Abstract A031: Proteogenomic analysis of the PDAC epithelium reveals tissue markers of subtype identity and biology

Abstract Effective treatments for Pancreatic ductal adenocarcinoma (PDAC) remain an urgent need. Integration of molecular PDAC subtypes into clinical trials could enable translational insights into how we might refine existing and emerging therapies to improve treatment options, yet this requires robust clinically suitable marker genes and a better understanding of subtype-related biology. Here, we deeply profiled the molecular composition of human PDAC epithelia and assessed differentially expressed genes for their ability to discriminate between subtypes and mirror their key biological traits. Using well-annotated resected & advanced biospecimens, we mapped the stromal and epithelial landscapes of PDAC subtypes by combining compartment-specific transcriptomics and proteomics with quantitative image analysis of a 42-marker IHC panel and single cell RNA sequencing analyses. The integrated profiling yielded a shortlist of 30 genes that were differentially expressed at both transcriptomic and proteomic levels, and across primary and metastatic sites. These were then scrutinized for their suitability as potential single gene subtype markers through association with subtype-related epithelial and stromal biology and clinical outcomes, and via practical considerations such as immunohistochemical staining quality and cell type-specific expression patterns. Since PDAC subtypes frequently co-occur intratumorally, we furthermore assessed complementarity of different subtype marker combinations and tested association of individual markers with regional subtype biology. Annexin A8 emerged as strong IHC-suitable marker gene of the basal/squamous subtype, that exhibited prognostic and predictive value. Concordantly, Annexin A8 expression was highly correlated with TP63, a master transcription factor for the squamous subtype, and CK5, a well-established basal cell marker. In tissue stains and single cell RNAseq data, Annexin A8 specifically marked malignant epithelia but was absent from adjacent normal acini and stroma cell populations. Annexin A8 expression in PDAC epithelia was spatially distinct from the known classical subtype biomarker GATA6, as well as Claudin 18, which was the top classical/pancreatic progenitor marker gene in our integrated multiOMIC analysis. Furthermore, Annexin A8high tumors as well as Annexin A8high intratumoral regions both recapitulated key biological traits of the basal-like/squamous PDAC subtype, such as increased EMT marker expression, proliferation, hypoxia, macrophage attraction and T cell repulsion. In conclusion, integrated proteogenomic characterization of PDAC subtypes and their tissue features uncovers complementary subtype marker pairs with clinical potential and provides insights into subtype-specific biology with implications in the development of future therapeutic approaches tailored to each PDAC subtype. Citation Format: Barbara T. Grünwald, Foram Vyas, Michael Geuenich, Nathan Chan, Ricardo Gonzalez, Kazeera Aliar, Niklas Krebs, Antoine Devisme, Geoffroy Andrieux, Gun Ho Jang, Grainne O'Kane, Julie Wilson, Jennifer Knox, Faiyaz Notta, Kieran Campbell, Steven Gallinger, Melanie Boerries, Sandra Fischer, Thomas Kislinger, Rama Khokha. Proteogenomic analysis of the PDAC epithelium reveals tissue markers of subtype identity and biology [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A031.