CaSH (Cancer-specific hypermethylated) Regions: quantifying ctDNA for non-invasive screening and monitoring of colon cancer

Abstract

Colon cancer is the second leading cause of cancer-related mortality globally. Recently, liquid biopsy utilizing the methylation profiles of circulating tumor DNA (ctDNA) in blood plasma has emerged as a promising approach for diagnosing and monitoring colon cancer. I propose a liquid biopsy-based method to identify regions for quantifying colon cancer tissue-derived ctDNA by considering adjacent colon cancer-specific hypermethylated CpGs. Using this approach, I identified 901 colon cancer- specific hypermethylated (CaSH) regions in tissues from 49 cancer patients and 260 healthy controls for colon cancer screening and monitoring. These CaSH regions were subsequently used to precisely quantify the amount of circulating tumor DNA (ctDNA) in blood samples from the same patients by cell-free DNA methylation profiles. Remarkably, the ctDNA methylation profiles in blood demonstrated high sensitivity (82%) and specificity (93%) in distinguishing colon cancer patients from the healthy control group, with an area under the curve (AUC) of 0.903. Additionally, I validated that this method for ctDNA quantification is effective for monitoring cancer patients and can serve as valuable tools for postoperative prognosis. This study successfully applied ctDNA quantification within cfDNA, utilizing colon cancer tissue-derived CaSH regions, for screening and monitoring colon cancer.