Abstract C111: Whole genome bisulfite sequencing of human and mouse organoid models of PDAC progression identifies stage- and subtype-specific DNA methylation signatures
Authors: Sarah S. Wang, Madison Hall, Eun Jung Lee, Neha Ramesh, Sang Hyub Lee, Jin-Young Jang, Ja-Lok Ku, Chang-Il Hwang
Journal: Cancer Research (2024)

Abstract The genetic underpinnings of PDAC progression from normal ductal cells to pancreatic intraepithelial neoplasms (PanINs) and primary tumors have been uncovered through the identification of common somatic point mutations and copy number variants in exome sequencing studies. However, attempts to identify recurrent metastasis-specific genetic mutations have been unsuccessful, suggesting that late-stage disease progression is predominantly driven by epigenetic alterations. Previous genome-wide DNA methylation studies have made it increasingly clear that DNA methylation is an important regulator of PDAC molecular pathobiology with impacts on clinical phenotypes and patient survival. While providing invaluable insights into functional roles of aberrant DNA methylation in PDAC, these studies were limited due to use of microarrays which assay less than 5% of CpG sites in the human genome, use of primary tumor samples with a high stromal content that can interfere with detection of tumor cell specific DNA methylation changes, and/or a limited sample size. To assay a larger portion of the PDAC methylome without stromal interference, we performed whole genome bisulfite sequencing (WGBS) analysis on a panel of 35 patient-derived organoid (PDO) models and 12 mouse organoid models of PDAC. Thus, this study is the first comprehensive analysis of genome-wide DNA methylation landscape in PDAC progression. With this approach, we assayed over 70% of the CpGs in the human and mouse genome and provide novel insight into the role of DNA methylation in PDAC progression and subtype differentiation. First, we uncovered thousands of DMRs that distinguish metastases from primary tumors and preneoplastic tissue in mouse organoids, early-stage primary tumors from late-stage primary tumors in PDOs, and primary tumors from normal pancreata in PDOs. Second, we showed that these stage-specific DMRs are enriched in promoters and bivalent enhancers and are associated with genes related to neurodevelopment and Ras signaling. Third, we identified DMRs whose DNA methylation correlate with expression of genes that have prognostic value. Lastly, we demonstrated that squamous and progenitor core gene programs are differentially methylated and separate the two subtypes based on their DNA methylation profiles. Together, these results show that DNA methylation changes underlie the disease stages and molecular subtypes of PDAC, resulting in significant and reoccurring DNA methylation patterns with diagnostic and prognostic potential. Citation Format: Sarah S. Wang, Madison Hall, Eun Jung Lee, Neha Ramesh, Sang Hyub Lee, Jin-Young Jang, Ja-Lok Ku, Chang-Il Hwang. Whole genome bisulfite sequencing of human and mouse organoid models of PDAC progression identifies stage- and subtype-specific DNA methylation signatures [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C111.