Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology

Abstract

Technological advancements in cell-free DNA (cfDNA) liquid biopsy have triggered exponential growth in numerous clinical applications. While cfDNA-based liquid biopsy has made significant strides in personalizing cancer treatment, the exploration and translation of epigenetics in liquid biopsy to clinical practice is still nascent. This comprehensive review seeks to provide a broad yet in-depth narrative of the present status of epigenetics in cfDNA liquid biopsy and its associated challenges. It highlights the potential of epigenetics in cfDNA liquid biopsy technologies with the hopes of enhancing its clinical translation. The momentum of cfDNA liquid biopsy technologies in recent years has propelled epigenetics to the forefront of molecular biology. We have only begun to reveal the true potential of epigenetics in both our understanding of disease and leveraging epigenetics in the diagnostic and therapeutic domains. Recent clinical applications of epigenetics-based cfDNA liquid biopsy revolve around DNA methylation in screening and early cancer detection, leading to the development of multi-cancer early detection tests and the capability to pinpoint tissues of origin. The clinical application of epigenetics in cfDNA liquid biopsy in minimal residual disease, monitoring, and surveillance are at their initial stages. A notable advancement in fragmentation patterns analysis has created a new avenue for epigenetic biomarkers. However, the widespread application of cfDNA liquid biopsy has many challenges, including biomarker sensitivity, specificity, logistics including infrastructure and personnel, data processing, handling, results interpretation, accessibility, and cost effectiveness. Exploring and translating epigenetics in cfDNA liquid biopsy technology can transform our understanding and perception of cancer prevention and management. cfDNA liquid biopsy has great potential in precision oncology to revolutionize conventional ways of early cancer detection, monitoring residual disease, treatment response, surveillance, and drug development. Adapting the implementation of liquid biopsy workflow to the local policy worldwide and developing point-of-care testing holds great potential to overcome global cancer disparity and improve cancer outcomes.

Keywords: DNA methylation; cancer disparity; cancer screening; cell-free DNA; chromatin remodeling; circulating tumor DNA; early cancer detection; epigenetic drugs; epigenetics; epigenomics; fragmentomics; histone modification; liquid biopsy; nucleosome positioning; personalized medicine; precision oncology; targeted therapy; translational medicine.

Figure 1

Impact of lifetime exposure on epigenetics plasticity and the development and progression of chronic diseases such as cancer. An individual’s genetic makeup is influenced by ethnicity, race, geography, and family history via trans-generation inheritance. Genes may undergo mutations because of prolonged exposures to the local environment and lifestyle habits, which accumulate throughout a lifetime. These genetic mutations may be passed down through generations. Epigenetic changes are highly dynamic and plastic, influencing gene expressions in response to changes and insults from the local environment. Crucial epigenetic alterations are passed on from ancestors and inherited by subsequent generations. This may lead to the priming of accelerated aging and the development of various diseases.

Figure 2

Epigenetic mechanisms and cfDNA biomarkers with detection methods in liquid biopsy. Arrows show the detection method. Abbreviations: Seq: sequencing, MBD-Seq: methyl-CpG-binding domain sequencing, MSQPCR: methylation-specific polymerase chain reaction, WGBS: whole genome bisulfite sequencing, Enz-Seq: enzymatic converted sequencing, MeDIP-Seq: methylated DNA immunoprecipitation followed by sequencing, CHIP: chromatin immunoprecipitation, MNase-Seq: micrococcal nuclease digestion with deep sequencing, CUT&RUN: cleavage under targets and release using nuclease, CUT&Tag: cleavage under targets and tagmentation, ATAC-Seq: assay for transposase-accessible chromatin with high-throughput sequencing, DNase-Seq: DNase I hypersensitive sites sequencing, qPCR: quantitative polymerase chain reaction, ddPCR: droplet digital polymerase chain reaction, DELFI: DNA evaluation of fragments for early interception.

Figure 3

cfDNA Liquid Biopsy Analytical Pipeline in Precision Oncology. Molecular biomarkers can be harnessed from a patient’s bodily fluids and stool samples. These biomarkers can be combined, and when integrated with machine learning, they can be used to develop tests for early disease detection, monitoring of residual disease, and targeted therapy. The vast molecular data from liquid biopsy can be stored in a long-term repository. These data can be integrated with real-time epigenetic sensing of long-term lifetime exposures and can be used to refine precision oncology prediction models for next-generation testing and applications.