Isolation and Quantification of Methylated Cell-Free DNA in Plasma on an Integrated Microfluidic System

A Fully Integrated ICP-Enriched and Nanozyme-Catalyzed Lateral Flow Assay for cfDNA Detection in Whole Blood

Rapid and sensitive detection of Epstein-Barr virus cell-free DNA (EBV cfDNA) is crucial for early diagnosis and monitoring of nasopharyngeal carcinoma (NPC), but accessibility to screening is limited by complicated and costly conventional DNA isolation and purification approaches. Here, a fully integrated ion concentration polarization (ICP)-enriched and nanozyme-catalyzed lateral flow assay (ICP-cLFA) is developed, enabling total analysis of EBV cfDNA in whole blood samples, with DNA isolation, pre-concentration, and amplification performed on a microfluidic chip, consequently providing the signal readout within 75 min. Specifically, ICP preconcentration and amplification steps, together with target recognition catalyzed by a platinum-decorated mesoporous gold nanosphere (MGNS@Pt) nanozyme, result in an ultralow detection limit of 4 aM in standard cfDNA samples and 100 aM in whole blood from NPC-bearing rats. The high sensitivity and specificity of the ICP-cLFA suggest strong potential for cfDNA screening in resource-limited clinical and field applications.

An all-in-one strategy for bisulfite-free DNA methylation detection by temperature-programmed enzymatic reactions

The fragmentation and low concentration of cell-free DNA (cfDNA) pose higher challenges for the cfDNA methylation detection technologies. Conventional bisulfite conversion-based methods are inadequate for cfDNA methylation analysis due to cumbersome operation and exacerbating cfDNA degradation. Herein, we proposed temperature-programmed enzymatic reactions for cfDNA methylation analysis in a single tube. Endonuclease was used to mildly recognize DNA methylation to avoid the degradation of cfDNA. And two stages of amplification reactions significantly improved the detection sensitivity for GC-rich sequence. With vimentin as the target, the detection sensitivity was 10 copies of methylated DNA. Meanwhile, the proposed method can accurately quantify the methylation level of target sequence from 1000-fold of unmethylated DNA background. Further, the methylated vimentin gene in 20 clinical plasma samples was successfully detected. The results shown significant differences in methylation levels of the vimentin gene between healthy volunteers and colorectal cancer patients. These results lead us to believe that the proposed method has great application potential for DNA methylation analysis as a complement to bisulfite conversion-based methods.