title: shRNA library screening identifies nucleocytoplasmic transport as a mediator of BCR-ABL1 kinase-independent resistance.
abstract: The mechanisms underlying tyrosine kinase inhibitor (TKI) resistance in chronic myeloid leukemia (CML) patients lacking explanatory BCR-ABL1 kinase domain mutations are incompletely understood. To identify mechanisms of TKI resistance that are independent of BCR-ABL1 kinase activity, we introduced a lentiviral short hairpin RNA (shRNA) library targeting ∼5000 cell signaling genes into K562(R), a CML cell line with BCR-ABL1 kinase-independent TKI resistance expressing exclusively native BCR-ABL1. A customized algorithm identified genes whose shRNA-mediated knockdown markedly impaired growth of K562(R) cells compared with TKI-sensitive controls. Among the top candidates were 2 components of the nucleocytoplasmic transport complex, RAN and XPO1 (CRM1). shRNA-mediated RAN inhibition or treatment of cells with the XPO1 inhibitor, KPT-330 (Selinexor), increased the imatinib sensitivity of CML cell lines with kinase-independent TKI resistance. Inhibition of either RAN or XPO1 impaired colony formation of CD34(+) cells from newly diagnosed and TKI-resistant CML patients in the presence of imatinib, without effects on CD34(+) cells from normal cord blood or from a patient harboring the BCR-ABL1(T315I) mutant. These data implicate RAN in BCR-ABL1 kinase-independent imatinib resistance and show that shRNA library screens are useful to identify alternative pathways critical to drug resistance in CML.
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Jamshid S
authors.initials: JS
authors.lastname: Khorashad
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Anna M
authors.initials: AM
authors.lastname: Eiring
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Clinton C
authors.initials: CC
authors.lastname: Mason
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Gantz
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Amber D
authors.initials: AD
authors.lastname: Bowler
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Hannah M
authors.initials: HM
authors.lastname: Redwine
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Beijing Tsinghua Chang Gung Hospital, Tsinghua University, Beijing, China;
authors.forename: Fan
authors.initials: F
authors.lastname: Yu
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Ira L
authors.initials: IL
authors.lastname: Kraft
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Anthony D
authors.initials: AD
authors.lastname: Pomicter
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Kimberly R
authors.initials: KR
authors.lastname: Reynolds
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Iovino
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Zabriskie
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: William L
authors.initials: WL
authors.lastname: Heaton
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, UT;
authors.forename: Srinivas K
authors.initials: SK
authors.lastname: Tantravahi
authors.affiliation: Karyopharm Therapeutics, Natick, MA; and.
authors.forename: Michael
authors.initials: M
authors.lastname: Kauffman
authors.affiliation: Karyopharm Therapeutics, Natick, MA; and.
authors.forename: Sharon
authors.initials: S
authors.lastname: Shacham
authors.affiliation: Cellecta, Mountain View, CA.
authors.forename: Alex
authors.initials: A
authors.lastname: Chenchik
authors.affiliation: Cellecta, Mountain View, CA.
authors.forename: Kyle
authors.initials: K
authors.lastname: Bonneau
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
authors.forename: Katharine S
authors.initials: KS
authors.lastname: Ullman
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, UT;
authors.forename: Thomas
authors.initials: T
authors.lastname: O'Hare
authors.affiliation: Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, UT;
authors.forename: Michael W
authors.initials: MW
authors.lastname: Deininger
mesh_terms: D021581:Active Transport, Cell Nucleus / Q000235:genetics; D001549:Benzamides / Q000494:pharmacology; D045744:Cell Line, Tumor; D002470:Cell Survival; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D016044:Fusion Proteins, bcr-abl / Q000235:genetics / Q000378:metabolism*; D055785:Gene Knockdown Techniques; D015723:Gene Library; D006801:Humans; D006834:Hydrazines / Q000494:pharmacology; D000068877:Imatinib Mesylate; D020014:K562 Cells; D028884:Karyopherins / Q000037:antagonists & inhibitors / Q000235:genetics; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000188:drug therapy* / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D010879:Piperazines / Q000494:pharmacology; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D011743:Pyrimidines / Q000494:pharmacology; D034741:RNA, Small Interfering / Q000235:genetics*; D018160:Receptors, Cytoplasmic and Nuclear / Q000037:antagonists & inhibitors / Q000235:genetics; D015398:Signal Transduction; D014230:Triazoles / Q000494:pharmacology; D014410:Tumor Stem Cell Assay; D020931:ran GTP-Binding Protein / Q000037:antagonists & inhibitors / Q000235:genetics; D000097606:Exportin 1 Protein
chemical_list: D001549:Benzamides; D016044:Fusion Proteins, bcr-abl; D006834:Hydrazines; D000068877:Imatinib Mesylate; D028884:Karyopherins; D010879:Piperazines; D047428:Protein Kinase Inhibitors; D011743:Pyrimidines; D034741:RNA, Small Interfering; D018160:Receptors, Cytoplasmic and Nuclear; D014230:Triazoles; D020931:ran GTP-Binding Protein; D000097606:Exportin 1 Protein; C581634:BCR-ABL1 fusion protein, human; C120587:RAN protein, human; C585161:selinexor