Multi-Biofluid Approaches for cftDNA and cftRNA Biomarker Detection: Advances in Early Cancer Detection and Monitoring

Cell-free tumor DNA (cftDNA) and cell-free tumor RNA (cftRNA) are emerging as powerful biomarkers for cancer detection, monitoring, and prognosis. These nucleic acids, released into the bloodstream by tumor cells, carry cancer-specific genetic and epigenetic alterations and can be detected non-invasively. Detection before clinical diagnosis offers a unique opportunity for earlier intervention yet requires longitudinal cohort studies to establish pre-diagnostic biomarker profiles. Current technologies enable sensitive quantification of cftDNA and cftRNA, with spike-in controls allowing for absolute quantification of single nucleosome-bound cftDNA, addressing a key limitation in liquid biopsy assays. Advances, such as DNA-PAINT, now permit single-molecule resolution detection of point mutations and methylation patterns characteristic of cancer, while new proteomics methods can identify the tissue of origin of exosome-derived nucleic acid. This review discusses the state-of-the-art detection strategies for cftDNA and cftRNA, highlights the gaps in longitudinal sampling, and outlines future research directions toward integrating multiomic liquid biopsy approaches for improved early diagnosis, monitoring, and relapse detection.