Deciphering the role of cell-free extrachromosomal circular DNA in human heart failure

Extrachromosomal circular DNAs (eccDNAs) are well-established drivers of tumorigenesis, yet their landscape and functional significance in human heart failure (HF) remain largely unknown. Using Tn5 transposase-based sequencing, we comprehensively profiled plasma eccDNAs from healthy controls and HF patients with myocardial ischemia (MI-HF) or non-myocardial ischemia (NMI-HF). Bioinformatics was employed to probe their chromosomal origins, genomic features, and potential roles in the development of HF. Circular structures of candidate eccDNAs were validated by inward and outward PCR followed by Sanger sequencing. Their clinical prognostic value was assessed by Kaplan–Meier and Cox regression analyses in a patient cohort. Most plasma eccDNAs were shorter than 1 kb and originated from all chromosomes, with selective enrichment from specific genomic regions including 5′ UTRs, CpG islands, and Alu elements. Characteristic nucleotide repeats were identified at eccDNA junction sites. The circular structure of eccDNAs was confirmed. Furthermore, we discovered that the eccDNA ENPP1 circle exon 25 was specifically detected in MI-HF patients. Its presence was significantly associated with a higher incidence of major adverse cardiac events (MACEs), and it served as an independent prognostic biomarker in multivariate analysis. This study delineates the first detailed landscape of plasma eccDNAs in HF and reveals their potential as noninvasive biomarkers for risk stratification. Our findings lay a crucial foundation for future research into eccDNA biology and their translational applications in cardiovascular disease.