Liquid biopsies: epigenetic clues for early cancer detection
November 17, 2021
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 tumour types, such as the smear test for cervical cancer and mammography for breast cancer1,2. 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 discomfort3. Furthermore, few early non-invasive screening tools exist for the majority of cancer types4. 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 tumours. Liquid biopsies aim to identify the presence of tumour-derived biological material, such as DNA or proteins, in the bodily fluids or blood of patients5. 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 body6. 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 tumour size and stage7. This tumour-derived portion of cfDNA is termed circulating tumour DNA (ctDNA) and can represent up to 90% of the total cfDNA of an individual8. 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 2 years before a clinical diagnosis of cancer9. However, analysis of mutations per se does not provide information about the origin or location of the potential tumour. 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 characterised by different DNA methylation patterns10 and the methylation pattern of cfDNA is consistent with the cells and tissue/organ from which the DNA originated11. Furthermore, aberrant methylation processes contribute to tumour development and progression. Therefore, analysis of tumour-specific methylation signatures appears to be the ideal diagnostic method to determine not only the presence but also the location of an asymptomatic tumour.
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 exist12 and more are under development. 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.
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 clinic13. 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
1. Hovda, T. et al (2021). Radiological review of prior screening mammograms of screen-detected breast cancer European Radiology, 31(4), 2568-2579.
2. Lin, J. S. et al (2021). Screening for Colorectal Cancer: Updated Evidence Report and Systematic Review for the US Preventive Services Task Force JAMA, 325(19).
3.Subramanian, S. et al (2004). Adherence with colorectal cancer screening guidelines: A review Preventive Medicine, 38(5), 536-550.
4. X., Cheng. et al. (2020). Non-invasive early detection of cancer four years before conventional diagnosis using a blood test Nature Communications, 11(1), 3475.
5. Luo, H. et al (2021). Liquid Biopsy of Methylation Biomarkers in Cell-Free DNA Trends in Molecular Medicine, 27(5), 482-500.
6. Thierry, A. R. et al (2016). Origins, structures, and functions of circulating DNA in oncology. Cancer and Metastasis Reviews, 35(3), 347-376.
7. Chen, M., & Zhao, H. (2019). Next-generation sequencing in liquid biopsy: Cancer screening and early detection Human Genomics, 13(1), 34.
8. Elazezy, M., & Joosse, S. A. (2018). Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management Computational and Structural Biotechnology Journal, 16, 370-378.
9. Gormally, E. et al (2006). TP53 and KRAS2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: A prospective study Cancer Research, 66(13), 6871-6876.
10. Moore, L. et al (2013). DNA Methylation and Its Basic Function Neuropsychopharmacology, 38(1), 23-38.
11. Moss, J. et al (2018). Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease Nature Communications, 9(1), 5068.
12. Locke, W. J. et al (2019). DNA Methylation Cancer Biomarkers: Translation to the Clinic Frontiers in Genetics, 10, 1150.
13. Luo, H. et al (2021). Liquid Biopsy of Methylation Biomarkers in Cell-Free DNA Trends in Molecular Medicine, 27(5), 482-500.