The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma.

Jacob T Polaski,Dylan B Udy,Andrea Ventura,Luisa F Escobar-Hoyos,Steven D Leach,Ram Kannan,Gokce Askan,Robert K Bradley

doi:10.7554/elife.62209

Abstract

Pancreatic adenosquamous carcinoma (PASC) is an aggressive cancer whose mutational origins are poorly understood. An early study reported high-frequency somatic mutations affecting UPF1, a nonsense-mediated mRNA decay (NMD) factor, in PASC, but subsequent studies did not observe these lesions. The corresponding controversy about whether UPF1 mutations are important contributors to PASC has been exacerbated by a paucity of functional studies. Here, we modeled two UPF1 mutations in human and mouse cells to find no significant effects on pancreatic cancer growth, acquisition of adenosquamous features, UPF1 splicing, UPF1 protein, or NMD efficiency. We subsequently discovered that 45% of UPF1 mutations reportedly present in PASCs are identical to standing genetic variants in the human population, suggesting that they may be non-pathogenic inherited variants rather than pathogenic mutations. Our data suggest that UPF1 is not a common functional driver of PASC and motivate further attempts to understand the genetic origins of these malignancies.

Highlights

Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive disease that constitutes 1-4% of pancreatic exocrine tumors (Madura, Jarman, Doherty, Yum, & Howard, 1999)
We modeled UPF1 mutation-induced exon skipping by designing paired guide RNAs flanking Upf1 exons 10 and 11, such that these exons would be deleted upon Cas9 expression
We introduced each mutation into its endogenous context by transiently transfecting a plasmid expressing Cas9 and a single guide RNA targeting UPF1 intron 10 as well as appropriate donor

Summary

Introduction

Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive disease that constitutes 1-4% of pancreatic exocrine tumors (Madura, Jarman, Doherty, Yum, & Howard, 1999). Liu et al (Liu et al, 2014) reported high-frequency mutations affecting UPF1, which encodes a core component of the nonsense-mediated mRNA decay (NMD) pathway, in 78% (18 of 23) of PASC patients. These mutations were absent from patient-matched normal pancreatic tissue (0 of 18) and from non-PASC tumors (0 of 29 non-adenosquamous pancreatic carcinomas and 0 of 21 lung squamous cell carcinomas)

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Conclusion