Ultrasensitive eccDNA Detection for Tumor Diagnostics by Using CRISPR/Cas12a-Coupled Nested PCR

Extrachromosomal circular DNA (eccDNA) has emerged as a novel biomarker for cancer detection due to its tumor-specific amplification and stable structure in circulation. However, its clinical application is hindered by extremely low abundance in biofluids and the lack of robust detection techniques. To address this, we screened for tumor-associated eccDNA biomarkers and developed NPCC (Nested PCR-CRISPR/Cas12a), a novel method combining nested PCR for ultrasensitive amplification with CRISPR/Cas12a for sequence-specific detection. The assay employs two rounds of junction-specific PCR to enrich eccDNA, followed by CRISPR/Cas12a-mediated cleavage guided by target-specific crRNA. Validation using synthetic circular DNA standards demonstrated a limit of detection (LoD) of 10 –6 fM, representing a >100-fold improvement over conventional PCR, with no cross-reactivity to linear or genomic DNA fragments. In plasma samples from 88 cancer patients, NPCC successfully detected multiple tumor-specific eccDNAs, including the hepatocellular carcinoma marker eccDNA-HCC-1 (AUC = 0.8977). NPCC overcomes key technical barriers in liquid biopsy, offering a cost-effective, highly sensitive, and specific platform for noninvasive cancer diagnostics.