title: Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen.
abstract: Targeted cancer therapeutics aim to exploit tumor-specific, genetic vulnerabilities specifically affecting neoplastic cells without similarly affecting normal cells. Here we performed sequencing-based screening of an shRNA library on a panel of cancer cells of different origins as well as normal cells. The shRNA library was designed to target a subset of genes previously identified using a whole genome screening approach. This focused shRNA library was infected into cells followed by analysis of enrichment and depletion of the shRNAs over the course of cell proliferation. We developed a bootstrap likelihood ratio test for the interpretation of the effects of multiple shRNAs over multiple cell line passages. Our analysis identified 44 genes whose depletion preferentially inhibited the growth of cancer cells. Among these genes ribosomal protein RPL35A, putative RNA helicase DDX24, and coatomer complex I (COPI) subunit ARCN1 most significantly inhibited growth of multiple cancer cell lines without affecting normal cell growth and survival. Further investigation revealed that the growth inhibition caused by DDX24 depletion is independent of p53 status underlining its value as a drug target. Overall, our study establishes a new approach for the analysis of proliferation-based shRNA selection strategies and identifies new targets for the development of cancer therapeutics.
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: David
authors.initials: D
authors.lastname: Oliver
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Ji
authors.affiliation: University of South Carolina, College of Arts and Sciences, Department of Statistics, Columbia, SC 29208, USA.|Bentley University, Waltham, MA 02452, USA.
authors.forename: Piaomu
authors.initials: P
authors.lastname: Liu
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Gasparian
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Ellen
authors.initials: E
authors.lastname: Gardiner
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Samuel
authors.initials: S
authors.lastname: Lee
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Adrian
authors.initials: A
authors.lastname: Zenteno
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Lillian O
authors.initials: LO
authors.lastname: Perinskaya
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Mengqian
authors.initials: M
authors.lastname: Chen
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Phillip
authors.initials: P
authors.lastname: Buckhaults
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Eugenia
authors.initials: E
authors.lastname: Broude
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Wyatt
authors.affiliation: University of South Carolina, College of Engineering and Computing, Department of Computer Sciences and Engineering, Columbia, SC 29208, USA.
authors.forename: Homayoun
authors.initials: H
authors.lastname: Valafar
authors.affiliation: University of South Carolina, College of Arts and Sciences, Department of Statistics, Columbia, SC 29208, USA.
authors.forename: Edsel
authors.initials: E
authors.lastname: Peña
authors.affiliation: University of South Carolina, College of Pharmacy, Department of Drug Discovery and Biomedical Sciences, Columbia, SC 29208, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Shtutman
mesh_terms: D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000187:drug effects; D020756:Coatomer Protein / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D053487:DEAD-box RNA Helicases / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D015195:Drug Design; D015723:Gene Library; D006801:Humans; D016013:Likelihood Functions; D009369:Neoplasms / Q000188:drug therapy / Q000235:genetics / Q000473:pathology; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism* / Q000494:pharmacology / Q000627:therapeutic use; D012269:Ribosomal Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D016159:Tumor Suppressor Protein p53 / Q000235:genetics / Q000378:metabolism
chemical_list: D020756:Coatomer Protein; D034741:RNA, Small Interfering; C489281:RPL35A protein, human; D012269:Ribosomal Proteins; D016159:Tumor Suppressor Protein p53; C412870:DDX24 protein, human; D053487:DEAD-box RNA Helicases