A highly sensitive linear amplification based DNA methylation profiling technique for clinical cancer research

The goal of this investigation is to validate the T7-Linear Amplification based Bisulfite Sequencing (LABS-seq), a highly sensitive whole-genome amplification-based bisulfite sequencing technology developed by our team, to profile 5-methylcytosines (5mC) in tissues/tumor cells and circulating cell-free DNA (cfDNA), and implement this technique in clinical applications (e.g., biomarker discovery). At present, biopsies and imaging are the standard for cancer diagnosis and prognosis, which are either invasive, associated with radiation exposure, or prone to sampling bias due to intra-tumoral and spatial heterogeneity, i.e., mutations or molecular alterations represented only in the single biopsied loci. Liquid biopsy-based approaches, however, have been limited by the availability of enabling technologies that can robustly detect molecular targets (e.g., epigenetic modifications) in clinically convenient biospecimens (e.g., cfDNA from a few mL of plasma). In this proposal, taking advantage of our on-going sample collection programs at the University of Chicago Medical Center and NIH-funded projects, we will validate the LABS-seq technique in banked tumor tissues/cells from a diverse list of common solid tumors and hematological malignancies, and cfDNA to provide a transformative epigenomic approach for cancer research and clinical applications. Specifically, we will 1) validate the LABS-seq technique for advancing cancer type-specific epigenetic biomarkers using tissue samples (Aim 1); and 2) validate the LABS-seq technique for biomarker detection using liquid biopsy (Aim 2). This proposed project will not only provide a transformative approach for precise, specific, and sensitive 5hmC profiling at base resolution, but also open up opportunities for future development of more convenient, minimally-invasive tools for management, treatment selection, and monitoring disease burden in oncology.