Fei Xiao from the Beijing Hospital in China presented at London Calling 2023 a session entitled “Small extrachromosomal circular DNAs as biomarkers for potential pan-cancer diagnosis and prognosis.” They defined extrachromosomal DNA (eccDNA) as “circular DNA molecule that is independent of conventional chromosomes and exists widely in eukaryotes” and can vary in length, though most are smaller than 10 kb. The role of eccDNA in cancer is still unclear, and short-read sequencing has been mostly used to study eccDNA. Xiao used Oxford Nanopore Technologies to profile eccDNA using a customized extraction, purification, and sequencing system. The system generates loop DNA for sequencing. Tumor tissues had more eccDNA than tissues from healthy people. The studies allowed exploration of the biogenesis mechanism of small eccDNA. The characteristics of small eccDNA were studies. Genomic annotation of small eccDNA allowed for comparison of characteristics of eccDNA in cancer patients. Targets are being validated. These advances con help refine a biomarker and diagnostic system with eccDNA. Small eccDNA associated with cancers were identified. Small eccDNA with retrotransposon sequences can move across the nuclear membrane, and Xiao noted that small eccDNA may fuse together to form megabase-sized elements. I had not heard about this! I learned about eccDNA and will now remember that these plasmid-like elements may serve a role in cancer diagnosis.
