Epigenetic alteration of circulating tumor DNA in the ethylenediaminetetraacetic acid (EDTA) plasma of breast cancer patients

This proof-of-concept study with the title “Epigenetic alteration of circulating tumor DNA in the ethylenediaminetetraacetic acid (EDTA) plasma of breast cancer patients” discussed whether hypermethylated gene sequences in the promoter regions of APC, ESR1, DKK3, HOXB4, MAL, RARß2, RASSF1A and SOX17 are detectable in the plasma of patients with breast cancer of different tumor stages and selected breast cancer cell lines. Another consideration was whether alcohol or nicotine consumption, ethnic origin and / or age had an impact on the methylation status of the promoter regions mentioned. For this purpose, plasma samples from a total of 40 blood donors and 28 breast cancer patients as well as three cell lines were analysed for potential DNA hypermethylation in a newly established, quantitative, methylation-specific one-step real-time PCR. The testing was carried out as a multiplex PCR using a methylation-dependent restriction endonuclease BstUI to establish an alternative and efficient method. The experimental setup and the protocol established for MAL, RARß2, RASSF1A and SOX17 showed satisfactory results in regards to the validation of the breast cancer cell lines MDA-MB-231, T47D and MCF7. In contrast, the investigation of APC, ESR1, DKK3 and HOXB4 showed a low signal-to-noise ratio between methylated and unmethylated control DNA. The cell line MDA-MB-231 exhibited a gene expression pattern with hypermethylation of the genes MAL, RASSF1A and SOX17. In the breast cancer cell line T47D a hypermethylation of the RASSF1A gene was detected, and the MCF7 analysis showed hypermethylation of all tested genes. These results suggest that due to the heterogeneity of the breast cancer types, an analysis using a gene panel is necessary. The method can also be used in histological analysis. The diagnostic test specificity of the promoter regions MAL, RARß2, RASSF1A and SOX17 was set at 95%. The sensitivity determined for the test genes was 0% for MAL, 3.6% for RARß2, 10.7% for RASSF1A and 3.6% for SOX17. Considering the low diagnostic sensitivities, no contribution could be made in the present study to develop a new PCR methylation detection for the ctDNA from EDTA plasma. Therefore, the four investigated promoter regions cannot be used as a screening method in this study, no biomarker could be established for early detection of breast cancer, in the prognosis assessment, in therapy stratification, the detection of the remission status or a presence of a relapse. The statistical analysis of the influence of alcohol and nicotine consumption, age and ethnicity also showed no significant correlation with promoter hypermethylation of the tested genes.2021-12-0