Alternative Polyadenylation Characterizes Epithelial and Fibroblast Phenotypic Heterogeneity in Pancreatic Ductal Adenocarcinoma

TL;DR

This study shows that alternative polyadenylation contributes to tumor cell diversity in pancreatic cancer by altering gene expression patterns in different cell types.

Contribution

The study identifies 3′ UTR-APA as a novel driver of phenotypic heterogeneity in pancreatic ductal adenocarcinoma.

Findings

Increased proximal 3′ UTR-APA is linked to PDAC progression and metastatic epithelial and inflammatory fibroblast subpopulations.

3′ UTR shortening in marker genes correlates with increased gene expression in specific cell states.

3′ UTR-APA patterns were resolved across PDAC cell states using single-cell sequencing.

Abstract

Human tumors are composed of a complex mixture of cell types, characterized by differences in gene expression. How these changes in gene expression are driven and maintained during tumor initial and progression is largely unknown. In this study, we characterize an important mediator of gene expression at the single-cell level in samples from human pancreatic cancer. We find that this process, alternative polyadenylation, regulates critical gene expression changes both within tumor cells and cells in the tumor microenvironment. We propose that alternative polyadenylation may be an important driver of tumor heterogeneity.

Human tumors are characterized by extensive intratumoral transcriptional variability within the cancer cell and stromal compartments. This variation drives phenotypic heterogeneity, producing cell states with differential pro- and anti-tumorigenic properties. While bulk RNA sequencing cannot achieve cell-type-specific transcriptional granularity, single-cell sequencing has permitted an unprecedented view of these cell states. Despite this knowledge, we lack an understanding of the mechanistic drivers of this transcriptional and phenotypic heterogeneity. 3′ untranslated region alternative polyadenylation (3′ UTR-APA) drives gene expression alterations through regulation of 3′ UTR length. These 3′ UTR alterations modulate mRNA stability, protein expression and protein localization, resulting in cellular phenotypes including differentiation, cell proliferation, and migration. Therefore, we sought to determine whether 3′ UTR-APA events could characterize phenotypic heterogeneity of tumor cell states. Here, we analyze the largest single-cell human pancreatic ductal adenocarcinoma (PDAC) dataset and resolve 3′ UTR-APA patterns across PDAC cell states. We find that increased proximal 3′ UTR-APA is associated with PDAC progression and characterizes a metastatic ductal epithelial subpopulation and an inflammatory fibroblast population. Furthermore, we find significant 3′ UTR shortening events in cell-state-specific marker genes associated with increased expression. Therefore, we propose that 3′ UTR-APA drives phenotypic heterogeneity in cancer.

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