Single cell analysis of an engineered organoid based model of pancreatic cancer identifies hypoxia as a contributing factor in the determination of transcriptional subtypes

Pancreatic ductal adenocarcinoma is a high-mortality cancer with an aggressive, treatment resistant phenotype and a complex tumour microenvironment featuring significant hypoxia. We leveraged a unique 3D in vitro platform (TRACER) to perform single-cell transcriptome analysis of organoids cultured in a spatially-defined microenvironmental gradient to explore the effect of oxygen and other microenvironmental gradients on organoid heterogeneity. Overall design: Pancreatic cancer patient-derived organoids (PDOs) were dissociated to single cells and cultured in the TRACER platform. After 24h of culture in the rolled configuration featuring microenvironmental gradients, cells from each of the 6 layers were isolated from the construct and analyzed by scRNA-seq.