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      shRNA library screening identifies nucleocytoplasmic transport as a mediator of BCR-ABL1 kinase-independent resistance.

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          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.

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          Author and article information

          Journal
          Blood
          Blood
          1528-0020
          0006-4971
          Mar 12 2015
          : 125
          : 11
          Affiliations
          [1 ] Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT;
          [2 ] Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Beijing Tsinghua Chang Gung Hospital, Tsinghua University, Beijing, China;
          [3 ] 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;
          [4 ] Karyopharm Therapeutics, Natick, MA; and.
          [5 ] Cellecta, Mountain View, CA.
          Article
          blood-2014-08-588855
          10.1182/blood-2014-08-588855
          4357584
          25573989
          461b477d-a15d-4da0-8a5f-d9f525bb2308
          © 2015 by The American Society of Hematology.

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