Abstract 4574: Epigenetic comparison of colorectal cancer tumors and patient-matched cfDNA
Authors: Seeta Rajpara, Chris Gooden, Dan Weisenberger, Raed Jaffal, Hanna Jaynes, Carmen Chavez, Mariana Stern, Heinz-Josef Lenz, David Craig, John Carpten, Bodour Salhia
Journal: Cancer Research (2025)

Abstract Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the U.S., with Hispanic/LatinX (HL) populations facing disproportionately higher mortality rates. Despite advancements in CRC screening and treatment, racial disparities in outcomes persist, partly due to limited access to early and precise detection tools. This study addresses these inequities by developing an innovative cfDNA methylation-based liquid biopsy for detecting minimal residual disease (MRD), a critical predictor of cancer recurrence that could improve outcomes in underrepresented populations. In this study, we performed methylation profiling using the EPIC v2 array on tumor tissue samples and cfDNA whole-genome bisulfite sequencing (WGBS) on 27 (16 females, 11 males; mean age 51.7 years) patient-matched blood plasma samples collected after tumor resection. Clinical data was abstracted to annotate each sample with tumor characteristics and the patient’s disease status. Disease status was determined as either no evidence of disease (NED) for over 2 years or active disease (AD). Next, to identify markers potentially associated with recurrence, we performed differential DNA methylation analysis between patients with AD (N = 14) and who have been NED (N = 13) for greater than 2 years and examined the overlap of differentially methylated regions (DMRs) between tissue and cfDNA. These markers would essentially represent tumor burden in patients with AD. We identified 175 DMRs in tissue, (88% hypermethylated and 12% hypomethylated) and 350 DMRs in cfDNA (94% hypermethylated and 6% hypomethylated) between patients with AD versus NED status. Tissue DMRs were significantly more promoter-enriched (78.3% tumor vs. 55.1% cfDNA, p=1.87x10-7) and had fewer gene body DMRs compared to cfDNA DMRs (10.9% tumor vs. 27.4% cfDNA, p=1.03x10-5). Enhancer regions were notably more frequent in tissue than cfDNA (10.9% tumor vs. 0% cfDNA, p=4.34 x10-10), while intergenic regions were more enriched in cfDNA than tumors (17.4% tumor vs. 5.1% cfDNA, p=5.94x10-5). Unsupervised clustering of showed clear separation of samples by disease status in both cfDNA and tissue samples. Furthermore, correlation analysis of beta values between matched tumors and cfDNA showed stronger correlations for AD samples (R2=0.68) compared to NED (R2=0.61), suggesting that tumor burden of AD samples are detectable in circulation to a higher degree and can have utility in biomarker development. The distinct methylation patterns observed between CRC tissue and cfDNA highlight the potential of liquid biopsies to capture tumor burden in circulation, particularly in active disease cases. Citation Format: Seeta Rajpara, Chris Gooden, Dan Weisenberger, Raed Jaffal, Hanna Jaynes, Carmen Chavez, Mariana Stern, Heinz-Josef Lenz, David Craig, John Carpten, Bodour Salhia. Epigenetic comparison of colorectal cancer tumors and patient-matched cfDNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4574.