Circulating cell-free DNA release in vitro: kinetics, size profiling, and cancer-related gene methylation

J Cell Physiol. 2019 Aug;234(8):14079-14089. doi: 10.1002/jcp.28097. Epub 2019 Jan 7.

Abstract

Circulating cell-free DNA (ccfDNA) is a biological entity of great interest due to its potential as liquid biopsy biomaterial carrying clinically valuable information. To better understand its nature, we studied ccfDNA in vitro in two human cancer cell lines MCF-7 and HeLa. Normalized indexes of ccfDNA per cell population decreased over time of culture but were significantly elevated after exposure to IC50 doses of the demethylating/apoptotic agent 5-azacytidine (5-AZA-CR). Fragment-size profiling was indicative of active release, whereas exposure to 5-AZA-CR induced the release of additional shorter fragments, indicative of apoptosis. Finally, the methylation profile of a panel of cancer-specific genes as assessed by quantitative methylation analysis in ccfDNA was identical to the corresponding genomic DNA and followed accurately changes caused by 5-AZA-CR. Overall, our in vitro findings support that ccfDNA can be a reliable biosource of clinically relevant information that can be further studied in these cell culture models.

Keywords: cancer; cell line; cell-free DNA; liquid biopsy; methylation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Azacitidine / pharmacology*
  • Biomarkers, Tumor / genetics
  • Cell-Free Nucleic Acids / drug effects
  • Cell-Free Nucleic Acids / genetics*
  • DNA Methylation / genetics*
  • HeLa Cells
  • Humans
  • Kinetics
  • MCF-7 Cells
  • Neoplasms / genetics*
  • Neoplasms / pathology

Substances

  • Biomarkers, Tumor
  • Cell-Free Nucleic Acids
  • Azacitidine