Abstract 4436: Phenotypic heterogeneity in pancreatic ductal adenocarcinoma revealed by single-cell lipidomics
Authors: Trajkovic-Arsic Marija , Delafiori Jeany , Shahraz Mohammed , Münch Corinna , Lueong Smiths S. , Liffers Sven T. , Hellerschmied Doris , Alexandrov Theodore , Siveke Jens T. 
Published: March 2024

Introduction: The high chemoresistance of pancreatic ductal adenocarcinoma (PDAC) is partly attributed to the phenotypic plasticity and high adaptability of PDAC cells to the challenges of the harsh microenviroment. Phenotypic presentation of the PDAC cell is also determined by the lipid composition of the plasma membrane and lipid species that organize the rigid or more flexible lipid bilayer and determine the cellular mobility and plasticity. Lipids are also important energy and signaling molecules that contribute to the aggressiveness of the cell. Here we focus on differences in lipid profile of PDAC cells in epithelial and mesenchymal cell state using single-cell lipidomics approach (SpaceM).

Methods: Lipid profile of 2D cultures of eight conventional and ten primary patient derived cell lines of different source (patient derived xenograft, ascites, primary tumor, organoid derived) was investigated. Epithelial (E) or mesenchymal (M) cell state was evaluated by gene and protein expression of EMT markers. Matrix-Assisted Laser Desorption/Ionization (MALDI)-imaging MS was used for data acquisition on positive ion mode at 25 µm step size and m/z range of 600-1000. For annotating lipids in MALDI-imaging data, we used the METASPACE cloud software. For constructing single-cell lipidomic profiles we used the SpaceM method. In total, around 150.000 cells were analyzed and 1400 lipid ions detected.

Results: Gene expression analysis suggested prominent metabolism of structural lipids in the conventional epithelial cells. In UMAP analysis of single cell lipidomics data, each cell line, conventional and primary, presented a unique lipid fingerprint with however prominent clustering into the two phenotypes, epithelial and mesenchymal. We detected enrichment of alkyl-acyl phosphatidylcholines, alkyl-acyl phospatidylethanolamines, ceramides and sphingolipids in the epithelial phenotype. Mesenchymal phenotype was enriched for lipids involved in lateral diffusion and low bilayer thickness supporting the increased fluidity of the mesenchymal cell membrane. Furthermore, mesenchymal phenotype was enriched for lipid droplets and energy storing triacylglycerols, also confirmed by histological lipid droplet staining.

Conclusions: Using the single cell lipid information, a successful grouping to epithelial or mesenchymal subtype could be performed regardless of sample source, suggesting a conserved lipid profile typical for the two states. Further detailed investigation of single cell lipidomics data aims to unveil the prominent epithelial-mesenchymal state lipid markers and open a niche for functional investigations of cell-state specific markers and potential cell-state targeting.

Citation Format: Marija Trajkovic-Arsic, Jeany Delafiori, Mohammed Shahraz, Corinna Münch, Smiths S. Lueong, Sven T. Liffers, Doris Hellerschmied, Theodore Alexandrov, Jens T. Siveke. Phenotypic heterogeneity in pancreatic ductal adenocarcinoma revealed by single-cell lipidomics [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 4436.