Cell-Free DNA Versus Circulating Tumor Cells: A Pilot Study of Alpha-Fetoprotein Analysis for Diagnosis and Treatment Monitoring in Hepatocellular Carcinoma

Serum alpha-fetoprotein (AFP) is widely used for hepatocellular carcinoma (HCC) management, yet its limited sensitivity and specificity restrict diagnostic and prognostic utility. In this study, we explore the clinical potential of AFP quantification from cell-free DNA (cfDNA) and circulating tumor cells (CTCs) using a novel bead-based liquid biopsy platform. Following isolation, AFP abundance in cfDNA was quantified by qPCR, while AFP protein expression in CTCs was assessed via immunohistochemistry. Compared to serum AFP, cfDNA-derived AFP demonstrated significantly greater diagnostic accuracy in distinguishing HCC patients from non-cancerous individuals (<i>p</i> < 0.0001, AUC = 0.998), while AFP⁺ CTCs showed high specificity. Post-treatment changes in AFP levels from cfDNA and CTCs were significantly associated with therapeutic response and overall survival, outperforming conventional serum AFP. Longitudinal monitoring further revealed that cfDNA AFP levels reliably captured recurrence events prior to clinical diagnosis. Moreover, a combined metric integrating AFP levels from cfDNA and CTCs significantly improved response stratification (AUC = 0.89), outperforming individual biomarkers. This pilot study highlights the potential of multimodal AFP profiling through cfDNA and CTCs as a promising, non-invasive approach for enhancing diagnosis, prognosis, and treatment monitoring in HCC, with direct implications for personalized therapeutic strategies.