Genome-wide CRISPR screen reveals PSMA6 to be an essential gene in pancreatic cancer cells

Jesse Bakke,Peter Oladimeji,Robert J Autry,Paul G Thomas,Jeremy Chase Crawford,Christopher T Brewer,William C Wright,Anthony E Zamora,William E Evans,Taosheng Chen

doi:10.1186/s12885-019-5455-1

Abstract

BackgroundDespite its relatively low incidence, pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer deaths because of the aggressive growth/metastasis of the tumor, the lack of early symptoms, and the poor treatment options. Basic research to identify potential therapeutic targets for PDAC is greatly needed.MethodsWe used a negative-selection genome-wide CRISPR screen to identify essential genes in the PANC-1 human pancreatic carcinoma cell line. We validated the top hits with follow-up siRNA screens, using the HPNE, HPAF-II, AsPC-1, and Mia PaCa-2 cell lines.ResultsThe PSMA6 gene was an identified candidate hit after the CRISPR screen, siRNA validation screen, and siRNA deconvolution screen. Spheroid formation assays and flow cytometry analysis showed that PSMA6 is critical for survival in many pancreatic ductal carcinoma cell models. Lastly, as PSMA6 protein is a proteosomal subunit of the 20S core complex, we showed that bortezomib, a proteasome inhibitor, was especially toxic in PANC-1 cells.ConclusionsFurther study of PSMA6 and the proteasome subunit that it encodes, along with other hits identified in our CRISPR screens, may provide valuable insights into potential therapeutic targets for PDAC.

Highlights

Despite its relatively low incidence, pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer deaths because of the aggressive growth/metastasis of the tumor, the lack of early symptoms, and the poor treatment options
By using the genome-wide CRISPR screening approach, we aimed to identify genes that were essential to the survival of PANC-1 cells and/or genes that sensitized PANC-1 cells to low-dose gemcitabine treatment
We hypothesized that those previously identified essential genes would not be of interest because of their lack of specificity for PDAC cell lines

Summary

Introduction

Despite its relatively low incidence, pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer deaths because of the aggressive growth/metastasis of the tumor, the lack of early symptoms, and the poor treatment options. Pancreatic ductal adenocarcinomas (PDACs) account for the vast majority of pancreatic cancer cases and are characterized by highly invasive mucin-producing neoplasms that commonly originate from noninvasive epithelial neoplasia of pancreatic ducts [2]. Driver mutations have been identified in four genes: the oncogene KRAS and the tumor suppressors CDKN2A, TP53, and SMAD4 [3]. To identify novel therapeutic targets of PDAC, we leveraged a genome-wide CRISPR screening approach that allowed us to quantify gene-specific phenotypic variation in PANC-1 cells in response to gemcitabine, the most commonly used PDAC chemotherapeutic. Genome-wide CRISPR screens are pool-based screening strategies that

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