High resolution and quantitative intra-ductal spatial analysis reveals phenotypic and functional diversification in pancreatic cancer

Activiteit: Talk or presentation at a conference


Introduction: Transcriptomic studies have identified two major subtypes of pancreatic ductal adenocarcinoma (PDAC), i.e. a ‘classical’ and a ‘basal-like’ subtype. These subtypes have differential expression of GATA6, with prognostic and potentially predictive value, and the basal-like subtype has reportedly increased gene dosage of mutant KRAS. Here, we project these findings to the tissue level by high resolution spatial analysis in human PDAC and derived organoids to gain additional biological insights.
Methods: We use formalin-fixed paraffin embedded (FFPE) human PDAC cell lines, surgical samples and tumour organoids that were subjected to hot spot mutation analysis and transcriptomic subtyping by DNA and RNA sequencing. A Basescope™ assay was optimized for specific in situ detection of KRAS point mutations in above FFPE samples. BaseScope™ and RNAScope™ were combined with multiplex immunostainings and whole tissue sections were analyzed with HALO (Indica™) software.
Results: Apart from inter-patient and intra-patient inter-ductal heterogeneity, we revealed and quantified phenotypic diversity of tumour cells within single ducts, i.e. intra-ductal spatial phenotypes with varying and anti-correlating mRNA expression levels of GATA6 and KRASG12D. Novel classical and basal-like mRNA marker panels, informed by published gene signatures, better captured the basal-like cell state at high resolution than widely used surrogate markers such as P40 or KRT5. These panels further underscore the intra-ductal co-existence of classical and basal-like regions, as well as co-expressor cells. The intra-ductal regions were also related to functional diversity with proliferative classical regions and epithelial to mesenchymal transition in basal-like regions. PDAC organoids recapitulate the intra-ductal phenotypic and functional diversification that can be shifted experimentally by co-culturing with CAFs.
Conclusion: We successfully established quantitative in situ profiling of single point mutations and transcriptomic subtypes. We reveal extensive intra-tumour heterogeneity suggestive of functional cooperation of plastic tumour cells that take on a different transcriptomic subtype. This will put extra challenges to novel therapeutic approaches.
Periode30 apr 2023
EvenementstitelGordon Research Seminar 2023: Pancreatic diseases
Mate van erkenningInternational