Correlation Between Tumor-Specific Mutated and Methylated DNA in Colorectal Cancer.

Abstract

Analysis of circulating tumor DNA (ctDNA) is a potential improvement in precision medicine. In colorectal cancer (CRC), somatic mutations such as <i>RAS</i> and <i>RAF</i> in the blood (mut-ctDNA) are investigated for prognostic and predictive purposes. However, they are only present in approximately 60% of patients. Recently, ctDNA has been detected in patients with <i>RAS</i>/<i>RAF</i> wild type (WT) by methylated ctDNA (meth-ctDNA). The aim of this study was to compare mutated DNA with methylated DNA in malignant and nonmalignant tissue and plasma from CRC cohorts to establish a universal biomarker for ctDNA in all patients with CRC. Tissue (n = 170) and plasma (n = 147) samples were analyzed for <i>RAS</i>/<i>RAF</i> mutations and neuropeptide Y methylation by droplet digital polymerase chain reaction. Tissue originated from nonmalignant WT and <i>RAS</i>/<i>RAF</i>-mutated adenomas, tumor-adjacent colorectal tissue, and WT and <i>RAS</i>/<i>RAF</i>-mutated tumor tissue. Plasma samples represented healthy donors and localized and metastatic CRCs. The level of neuropeptide Y-methylated DNA in the tissue cohorts differed between nonmalignant and malignant/premalignant tissues with minimal overlap. Furthermore, meth-ctDNA was detected in plasma from 100% of patients with metastatic disease, compared with 67% of those with localized disease and 8% of healthy donors. Median fraction of meth-ctDNA in metastatic and localized cancers was 13.25% and 0.04%, respectively. Correlation between mut-ctDNA and meth-ctDNA was high (<i>r</i> = 0.77 and 0.80 in localized and metastatic settings, respectively). Mut-ctDNA is interchangeable with meth-ctDNA in patients with CRC. On the basis of our results, meth-ctDNA should be considered a universal biomarker in metastatic CRC, but additional investigations of clinical utility are warranted.