Single-Cell Cross-Species Profiling identifies Conserved Transcriptional Networks in Early Pancreatic Tumourigenesis

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer and carries the poorest prognosis among all cancers, largely because it is frequently diagnosed at metastatic stages. It is therefore critical to identify reliable markers of preinvasive stages and to decipher the network driving preinvasive lesions to invasive carcinoma.

Here, we generated a zebrafish model in which KRAS
G12D
is specifically expressed in pancreatic acinar cells, inducing acinar-to-ductal metaplasia that faithfully mirrors mammalian tumorigenesis. Single cell RNA-seq allowed us to capture transcriptional changes occurring at early stages of the disease. Cross-species comparison with mouse and human scRNAseq transcriptomes revealed a striking conservation of the genes upregulated during metaplasia, triggering common signalling pathways and regulatory programs. Notably, metaplastic cells reactivate a broad set of developmental genes expressed in multipotent pancreatic progenitors.

Mapping the acinar-to-cancer trajectories revealed a set of cytoskeletal and migration-related genes specifically upregulated during the late phase of metaplasia, immediately prior to malignant transformation, likely conferring invasive potential to these cells. SCENIC analysis further identified regulatory networks that become progressively activated as cells transition toward cancer, suggesting their involvement in the acquisition of malignant traits.
In conclusion, our cross-species comparison demonstrates a high degree of conservation in the molecular mechanisms driving pancreatic cancer progression from early to late stages across evolutionarily distant species, including zebrafish, mouse, and human, highlighting critical pathways that should be targeted to prevent cancer progression.

To allow researchers to easily explore gene expression profiles during pancreatic cancer progression across all three species, the datasets are publicly accessible via a user-friendly web platform (
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)