A DNA Methylation-Based Test for Breast Cancer Detection in Circulating Cell-Free DNA

Abstract

Background: Breast cancer (BrC) is the most frequent neoplasm in women. New biomarkers, including aberrant DNA methylation, may improve BrC management. Herein, we evaluated the detection and prognostic performance of seven genes’ promoter methylation (APC, BRCA1, CCND2, FOXA1, PSAT1, RASSF1A and SCGB3A1). Methods: Methylation levels were assessed in primary BrC tissues by quantitative methylation-specific polymerase chain reaction (QMSP) and in circulating cell-free DNA (ccfDNA) by multiplex QMSP from two independent cohorts of patients (Cohort #1, n = 137; and Cohort #2, n = 44). Receiver operating characteristic (ROC) curves were constructed, and log-rank test and Cox regression were performed to assess the prognostic value of genes’ methylation levels. Results: The gene-panel APC, FOXA1, RASSF1A, SCGB3A1 discriminated normal from cancerous tissue with high accuracy (95.55%). In multivariable analysis, high PSAT1-methylation levels [>percentile 75 (P75)] associated with longer disease-free survival, whereas higher FOXA1-methylation levels (>P75) associated with shorter disease-specific survival. The best performing panel in ccfDNA (APC, FOXA1 and RASSF1A) disclosed a sensitivity, specificity and accuracy over 70%. Conclusions: This approach enables BrC accurate diagnosis and prognostic stratification in tissue samples, and allows for early detection in liquid biopsies, thus suggesting a putative value for patient management.

Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives

“…Further, for the management of pancreatic cancer and its early detection Eissa et al analyzed the methylation of ADAMTS1 and BNC1 in cfDNA using qMSP, which exhibited a sensitivity of 94.8% and specificity of 91.6% with a AUC of 0.95 reflecting diagnostic potential of this blood based two-gene panel in detection of pancreatic cancer at an early stage (Eissa et al, 2019). Methylation of APC, FOXA1, and RASSF1A in cell free DNA served as a best performing cassette in terms of diagnostic and prognostic value, revealing a sensitivity, specificity and accuracy over 70% suggesting its putative utility in management of breast cancer (Salta et al, 2018).…”

DNA Methylation in Human Breast Cancer Cell Lines Adapted to High Nitric Oxide

“…In order to make the role of NO clear epigenetically, we detected the level of methylation of a panel of five tumorsuppressor genes in the same model system of breast cancer cell lines in the current study. The tumor-suppressor genes BRCA1, DCC, RASSF1A, MGMT and SFRP1 were chosen since they have been shown to be subjected to epigenetic silencing by promoter hypermethylation in primary breast cancer (25)(26)(27)(28)(29)(30). We used Illumina MiSequncing to quantify methylation of these genes in parental and HNO-adapted breast cancer cell lines and observed diverse results in response to NO treatment.…”

“…The tumor-suppressor genes we studied (BRCA1, DCC, RASSF1A, MGMT and SFRP1) have been shown to be epigenetically silenced to various extents by promoter DNA hypermethylation in breast cancer (25)(26)(27)(28)(29)(30).…”

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

“…Nevertheless, a panel including DAPK1 me and RASSF1A me showed the highest sensitivity, i.e., 96% for BrC detection using methylation-specific PCR (MSP) [81]. Other studies attempted to assemble panels for BrC detection using quantitative methylation-specific PCR (qMSP), a quantitative method, achieving sensitivities above 80% [78,82]. Furthermore, several panels reached 100% specificity for BrC detection [83][84][85].…”