Early detection of the major male cancer types in blood-based liquid biopsies using a DNA methylation panel

Background Lung (LC), prostate (PCa) and colorectal (CRC) cancers are the most incident in males worldwide. Despite recent advances, optimal population-based cancer screening methods remain an unmet need. Due to its early onset, cancer specificity and accessibility in body fluids, aberrant DNA promoter methylation might be a valuable minimally invasive tool for early cancer detection. Herein, we aimed to develop a minimally invasive methylation-based test for simultaneous early detection of LC, PCa and CRC in males, using liquid biopsies. Results Circulating cell-free DNA was extracted from 102 LC, 121 PCa and 100 CRC patients and 136 asymptomatic donors' plasma samples. Sodium-bisulfite modification and whole-genome amplification was performed. Promoter methylation levels of APC(me), FOXA1(me), GSTP1(me), HOXD3(me), RAR beta 2(me), RASSF1A(me), SEPT9(me) and SOX17(me) were assessed by multiplex quantitative methylation-specific PCR. SEPT9(me) and SOX17(me) were the only biomarkers shared by all three cancer types, although they detected CRC with limited sensitivity. A PanCancer panel (FOXA1(me), RAR beta 2(me) and RASSF1A(me)) detected LC and PCa with 64% sensitivity and 70% specificity, complemented with CancerType panel (GSTP1(me) and SOX17(me)) which discriminated between LC and PCa with 93% specificity, but with modest sensitivity. Moreover, a HOXD3(me) and RASSF1A(me) panel discriminated small cell lung carcinoma from non-small cell lung carcinoma with 75% sensitivity, 88% specificity, 6.5 LR+ and 0.28 LR-. An APC(me) and RASSF1A(me) panel independently predicted disease-specific mortality in LC patients. Conclusions We concluded that a DNA methylation-based test in liquid biopsies might enable minimally invasive screening of LC and PCa, improving patient compliance and reducing healthcare costs. Moreover, it might assist in LC subtyping and prognostication.