DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types

Abstract

Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients' stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a "PanCancer" detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.

Keywords: DNA methylation; biomarker; breast cancer; cell-free DNA; colorectal cancer; detection; liquid biopsy; lung cancer; prognosis; prostate cancer.

Figure 1

Blood-based liquid biopsy. Circulating tumor cells (CTC), circulating cell-free DNA (ccfDNA) [including circulating tumor DNA (ctDNA)], circulating cell-free RNA (ccfRNA) and exosomes are released from tumor cells to the bloodstream. Hence, blood can be collected and analyzed in the context of a liquid biopsy.

Figure 2

Flow diagram of Pubmed available studies’ selection procedure using the key words “Lung Cancer/Breast Cancer/Colorectal Cancer/Lung Cancer”, “DNA methylation”, “Diagnosis/Detection/Prognosis” and “Serum/Plasma”.

Figure 3

Major studied epigenetic mechanisms involved in gene expression regulation. DNA methylation consists in the addition of a methyl group to a cytosine present in a cytosine-phosphate-guanine (CpG). Histone post-translational modifications refer to the addition of biochemical modifications on histone tails, such as methylation, acetylation, phosphorylation, ubiquitylation and SUMOylation that regulate gene expression. Histone variants differ a few amino acids from canonical histones and regulate chromatin remodeling and histone post-translational modifications. Chromatin remodeling complexes regulate the nucleosome structure by removing, relocate and shifting histones.

Figure 4

DNA methylation within a gene promoter region. Unmethylated CpG islands enable gene transcription. When CpG island is methylated, gene transcription is repressed.

Figure 5

Circulating cell-free DNA methylation-based biomarkers described in the literature for cancer detection common to at least two cancer types [Breast Cancer (pink box), Lung Cancer (blue box), Prostate Cancer (yellow box), Colorectal Cancer (orange box)].