Methylation-based ctDNA monitoring in metastatic breast cancer during CDK4/6 inhibitor therapy

Circulating tumor DNA (ctDNA) enables minimally invasive treatment monitoring, yet the clinical validity of longitudinal ctDNA surveillance in metastatic breast cancer remains incompletely defined. Here we show that methylation-based tumor fraction (mTF), a tissue-agnostic epigenomic measure of ctDNA, closely mirrors radiographic response and clinical outcomes in 57 patients with estrogen receptor-positive, HER2-negative metastatic breast cancer receiving endocrine therapy with a CDK4/6 inhibitor across 350 serial plasma timepoints. Baseline ctDNA is detectable in 94.7% of patients. Clearance of mTF on treatment is associated with prolonged time to treatment discontinuation (HR = 0.17, 95% CI: 0.07-0.41; p < 0.0001). A rise in mTF (molecular progression) precedes treatment discontinuation by a median of 5.8 months and outperforms mutation-based tracking, with resistance-associated alterations in ESR1 and RB1 frequently emerging at molecular progression. These findings support prospective evaluation of mTF-guided treatment strategies.