Abstract 4339: Chromatin landscapes of colorectal cancer development and cfDNA fragmentation
Authors: Nicholas A. Vulpescu, Zachariah H. Foda, Pieter H. Wisse, Jamie E. Medina, Vilmos Adleff, Remond J. Fijneman, Robert B. Scharpf, Gerrit A. Meijer, Beatriz Carvalho, Victor E. Velculescu
Journal: Cancer Research (2024)

Abstract Introduction: The stepwise progression of colorectal cancer from healthy epithelium, to premalignant adenoma, to cancer is accompanied by genome-wide epigenetic reprogramming. 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. Methods: Using 43 patient-derived colorectal organoids derived from healthy, adenoma, and cancer tissues, 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 stage and used principal component analyses to identify peaks that contributed the most variation across the collection of organoids. Consensus regions were linked to genes they overlapped, and intergenic consensus regions were linked to the nearest gene within 1 Mbp. Subsequently, we performed a gene set enrichment analysis to assess pathways affected by differential chromatin accessibility. To identify the transcription factor drivers of regulatory reprogramming, the DNA sequences within the consensus peaks were analyzed for enrichment of characteristic binding motifs. We analyzed regions of consensus peaks for fragmentation characteristics in the circulating cell-free DNA (cfDNA) of 250 healthy individuals and 51 patients with stage IV colorectal cancer. Results: Across all organoid samples, we identified &amp;gt;35 million nucleosome depleted regions that we coalesced into a consensus set of 61,755 regions. We excluded 13,040 regions that had low variation across the organoid tissues, leaving 48,715 regions that could potentially define tissue-specific signatures of chromatin accessibility. As 78% of these regions could be linked to genes, we assessed whether these signatures identify known pathways involved in colorectal cancer. We identified unique signatures of healthy tissues, adenomas, and cancers comprising genes of known and novel pathways, including those involved in WNT, hippo, and RAS signaling. We found that changes in chromatin accessibility can be detected in circulating cfDNA profiles and were associated with independent circulating tumor DNA abundance by droplet digital PCR (R=0.78, p&amp;lt;0.0001). Conclusions: These analyses highlight important targets of chromatin remodeling in colorectal tumorigenesis and provide an avenue for evaluating these through genome-wide analyses of cfDNA fragmentation. Citation Format: Nicholas A. Vulpescu, Zachariah H. Foda, Pieter H. Wisse, Jamie E. Medina, Vilmos Adleff, Remond J. Fijneman, Robert B. Scharpf, Gerrit A. Meijer, Beatriz Carvalho, Victor E. Velculescu. Chromatin landscapes of colorectal cancer development and cfDNA fragmentation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4339.