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Lewis G, Christiansen L, McKenzie J, Luo M, Pasackow E, Smurnyy Y, Harrington S, Gregory P, Veres G, Negre O, Bonner M. Staurosporine Increases Lentiviral Vector Transduction Efficiency of Human Hematopoietic Stem and Progenitor Cells. Mol Ther Methods Clin Dev 2018; 9:313-322. [PMID: 30038935 PMCID: PMC6054695 DOI: 10.1016/j.omtm.2018.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/01/2018] [Indexed: 11/19/2022]
Abstract
Lentiviral vector (LVV)-mediated transduction of human CD34+ hematopoietic stem and progenitor cells (HSPCs) holds tremendous promise for the treatment of monogenic hematological diseases. This approach requires the generation of a sufficient proportion of gene-modified cells. We identified staurosporine, a serine/threonine kinase inhibitor, as a small molecule that could be added to the transduction process to increase the proportion of genetically modified HSPCs by overcoming a LVV entry barrier. Staurosporine increased vector copy number (VCN) approximately 2-fold when added to mobilized peripheral blood (mPB) CD34+ cells prior to transduction. Limited staurosporine treatment did not affect viability of cells post-transduction, and there was no difference in in vitro colony formation compared to vehicle-treated cells. Xenotransplantation studies identified a statistically significant increase in VCN in engrafted human cells in mouse bone marrow at 4 months post-transplantation compared to vehicle-treated cells. Prostaglandin E2 (PGE2) is known to increase transduction efficiency of HSPCs through a different mechanism. Combining staurosporine and PGE2 resulted in further enhancement of transduction efficiency, particularly in short-term HSPCs. The combinatorial use of small molecules, such as staurosporine and PGE2, to enhance LVV transduction of human CD34+ cells is a promising method to improve transduction efficiency and subsequent potential therapeutic benefit of gene therapy drug products.
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Affiliation(s)
- Gretchen Lewis
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
| | | | | | - Min Luo
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
| | - Eli Pasackow
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
| | - Yegor Smurnyy
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
| | | | - Philip Gregory
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
| | - Gabor Veres
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
| | - Olivier Negre
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
| | - Melissa Bonner
- bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA
- Corresponding author: Melissa Bonner, bluebird bio, Inc., 60 Binney St., Cambridge, MA 02142, USA.
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Heffner GC, Bonner M, Christiansen L, Pierciey FJ, Campbell D, Smurnyy Y, Zhang W, Hamel A, Shaw S, Lewis G, Goss KA, Garijo O, Torbett BE, Horton H, Finer MH, Gregory PD, Veres G. Prostaglandin E 2 Increases Lentiviral Vector Transduction Efficiency of Adult Human Hematopoietic Stem and Progenitor Cells. Mol Ther 2017; 26:320-328. [PMID: 29102562 PMCID: PMC5763075 DOI: 10.1016/j.ymthe.2017.09.025] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 09/22/2017] [Accepted: 09/29/2017] [Indexed: 12/15/2022] Open
Abstract
Gene therapy currently in development for hemoglobinopathies utilizes ex vivo lentiviral transduction of CD34+ hematopoietic stem and progenitor cells (HSPCs). A small-molecule screen identified prostaglandin E2 (PGE2) as a positive mediator of lentiviral transduction of CD34+ cells. Supplementation with PGE2 increased lentiviral vector (LVV) transduction of CD34+ cells approximately 2-fold compared to control transduction methods with no effect on cell viability. Transduction efficiency was consistently increased in primary CD34+ cells from multiple normal human donors and from patients with β-thalassemia or sickle cell disease. Notably, PGE2 increased transduction of repopulating human HSPCs in an immune-deficient (nonobese diabetic/severe combined immunodeficiency/interleukin-2 gamma receptor null [NSG]) xenotransplantation mouse model without evidence of in vivo toxicity, lineage bias, or a de novo bias of lentiviral integration sites. These data suggest that PGE2 improves lentiviral transduction and increases vector copy number, therefore resulting in increased transgene expression. As a result, PGE2 may be useful in clinical gene therapy applications using lentivirally modified HSPCs.
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Affiliation(s)
| | - Melissa Bonner
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Dakota Campbell
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | - Yegor Smurnyy
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | - Wenliang Zhang
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | - Amanda Hamel
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | - Seema Shaw
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | - Gretchen Lewis
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | - Kendrick A Goss
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | - Olivia Garijo
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Holly Horton
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
| | | | | | - Gabor Veres
- bluebird bio, Inc., 60 Binney Street, Cambridge, MA 02142, USA
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Heffner G, Bonner M, Campbell D, Christiansen L, Pierciey FJ, Zhang W, Lewis G, Smurnyy Y, Hamel A, Shah S, Horton H, Ryu B, Goss K, Negre O, Veres G, Horvath C, Finer M, Gregory P. 229. PGE2 Increases Lentiviral Vector Transduction Efficiency of Human HSC. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)33038-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Smurnyy Y, Cai M, Wu H, McWhinnie E, Tallarico JA, Yang Y, Feng Y. DNA sequencing and CRISPR-Cas9 gene editing for target validation in mammalian cells. Nat Chem Biol 2014; 10:623-5. [PMID: 24929529 DOI: 10.1038/nchembio.1550] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 05/06/2014] [Indexed: 12/30/2022]
Abstract
Identification and validation of drug-resistant mutations can provide important insights into the mechanism of action of a compound. Here we demonstrate the feasibility of such an approach in mammalian cells using next-generation sequencing of drug-resistant clones and CRISPR-Cas9-mediated gene editing on two drug-target pairs, 6-thioguanine-HPRT1 and triptolide-ERCC3. We showed that disrupting functional HPRT1 allele or introducing ERCC3 point mutations by gene editing can confer drug resistance in cells.
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Affiliation(s)
- Yegor Smurnyy
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mi Cai
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Hua Wu
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Elizabeth McWhinnie
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - John A Tallarico
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yi Yang
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yan Feng
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
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Smurnyy Y, Toms AV, Hickson GR, Eck MJ, Eggert US. Binucleine 2, an isoform-specific inhibitor of Drosophila Aurora B kinase, provides insights into the mechanism of cytokinesis. ACS Chem Biol 2010; 5:1015-20. [PMID: 20804174 DOI: 10.1021/cb1001685] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Aurora kinases are key regulators of cell division and important targets for cancer therapy. We report that Binucleine 2 is a highly isoform-specific inhibitor of Drosophila Aurora B kinase, and we identify a single residue within the kinase active site that confers specificity for Aurora B. Using Binucleine 2, we show that Aurora B kinase activity is not required during contractile ring ingression, providing insight into the mechanism of cytokinesis.
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Affiliation(s)
- Yegor Smurnyy
- Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Angela V. Toms
- Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Gilles R. Hickson
- Sainte-Justine Hospital Research Center, Université de Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5 Canada
- Dept. Pathology & Cell Biology, Faculty of Medicine, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, QC, H3T 1J4 Canada
| | - Michael J. Eck
- Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Ulrike S. Eggert
- Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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Castoreno AB, Smurnyy Y, Torres AD, Vokes MS, Jones TR, Carpenter AE, Eggert US. Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis. Nat Chem Biol 2010; 6:457-63. [PMID: 20436488 PMCID: PMC2873065 DOI: 10.1038/nchembio.363] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 03/22/2010] [Indexed: 12/20/2022]
Abstract
We report the discovery of small molecules that target the Rho pathway, a central regulator of cytokinesis, the final step in cell division. We have developed a method to target a small molecule screen towards a specific pathway, which should be widely applicable to study any signaling pathway. In a chemical genetic variant of a classical modifier screen, we used RNA interference (RNAi) to sensitize cells and identified small molecules that suppressed or enhanced the RNAi phenotype. We have discovered promising candidate molecules, which we named Rhodblock 1–8, and we identified the target of Rhodblock 6 as Rho kinase. Several Rhodblocks inhibit a function of the Rho pathway in cells: the correct localization of phosphorylated myosin light chain during cytokinesis. Rhodblocks differentially perturb Rho pathway proteins in cells and can be used to dissect the mechanism of the Rho pathway during cytokinesis.
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Affiliation(s)
- Adam B Castoreno
- Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Elyashberg M, Blinov K, Smurnyy Y, Churanova T, Williams A. Empirical and DFT GIAO quantum-mechanical methods of (13)C chemical shifts prediction: competitors or collaborators? Magn Reson Chem 2010; 48:219-229. [PMID: 20108257 DOI: 10.1002/mrc.2571] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The accuracy of (13)C chemical shift prediction by both DFT GIAO quantum-mechanical (QM) and empirical methods was compared using 205 structures for which experimental and QM-calculated chemical shifts were published in the literature. For these structures, (13)C chemical shifts were calculated using HOSE code and neural network (NN) algorithms developed within our laboratory. In total, 2531 chemical shifts were analyzed and statistically processed. It has been shown that, in general, QM methods are capable of providing similar but inferior accuracy to the empirical approaches, but quite frequently they give larger mean average error values. For the structural set examined in this work, the following mean absolute errors (MAEs) were found: MAE(HOSE) = 1.58 ppm, MAE(NN) = 1.91 ppm and MAE(QM) = 3.29 ppm. A strategy of combined application of both the empirical and DFT GIAO approaches is suggested. The strategy could provide a synergistic effect if the advantages intrinsic to each method are exploited.
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Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development, Moscow Department, 6 Akademik Bakulev St, 117513 Moscow, Russian Federation
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Elyashberg M, Blinov K, Molodtsov S, Smurnyy Y, Williams AJ, Churanova T. Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream. J Cheminform 2009; 1:3. [PMID: 20142986 PMCID: PMC2816863 DOI: 10.1186/1758-2946-1-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 03/17/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be described using, as an example, the expert system Structure Elucidator. RESULTS The developers of CASE systems have been forced to overcome many obstacles hindering the development of a software application capable of drastically reducing the time and effort required to determine the structures of newly isolated organic compounds. Large complex molecules of up to 100 or more skeletal atoms with topological peculiarity can be quickly identified using the expert system Structure Elucidator based on spectral data. Logical analysis of 2D NMR data frequently allows for the detection of the presence of COSY and HMBC correlations of "nonstandard" length. Fuzzy structure generation provides a possibility to obtain the correct solution even in those cases when an unknown number of nonstandard correlations of unknown length are present in the spectra. The relative stereochemistry of big rigid molecules containing many stereocenters can be determined using the StrucEluc system and NOESY/ROESY 2D NMR data for this purpose. CONCLUSION The StrucEluc system continues to be developed in order to expand the general applicability, provide improved workflows, usability of the system and increased reliability of the results. It is expected that expert systems similar to that described in this paper will receive increasing acceptance in the next decade and will ultimately be integrated directly to analytical instruments for the purpose of organic analysis. Work in this direction is in progress. In spite of the fact that many difficulties have already been overcome to deliver on the spectroscopist's dream of "fully automated structure elucidation" there is still work to do. Nevertheless, as the efficiency of expert systems is enhanced the solution of increasingly complex structural problems will be achievable.
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Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development, Moscow Department, 6 Akademik Bakulev Street, Moscow 117513, Russian Federation
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Abstract
Protein structure determination by solid-state NMR of aligned samples relies on the fundamental characteristics of the anisotropic nuclear spin interactions present in isotopically labeled proteins. Progress in the implementation of algorithms that calculate protein structures from the orientational constraints in the chemical shift and heteronuclear dipolar coupling interactions is described using both simulated and experimental data.
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Affiliation(s)
- Yegor Smurnyy
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0307, USA
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Affiliation(s)
- Yegor Smurnyy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and M.V. Lomonosov Moscow State University, Moscow, Russia 119992
| | - Christine Bibal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and M.V. Lomonosov Moscow State University, Moscow, Russia 119992
| | - Maren Pink
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and M.V. Lomonosov Moscow State University, Moscow, Russia 119992
| | - Kenneth G. Caulton
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, and M.V. Lomonosov Moscow State University, Moscow, Russia 119992
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