Abstract 5926: Determining classical-basal transcriptional subtypes of pancreatic ductal adenocarcinoma using circulating tumor DNA epigenomic profiling
Authors: Karl Semaan, Marc Eid, Damien Vasseur, Gunsagar S. Gulati, Ji-Heui Seo, Alexander Jordan, Andressa Dias Costa, John Canniff, Leigh Culnane, Elizabeth Andrews, Emma C. Coleman, Noa Phillips, Brad Fortunato, Hunter Savignano, Rashad Nawfal, Razane El Hajj Chehade, Talal El Zarif, Ze Zhang, Paulo Cordeiro, Antoine Hollebecque, Antoine Italiano, Brandon M. Huffman, James M. Cleary, Jonathan Nowak, Jacob E. Berchuck, Toni K. Choueiri, Kimberly Perez, Andrew J. Aguirre, Sylvan C. Baca, Brian M. Wolpin, Matthew L. Freedman, Harshabad Singh
Journal: Cancer Research (2025)

Abstract Introduction: Classical (C) and basal (B) transcriptional subtypes are key prognostic biomarkers of pancreatic ductal adenocarcinoma (PDAC). The B subtype is associated with higher rates of metastases, chemoresistance and poor outcomes. Early data suggest that the B subtype may predict response to KRAS inhibition. Current subtyping methods rely on tissue biopsies, which may not capture subtype heterogeneity, and are difficult to implement clinically. Here, we report a novel non-invasive approach for PDAC subtyping based on profiling circulating tumor chromatin. Methods: RNA-seq, chromatin immunoprecipitation and sequencing (ChIP-seq) for H3K27ac and H3K4me3, assay for transposase-accessible chromatin sequencing (ATAC-seq), and methylated DNA immunoprecipitation sequencing (MeDIP-seq) were performed on PDAC patient derived xenografts (PDX, n = 17). C and B subtypes were called using PURIST algorithm on RNA-seq. Differential features between C and B PDXs for each epigenetic mark were identified using DESeq2. H3K27ac and H3K4me3 ChIP-seq, MeDIP-seq and low pass whole genome sequencing (LPWGS) were then performed on plasma of patients with metastatic PDAC from two clinical cohorts where C and B subtypes were previously determined. Circulating tumor DNA (ctDNA) fraction was estimated from LPWGS data using ichorCNA. A C/B score was derived for each epigenetic feature in individual patients by calculating the ratio of aggregate signal at classical:basal regions. Finally, a plasma integrated epigenomic score (PIES) was developed by combining various epigenetic features and its ability to distinguish subtypes was assessed using the area under the receiver operating characteristic (AUROC) curve. Results: Overall, 17 PDAC PDXs (C = 13, B = 4) were profiled with ChIP-seq (H3K27Ac, H3K4me3), ATAC-seq and MeDIP-seq. We identified 7, 855 differential H3K27ac sites that were also differentially accessible by ATAC-seq, 1, 603 differential H3K4me3 sites and 308 differentially methylated regions between the 2 subtypes. We then profiled 53 plasma samples from patients with metastatic PDAC who had previously undergone tissue-based RNA analysis (C = 33, B = 20). The median ctDNA fraction was comparable between the two subtypes (3.1 vs. 3.3%; p=0.4). The H3K27ac and H3K4me3 C/B scores were significantly higher in plasma from patients with classical PDAC (p&amp;lt;0.001) compared to basal PDAC. The methylation signature did not distinguish the two subtypes (p=0.2). PIES showed high discriminatory power between classical and basal samples, with an area under the curve (AUC) of 0.84 for all samples regardless of ctDNA fraction and an AUC of 0.88 for samples with &amp;gt;3% ctDNA. Conclusion: We present a non-invasive approach for distinguishing classical versus basal PDAC based on circulating tumor epigenomic profiles, which could facilitate subtyping to guide clinical decision making. Citation Format: Karl Semaan, Marc Eid, Damien Vasseur, Gunsagar S. Gulati, Ji-Heui Seo, Alexander Jordan, Andressa Dias Costa, John Canniff, Leigh Culnane, Elizabeth Andrews, Emma C. Coleman, Noa Phillips, Brad Fortunato, Hunter Savignano, Rashad Nawfal, Razane El Hajj Chehade, Talal El Zarif, Ze Zhang, Paulo Cordeiro, Antoine Hollebecque, Antoine Italiano, Brandon M. Huffman, James M. Cleary, Jonathan Nowak, Jacob E. Berchuck, Toni K. Choueiri, Kimberly Perez, Andrew J. Aguirre, Sylvan C. Baca, Brian M. Wolpin, Matthew L. Freedman, Harshabad Singh. Determining classical-basal transcriptional subtypes of pancreatic ductal adenocarcinoma using circulating tumor DNA epigenomic profiling [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 5926.