Abstract PR016: Dynamic chromatin landscapes of colorectal cancer development and cell-free DNA fragmentation
Authors: Vulpescu Nicholas A. , Foda Zachariah H. , Wisse Pieter H.A. , Cherry Christopher , Medina Jaime E. , Adleff Vilmos , Fijneman Remond J.A. , Scharpf Robert B. , Meijer Gerrit A. , Carvalho Beatriz , Velculescu Victor E. 
Published: November 2024

Abstract
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 complex mixtures of cells in normal, adenoma and cancer tissue samples, as well as absence of suitable adenoma model systems. Cultured colorectal organoids, comprised of pure epithelial cells, could enable insights on the epigenetic changes leading to progression from healthy tissue to cancer. Such features could be instrumental in the early cancer detection using genome-wide analyses of cfDNA fragmentation. 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 progression using transposase accessible chromatin analyses with next-generation sequencing. We defined a consensus set of nucleosome depleted regions for each disease state and identified loci with differential accessibility between PBMCs, colon healthy, colon adenoma, and colon cancer tissues. We analyzed these differential loci for fragmentation characteristics in the circulating cfDNA of 250 healthy individuals and 51 patients with metastatic CRC. Across all organoid samples, we identified &gt;35 million nucleosome depleted regions that we coalesced into a consensus set of 62,708 regions. As 78% of these regions could be linked to genes, we assessed whether these signatures identify known pathways involved in colorectal cancer. Within these regions, we identified unique colon tumor-related signatures comprising genes of known and novel pathways, including those involved in WNT, hippo, and RAS signaling. While the majority of chromatin accessibility differences were shared between adenomas and cancers, we identified 895 chromatin changes in adenomas that were not present in either healthy or malignant tissues. In healthy individuals, we found that the cfDNA coverage was negatively correlated with accessibility of white blood cell accessibility loci (Spearman ρ= - 0.60) while in individuals with cancer, changes in chromatin accessibility were associated with independent circulating tumor DNA abundance by droplet digital PCR (R2=0.69, p&lt;0.001). Chromatin accessibility profiles were correlated with genome-wide cell-free DNA fragmentation features and could be used to distinguish healthy individuals from those with colorectal cancer (AUC=0.97). These analyses are consistent with dynamic chromatin remodeling during colorectal tumor development and may provide an avenue for evaluating these through genome-wide analyses of cfDNA fragmentation.
Citation Format: Nicholas A. Vulpescu, Zachariah H. Foda, Pieter H.A. Wisse, Christopher Cherry, Jaime E. Medina, Vilmos Adleff, Remond J.A. Fijneman, Robert B. Scharpf, Gerrit A. Meijer, Beatriz Carvalho, Victor E. Velculescu. Dynamic chromatin landscapes of colorectal cancer development and cell-free DNA fragmentation [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR016.