Abstract 1958: Chromatin accessibility landscapes of colorectal cancer development and genome-wide cell-free DNA fragmentation
Authors: Nicholas A. Vulpescu, Zachariah H. Foda, Pieter H. Wisse, Christopher Cherry, Jamie E. Medina, Stephen B. Baylin, Kasper D. Hansen, Vilmos Adleff, Remond J. Fijneman, Michael A. Beer, Robert B. Scharpf, Gerrit A. Meijer, Beatriz Carvalho, Victor E. Velculescu
Journal: Cancer Research (2025)

Abstract Introduction: The stepwise progression of colorectal cancer (CRC) from healthy epithelium, to premalignant adenoma, to cancer is accompanied by genome-wide epigenetic reprogramming which may be reflected in circulating cell-free DNA (cfDNA). However, current analyses of these processes have been hampered by the complex mixture of cells associated with colonic epithelial tissue, as well as the absence of suitable adenoma model systems. Cultured colorectal organoids, comprised of pure epithelial cells, could enable insights into the epigenetic changes leading to progression from healthy tissue to cancer. Such features could be instrumental in early cancer detection using genome-wide analyses of cfDNA fragmentation. Methods: Using 43 patient-derived colorectal organoids derived from healthy, adenoma, and cancer tissues, as well as 10 freshly collected peripheral blood mononuclear cell (PBMC) control samples, we examined the chromatin landscape of tumor development using transposase accessible chromatin analyses with next-generation sequencing. We analyzed enrichment for gapped-kmer abundance to reveal gene regulatory networks underlying differences between tissue types. We defined a consensus set of nucleosome depleted regions (NDRs) for each disease state and identified loci with differential accessibility between PBMCs, colon healthy, adenoma, and cancer tissues. We analyzed these differential loci for fragmentation characteristics in the circulating cfDNA of 250 healthy individuals and 51 patients with metastatic CRC. Results: Across all organoid samples, we identified a consensus set of 62, 890 NDRs. Associating these regions with nearby genes, we identified unique CRC-related signatures comprising genes of known and novel pathways, including those involved in WNT, hippo, and RAS signaling. Additionally, we discovered a gene regulatory network which drives chromatin accessibility differences between the healthy, adenoma, and carcinoma tissue in colon. While most chromatin accessibility differences were shared between adenomas and cancers, we identified 895 chromatin changes which were unique to adenoma. In healthy individuals, we found that cfDNA coverage was negatively correlated with accessibility at white blood cell NDRs (Spearman ρ= -0.56), while in individuals with cancer, changes in NDRs were associated with independent circulating tumor DNA abundance by droplet digital PCR (R2=0.69, p&amp;lt;0.001). Consequently, genome-wide cfDNA fragmentation features could be used to distinguish healthy individuals from those with CRC (AUC=0.94). Conclusions: These analyses reveal chromatin accessibility landscapes that were unique to different pathologic stages of CRC development, highlighting important genes and networks regulated by chromatin remodeling and providing an avenue for evaluating these through genome-wide analyses of cfDNA fragmentation. Citation Format: Nicholas A. Vulpescu, Zachariah H. Foda, Pieter H. Wisse, Christopher Cherry, Jamie E. Medina, Stephen B. Baylin, Kasper D. Hansen, 1 Vilmos Adleff, Remond J. Fijneman, Michael A. Beer, Robert B. Scharpf, Gerrit A. MeijerBeatriz Carvalho, Victor E. Velculescu. {TTT} [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 1958.