Cell-free DNA in hepatocellular carcinoma: Biology to treatment response

Abstract

Hepatocellular carcinoma (HCC) is frequently diagnosed without tissue confirmation, and single-site biopsies often fail to capture intratumor heterogeneity, underscoring the need for liquid biopsy approaches. Circulating cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) provide access to genetic, epigenetic, copy-number, and fragmentomic biomarkers that can support diagnosis, prognostication, and treatment monitoring. Current monitoring modalities, such as alpha-fetoprotein and radiographic assessment, lack sensitivity and typically lag behind molecular changes, whereas cfDNA/ctDNA-based analyses offer the potential for earlier and more accurate prediction of treatment response and disease dynamics. Literature review (PubMed, Google Scholar, 2015-2025) evaluated cfDNA biomarkers for predicting and monitoring treatment response across immune checkpoint inhibitors, tyrosine kinase inhibitors, transarterial chemoembolization, and radiotherapy in HCC. ctDNA profiling detects recurrent mutations in TERT, TP53, CTNNB1, and phosphatidylinositol 3-kinase/mammalian target of rapamycin pathways with variable prognostic associations across therapies. Limited evidence suggests phosphatidylinositol 3-kinase/mammalian target of rapamycin alterations may predict tyrosine kinase inhibitor resistance. Serial ctDNA monitoring shows promise for early response assessment, with variant allele frequency changes correlating with outcomes in small cohorts, though superiority to alpha-fetoprotein remains inconsistently demonstrated. Baseline cfDNA burden associates with survival across multiple treatment modalities. Copy-number variation dynamics correlate with transarterial chemoembolization response. Postoperative ctDNA detection enables recurrence risk stratification. Fragmentomic and methylation signatures demonstrate high diagnostic accuracy but lack treatment-response validation. cfDNA shows potential for treatment monitoring in HCC but faces critical limitations: Low analytical sensitivity, platform heterogeneity, absence of validated thresholds, and limited prospective evidence. Standardized multicenter trials demonstrating clinical utility are essential before routine implementation.

Keywords: Cell-free DNA; Circulating tumor DNA; Hepatocellular carcinoma; Liquid biopsy; Methylation; Fragmentomics; Copy number variation; Chromosomal instability; Minimal residual disease; Treatment response

Core Tip: The study evaluated circulating tumor DNA as a potential indicator of treatment response in hepatocellular carcinoma. Quantitative aspects of cell-free DNA, such as concentration and variant allele frequency, were analyzed in conjunction with qualitative genomic and epigenetic features, including copy-number variation and methylation-associated changes, to assess tumor dynamics during therapy. The findings indicate that cell-free DNA profiling captures both quantitative changes and molecular alterations, including genomic and epigenetic variation, that may reflect treatment-related tumor dynamics in hepatocellular carcinoma.