Integrative single-cell transcriptome analysis of human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis [Spatial]

We identified five distinct functional subclusters of pancreatic cancer cells and six distinct cancer-associated fibroblast subclusters. We deeply profiled their characteristics, and we found that these subclusters successfully deconvoluted most of the features suggested in bulk transcriptome analysis of pancreatic cancer. Among those subclusters, we identified a novel cancer cell subcluster, Ep_VGLL1, showing intermediate characteristics between the extremities of basal-like and classical dichotomy, despite its prognostic value. Molecular features of Ep_VGLL1 suggest its transitional properties between basal-like and classical subtypes, which is strongly supported by spatial transcriptome data. We performed single cell RNA sequencing using enriched non-immune cell populations from 17 pancreatic cancer tumor tissues, and also generated paired spatial transcriptome data from 7 of the patient samples.