Extracellular Vesicle-Derived DNA vs. CfDNA as a Biomarker for the Detection of Colon Cancer

Abstract

Liquid biopsy has emerged as a promising non-invasive way to diagnose tumor and monitor its progression. Different types of liquid biopsies have different advantages and limitations. In the present research, we compared the use of two types of liquid biopsy, extracellular vesicle-derived DNA (EV-DNA) and cell-free DNA (cfDNA) for identifying tumor mutations in patients with colon carcinoma. Method: DNA was extracted from the tumor tissue of 33 patients diagnosed with colon carcinoma. Targeted NGS panel, based on the hotspots panel, was used to identify tumor mutations. Pre-surgery serum and plasma were taken from the patients in which mutation was found in the tumor tissue. Extracellular vesicles were isolated from the serum followed by the extraction of EV-DNA. CfDNA was extracted from the plasma. The mutations found in the tumor were used to detect the circulating tumor DNA using ultra-deep sequencing. We compared the sensitivity of mutation detection and allele frequency obtained in EV-DNA and cfDNA. Results: The sensitivity of mutation detection in EV-DNA and cfDNA was 61.90% and 66.67%, respectively. We obtained almost identical sensitivity of mutation detection in EV-DNA and cfDNA in each of the four stages of colon carcinoma. The total DNA concentration and number mutant copies were higher in cfDNA vs. EV-DNA (p value = 0.002 and 0.003, respectively). Conclusion: Both cfDNA and EV-DNA can serve as tumor biomarkers. The use of EV-DNA did not lead to improved sensitivity or better detection of tumor DNA in the circulation.

Isolation and Characterization of Extracellular Vesicles in Human Bowel Lavage Fluid

“…In contrast to our results, Bryzgunova and collaborators demonstrated that EVs of urine samples from patients with prostate cancer presented higher DNA concentrations than healthy samples [ 36 ], although these variances could be attributed to the different type of sample and cancer from which EVs were isolated. Despite this, DNA from EVs can be studied [ 31 ], and our results indicate a sufficient concentration of DNA for use, as shown in studies by Thakur and collaborators, who found that DNA concentration in serum EVs was 10.59 ± 13.19 ng/mL [ 37 ], or in studies by Choi et al, who determined that the amount of DNA in plasma EVs ranged from 0.1 to 2.48 ng [ 38 ]. Finally, protein expression levels can be directly determined in BLF samples, as shown in studies by Kayazawa and collaborators, in which lactoferrin, polymorphonuclear neutrophil elastase, myeloperoxidase, and lysozyme concentrations were determined in BLF samples by ELISA [ 39 ].…”

Extracellular Vesicles in Liquid Biopsies as Biomarkers for Solid Tumors

“…In turn, Thakur et al reported similar detection rates when using either circulating EV-DNA or cfDNA for the identification of several mutations in CRC patients [109]. In the future, however, a combination of both EV-derived nucleic acids and cfDNA might represent the most efficient procedure for non-invasive cancer-associated mutation screenings [110,111]. This approach was also applied for the development of a clinical test developed by Exosomes Diagnostics (ExoDx Lung(EGFR T790M)), which efficiently identified different EGFR mutations (L858R, T790M, and exon 19 indels) in plasma sEVs from a large cohort of non-small cell lung carcinoma (NSCLC) patients [112].…”

Extracellular Vesicle DNA Extraction and Sequencing in Ancient Serum Samples From Patients With Breast Cancer

“…The most widely used tools are circulating tumor cells (CTC) and cell-free DNA (cfDNA) (1)(2)(3). Extracellular vesicle (EV) DNA (EV-DNA) has recently emerged as informative cancer biomarker (4)(5)(6)(7)(8). EVs constitute a diverse and heterogeneous category of vesicles released by every cell type.…”