Enhancing the cancer metastasis diagnosis: Ultrasensitive nano sensors exploiting Cancer stem cell associated DNA methylation as a liquid biopsy marker

Cancer metastasis presents a significant clinical challenge due to its impact on patient survival rates. Early detection of metastasis is pivotal for effective intervention and improved patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, holds promise for cancer detection, yet its utility in metastasis detection remains underexplored. Stable and accurate, DNA methylation reflects early tumor stages and enables molecular characterization, providing valuable longitudinal information. Despite its potential, clinical translation of DNA methylation biomarkers is limited, partially due to technology constraints and tumor heterogeneity. To enable clinical translation, an assay is needed that 1) quantifies DNA methylation, 2) integrates seamlessly into clinical workflows, and 3) ensures accuracy and sensitivity. In this study, we introduce an ultrasensitive nanosensor, Methylprobe, for DNA methylation-based liquid biopsy of metastasis. Methylprobe, synthesized via ultrashort pulsed ionization, provides signal amplification, enabling direct detection of methylated DNA in plasma. The technology is scalable and adaptable for clinical settings. The assay comprises the Methylprobe, metastasis-specific biomarkers, and a machine-learning algorithm. Tumor heterogeneity is addressed by integrating DNA-methylation signatures from distinct cancer stem cell phenotypes, enhancing assay reliability. The Methylprobe assay is validated on breast, lung, and colorectal cancer samples, demonstrating 99.8% accuracy in metastasis detection. This innovative approach offers potential as a reliable, sensitive, and accurate platform for assessing metastasis-associated DNA methylation patterns in blood plasma. Integrating Methylprobe into clinical practice could revolutionize metastasis detection, providing comprehensive insights into metastatic phenotypes and informing tailored therapeutic strategies.