Characterization of extrachromosomal circular DNA associated with genomic repeat sequences in breast cancer

Extrachromosomal circular DNA (eccDNA) has emerged as a potential biomarker for disease due to its stable closed circular structure. However, the diagnostic utility of eccDNA remains underexplored. In this study, we demonstrate that the characteristics of eccDNA associated with genomic repetitive elements change in breast cancer patient tissues and plasma. These changes can serve as signatures for accurate cancer classification. We profiled eccDNA annotated to repeat elements across the genome in tissues and plasma, aggregating each repeat element to the superfamily and subfamily level. Our findings indicate that eccDNA associated with repetitive elements in cancer exhibits regular patterns of enrichment or depletion in specific elements, particularly at the family level. Additionally, these repeat element changes are present in different subtypes of breast cancer, correlated with varying hormone receptor expression. Although there are differences in the landscapes of eccDNA on repetitive elements between cancer tissues and paired plasma, the unique characteristics of eccDNA associated with repetitive sequences in the plasma of cancer patients facilitate better differentiation from normal individuals. These analyses reveal that changes in eccDNA associated with repeat sequences in human cancers can be used as diagnostic biomarkers for cancer patients.