Liquid biopsies: epigenetic clues for early cancer detection

Written November 17, 2021.  Reviewed by Celina Whalley April 26, 2024

Liquid biopsies

Current screening limitations

Cancer is a leading cause of morbidity and mortality globally. Despite early diagnosis and treatment being one of the most effective methods to improve outcomes for cancer patients, early detection remains challenging. Screening methods are available for some tumor types, such as the smear test for cervical cancer and mammography for breast cancer.1,2 However, these early detection strategies are not entirely reliable, have limited sensitivity and patient adherence to these screening methods may not be optimal due to patient discomfort.3 Furthermore, few early non-invasive screening tools exist for the majority of cancer types.4 As a result, many cancers are detected when they become symptomatic, and at a stage in which treatment may no longer be possible or as effective.

The liquid biopsy revolution

Driven by these shortcomings, scientists and clinicians have turned their attention to liquid biopsies as a novel non- or minimally invasive screening strategy for early diagnosis of different tumors. Liquid biopsies aim to identify the presence of tumor-derived biological material, such as DNA or proteins, in the bodily fluids or blood of patients.5 Among those analytes the most widely published is cell-free circulating DNA (cfDNA). This cfDNA consists of short fragments of DNA released into circulation from cells during apoptosis or necrosis elsewhere in the body.6 The levels of cfDNA are generally low in healthy individuals but tend to be increased upon specific insults such as physical trauma, myocardial infarction, diabetes mellitus, infection and cancer. Indeed, the concentration of cfDNA correlates both with tumor size and stage.7 This tumor-derived portion of cfDNA is termed circulating tumor DNA (ctDNA) and can represent up to 90% of the total cfDNA of an individual.8 With the developments in next-generation sequencing (NGS) technologies, ctDNA has arisen as a promising biomarker that can be inexpensively and non-invasively analysed as a novel method for early cancer detection.

Evidence suggests mutations in oncogenes can be observed in the ctDNA of individuals as early as two years before a clinical diagnosis of cancer.9 However, analysis of mutations per se does not provide information about the origin or location of the potential tumor. Here, looking at the methylation pattern(s) of ctDNA may provide useful clues.

DNA methylation as a diagnostic tool

DNA methylation is an epigenetic modification that consists of the addition of a methyl group to cytosine in DNA chains. Different tissues in the body can be characterized by different DNA methylation patterns and the methylation pattern of cfDNA is consistent with the cells and tissue/organ from which the DNA originated10,11. Furthermore, aberrant methylation processes contribute to tumor development and progression. Therefore, analysis of tumor-specific methylation signatures appears to be the ideal diagnostic method to determine not only the presence but also the location of an asymptomatic tumor.

Finding specific DNA methylation patterns that can be tested for and used as a diagnostic tool is a topic of intense research. Many commercially available options for the diagnosis of cancers exist and more are under development.12

As a recent example, researchers working at the Centre For Genomic and Experimental Medicine at the University of Edinburgh have used the Nonacus Cell3 Target Technology to generate targeted methylation (NGS) sequencing libraries from cfDNA that can then be analysed for its methylation patterns. The researchers were able to successfully sequence as little as 20 ng of cfDNA. Using the MCF-7 breast cancer cell line as a source of artificial cfDNA, they found it was possible to establish that DNA originating from these cells displayed a higher amount of methylation in specific regions (CpG loci) when compared to lymphocyte-derived DNA.13

In the future, the group plans to perform similar experiments to identify the presence of ctDNA in samples from patients with breast, prostate, and kidney cancer, which would be the next step in bringing this tool into the clinic. The next decade is expected to bring together advances in biology, statistics, and computational tools to develop multi-parameter screening tests combining mutation, epigenetic, and/or protein biomarkers to increase the diagnostic accuracy of liquid biopsies and bring more early screening tools from the laboratory bench to the clinic.14 Nonacus plans to continue to support this valuable translational R&D work through provision of innovative products, informatics and software for liquid biopsy research and testing.

References

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  2. Lin JS, Piper MA, Perdue LA, Rutter CM, Webber EM, O’Connor E, et al. Screening for colorectal cancer: updated evidence report and systematic review for the US Preventive Services Task Force. JAMA. 2016;315(23):2576-94.
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  11. Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nature communications. 2018;9(1):5068.
  12. Locke WJ, Guanzon D, Ma C, Liew YJ, Duesing KR, Fung KY, et al DNA methylation cancer biomarkers: translation to the clinic. Frontiers in genetics. 2019;10:1150.
  13. de Procé SM, Adamowicz M, Dutta P, Warlow SJ, Moss J, Shemer R, et al. Development of methylation-based biomarkers for breast cancer detection by model training and validation in synthetic cell-free DNA. bioRxiv. 2022;2022-02.
  14. Luo H, Wei W, Ye Z, Zheng J, Xu RH. Liquid biopsy of methylation biomarkers in cell-free DNA. Trends in molecular medicine. 2021;27(5):482-500.