Universal methylated ctDNA markers for minimal residual disease detection and therapy response prediction in colorectal cancer

/Abstract Colorectal cancer (CRC) is the third and fourth leading cause of cancer mortality in U.S. men and women, respectively. Despite curative intent surgery being offered to most with stage I-III CRC, nearly half of all CRC cases will develop incurable metastatic disease. This underscores limitations to detect and clear minimal residual disease (MRD) with current approaches in the postoperative CRC setting. Metastatic or stage IV CRC is widely regarded as incurable where the standard of care remains palliative and indefinite systemic therapy in this setting. Despite serial carcinoembryonic antigen (CEA) testing and computed tomography scans serving as the consensus guidelines-recommended strategy for measuring systemic therapy response in stage IV CRC, there lacks a reliable biomarker for early tumor response assessments due to limited sensitivity and specificity of existing tumor markers that could prognosticate and guide systemic therapy sequencing or clinical trial participation on a more dynamic level in anticipation of interval radiographic assessments. Plasma circulating tumor DNA (ctDNA) has shown superior performance in detecting postoperative recurrences over the conventional tumor marker CEA in stage I-III CRC, while also having been shown to be prognostic of outcomes to systemic therapies, correlative with changes in tumor burden, and potentially predictive of early response to systemic therapies prior to radiographic assessments in stage IV CRC. Both tumor-informed and tumor-agnostic plasma ctDNA assays are undergoing development for MRD detection in CRC. Tumor-informed ctDNA assays, owing to their reliance on next-generation sequencing (NGS) of colorectal tumors to identify somatic mutations that are then detected as ctDNA in plasma, are widely regarded for their superior limits of ctDNA detection. The purpose of this study is to validate the performance of a novel tumor-agnostic ctDNA assay, comprised of a minimal panel of markers that are “universally” methylated in CRC, to detect postoperative recurrence and predict early treatment response in prospective cohorts of resected stage II-III CRC and stage IV CRC subjects, respectively. We will compare the performance of our plasma methylated ctDNA marker panel against CEA, which remains the standard of care blood-based biomarker in routine clinical use for CRC, and the commercial NGS-based ctDNA platform, SignateraTM, to detect postoperative recurrences in stage II-III CRC. This prospective validation against comparators in matched blood samples from the same patient cohort has never been performed with other plasma-based ctDNA assays in development. In stage IV CRC, we will evaluate our ctDNA assay's ability to predict for tumor response to conventional and novel systemic therapies compared to CEA. Establishing superiority to CEA and comparable performance to the Signatera NGS-based ctDNA assay represents a provocative opportunity to offer a rapid, cost-effective, and noninvasive test that is independent of tumor-to-plasma tailoring for MRD detection in stage II-III CRC. The potential of methylated ctDNA to predict early treatment response could also inform systemic therapy and surgical decision-making in stage IV CRC. Project Number: 1R37CA300232-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: JUN GONG | Institution: CEDARS-SINAI MEDICAL CENTER, LOS ANGELES, CA | Award Amount: $662,610 | Activity Code: R37 | Study Section: Molecular Cancer Diagnosis and Classification Study Section[MCDC] View on NIH RePORTER: https://reporter.nih.gov/project-details/11298504