Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies

Abstract

Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term “liquid biopsy” (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from “bench to bedside”.

Interrogating Epigenome toward Personalized Approach in Cutaneous Melanoma

“…These genes appear to be involved in various signaling pathways, usually disrupted in CM, such as the phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) and MAPK pathways, cell cycle, DNA repair, retinoblastoma (RB) and Wnt signaling [ 86 ]. Furthermore, it was also observed that three TSGs are frequently inactivated by methylation: RASSF1A (55%), RAR-β2 (70%), and MGMT (34%) can also be identified in the circulating tumor DNA of CM patients, which makes them useful diagnostic and prognostic biomarkers in the clinical setting [ 88 , 89 ]. In several cancers, but also in a significant proportion of melanomas, a gradual increase in DNA hypermethylation was observed along with tumor aggressiveness; this phenomenon, called CpG methylator phenotype (CIMP), was reported for the first time in colorectal cancers, a finding that highlighted a tight correlation between altered DNA methylation patterns and the clinical outcome of the affected patients.…”

“…Given the critical roles of epigenetic alterations in CM development and its drug resistance, targeting or co-targeting these epigenetic events appears to be a promising strategy for improving the clinical condition of CM patients [ 109 ]. Although epigenetic biomarkers have not yet found their place in clinical practice, an impressive number of epigenetic drugs are constantly being developed and tested for their cytotoxicity and efficacy in clinical trials in various human cancers, including CM [ 89 , 202 ]. These epigenetic drugs include both general epigenetic inhibitors such as HDACi or DNMTi, but also more specific inhibitors targeting enhancer of zeste homolog 2 (EZH2i), bromodomain and extra-terminal domain proteins (BETi), or JMJD3 and JARID1B demethylases [ 203 ].…”

Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy

“…Liquid biopsy evaluation of epigenetic biomarkers is an emerging field in oncology that might have a putative impact in improving diagnostic and screening procedures [ 196 ]. Several benefits may address the use of DNA methylation as a biomarker, such as its high stability in several biofluids and its dynamism during disease evolution.…”

DNA Methylation Analysis in Plasma Cell-Free DNA and Paired CTCs of NSCLC Patients before and after Osimertinib Treatment

“…Liquid biopsy has drawn major attention in the last few years as a highly useful tool for the management of cancer patients and has already shown its clinical impact on the early detection, minimal residual disease and tracking of treatment resistance [ 17 , 18 ]. The identification of circulating epigenetic biomarkers through DNA methylation studies is of utmost clinical importance in the liquid biopsy field and can be used for the diagnosis, prognosis, and prediction of drug response [ 19 , 20 ]. Notwithstanding that mutation analysis in liquid biopsy is already established through its clinical utility, it cannot always provide consistent results due to tumoral heterogeneity.…”

“…Wnt inhibitory factor-1 ( WIF-1 ) has been identified as an important Wnt antagonist which inhibits Wnt/β- catenin signaling by directly binding to Wnt proteins. Methylation of the WIF-1 gene can lead to the loss of WIF-1 expression which has been observed in numerous types of cancer including NSCLC [ 16 , 17 , 18 , 19 , 20 ]. Another important Wnt antagonist with tumor suppressor activity is the APC gene that is involved in cell migration and adhesion, transcriptional activation, and apoptosis; APC promoter methylation has a diagnostic role in NSCLC [ 36 , 37 ].…”