concentration remains a challenge. However, HPV cell-free DNA is an available biomarker in head and neck cancer that defines HPV status and predicts recurrence. Its promise to significantly improve clinical management has us at BioCaptiva very excited and we look forward to seeing its impact.
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