Extrachromosomal DNA and cell-free DNA in breast cancer liquid biopsy: current evidence and future perspectives

Extrachromosomal DNA (ecDNA) has emerged as a pivotal factor in the amplification of oncogenes, the heterogeneity of tumors, and the development of therapeutic resistance in breast cancer (BC). EcDNA comprises large, acentric, circular DNA molecules that replicate independently and segregate in a non-Mendelian fashion, setting them apart from chromosomal DNA and the smaller extrachromosomal circular DNA (eccDNA) observed in normal cells. The ability to detect ecDNA in plasma has generated interest in its potential role as a biomarker for liquid biopsy in BC. This review synthesizes current evidence concerning plasma ecDNA in BC, while also integrating relevant studies on circulating free DNA (cfDNA) and circulating tumor DNA (ctDNA) as contextual background. However, direct evidence supporting the clinical applicability of plasma ecDNA in BC remains limited and predominantly exploratory. The majority of diagnostic and prognostic research within this domain has focused on assessing cell-free DNA (cfDNA) methylation, cfDNA integrity, chromosomal instability scores, circulating tumor DNA (ctDNA) mutations, and ctDNA-based minimal residual disease (MRD). Recent evidence indicates that extrachromosomal DNA (ecDNA) may offer supplementary insights into oncogene amplification, structural heterogeneity, and treatment resistance. There is an urgent need for the standardization of pre-analytical procedures, extraction methodologies, quantification strategies, structural validation, and the implementation of multicenter prospective studies.