1
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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2
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Kumar D, Kashyap MK, Yu Z, Spaanderman I, Villa R, Kipps TJ, La Clair JJ, Burkart MD, Castro JE. Modulation of RNA splicing associated with Wnt signaling pathway using FD-895 and pladienolide B. Aging (Albany NY) 2022; 14:2081-2100. [PMID: 35230971 PMCID: PMC8954975 DOI: 10.18632/aging.203924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Alterations in RNA splicing are associated with different malignancies, including leukemia, lymphoma, and solid tumors. The RNA splicing modulators such as FD-895 and pladienolide B have been investigated in different malignancies to target/modulate spliceosome for therapeutic purpose. Different cell lines were screened using an RNA splicing modulator to test in vitro cytotoxicity and the ability to modulate RNA splicing capability via induction of intron retention (using RT-PCR and qPCR). The Cignal Finder Reporter Array evaluated [pathways affected by the splice modulators in HeLa cells. Further, the candidates associated with the pathways were validated at protein level using western blot assay, and gene-gene interaction studies were carried out using GeneMANIA. We show that FD-895 and pladienolide B induces higher apoptosis levels than conventional chemotherapy in different solid tumors. In addition, both agents modulate Wnt signaling pathways and mRNA splicing. Specifically, FD-895 and pladienolide B significantly downregulates Wnt signaling pathway-associated transcripts (GSK3β and LRP5) and both transcript and proteins including LEF1, CCND1, LRP6, and pLRP6 at the transcript, total protein, and protein phosphorylation's levels. These results indicate FD-895 and pladienolide B inhibit Wnt signaling by decreasing LRP6 phosphorylation and modulating mRNA splicing through induction of intron retention in solid tumors.
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Affiliation(s)
- Deepak Kumar
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- ThermoFisher Scientific, Carlsbad, CA 92008, USA
| | - Manoj K. Kashyap
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Zhe Yu
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Ide Spaanderman
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Januario E. Castro
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Hematology-Oncology Division, Mayo Clinic, Phoenix, AZ 85054, USA
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3
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Cretu C, Gee P, Liu X, Agrawal A, Nguyen TV, Ghosh AK, Cook A, Jurica M, Larsen NA, Pena V. Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Nat Commun 2021; 12:4491. [PMID: 34301950 PMCID: PMC8302644 DOI: 10.1038/s41467-021-24741-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/27/2022] Open
Abstract
Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)—a complex chaperoning the selection of branch and 3′ splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept. Chemical modulation of intron selection has emerged as a route for cancer therapy. Here, structures of the U2 snRNP’s SF3B module and of prespliceosome- both in complexes with splicing modulators- provide insight into the mechanisms of intron recognition and branch site inactivation.
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Affiliation(s)
- Constantin Cretu
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.,Cluster of Excellence Multiscale Bioimaging (MBExC), Universitätsmedizin Göttingen, Göttingen, Germany
| | | | - Xiang Liu
- H3 Biomedicine, Inc, Cambridge, MA, USA
| | | | | | - Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Melissa Jurica
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | | | - Vladimir Pena
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.
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4
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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5
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Nicolaou KC, Rekula SR, Kumar SM, Podilapu AR, Matuszak RP, Jung PM, Lam LT, Phillips AC, Lyssikatos J, Munneke S, Gu C, Sarvaiya H, Sandoval J, Hammond M, Aujay M, Purcell JW, Reilly RM, Gavrilyuk J. Design, Synthesis, and Biological Investigation of Thailanstatin A and Spliceostatin D Analogues Containing Tetrahydropyran, Tetrahydrooxazine, and Fluorinated Structural Motifs. J Org Chem 2021; 86:2499-2521. [PMID: 33417458 DOI: 10.1021/acs.joc.0c02643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thailanstatin A and spliceostatin D, two naturally occurring molecules endowed with potent antitumor activities by virtue of their ability to bind and inhibit the function of the spliceosome, and their natural siblings and designed analogues, constitute an appealing family of compounds for further evaluation and optimization as potential drug candidates for cancer therapies. In this article, the design, synthesis, and biological investigation of a number of novel thailanstatin A analogues, including some accommodating 1,1-difluorocyclopropyl and tetrahydrooxazine structural motifs within their structures, are described. Important findings from these studies paving the way for further investigations include the identification of several highly potent compounds for advancement as payloads for antibody-drug conjugates (ADCs) as potential targeted cancer therapies and/or small molecule drugs, either alone or in combination with other anticancer agents.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Santhosh Reddy Rekula
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - S Mothish Kumar
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ananda Rao Podilapu
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ryan P Matuszak
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Paul M Jung
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Lloyd T Lam
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Andrew C Phillips
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Joseph Lyssikatos
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Stefan Munneke
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Christine Gu
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Hetal Sarvaiya
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Joseph Sandoval
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Mikhail Hammond
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Monette Aujay
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - James W Purcell
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Regina M Reilly
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Julia Gavrilyuk
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
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6
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Zhang D, Meng F. A Comprehensive Overview of Structure-Activity Relationships of Small-Molecule Splicing Modulators Targeting SF3B1 as Anticancer Agents. ChemMedChem 2020; 15:2098-2120. [PMID: 33037739 DOI: 10.1002/cmdc.202000642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/19/2020] [Indexed: 02/06/2023]
Abstract
The pre-mRNA splicing factor SF3B1 shows recurrent mutations among hematologic malignancies and some solid tumors. In 2007, the identification of two cytotoxic natural products, which showed splicing inhibition by binding to SF3b, prompted the development of small-molecule splicing modulators of SF3B1 as therapeutics for cancer. Recent studies suggested that spliceosome-mutant cells are preferentially sensitive to pharmacologic splicing modulation; therefore, exploring the clinical utility of splicing modulator therapies in patients with spliceosome-mutant hematologic malignancies who have failed current therapies is greatly needed, as these patients have few treatment options. H3B-8800 had unique pharmacological activity and exhibited favorable data in phase I clinical trials to treat patients with advanced myeloid malignancies, indicating that further clinical trials are promising. The most established small-molecule modulators of SF3B1 can be categorized into three classes: the bicycles, the monopyranes, and the 12-membered macrolides. This review provides a comprehensive overview of the structure-activity relationships of small-molecule SF3B1 modulators, with a detailed analysis of interactions between modulators and protein binding pocket. The future strategy for splicing modulators development is also discussed.
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Affiliation(s)
- Datong Zhang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, P. R. China
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, 306 Huiren Road, Tianjin, 300301, P. R. China
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7
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Gartshore C, Tadano S, Chanda PB, Sarkar A, Chowdari NS, Gangwar S, Zhang Q, Vite GD, Momirov J, Boger DL. Total Synthesis of Meayamycin and O-Acyl Analogues. Org Lett 2020; 22:8714-8719. [PMID: 33074680 DOI: 10.1021/acs.orglett.0c03308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A short, scalable total synthesis of meayamycin is described by an approach that entails a longest linear sequence of 12 steps (22 steps overall) from commercially available chiral pool materials (ethyl l-lactate, BocNH-Thr-OH, and d-ribose) and introduces the most straightforward preparation of the right-hand subunit detailed to date. The use of the approach in the divergent synthesis of a representative series of O-acyl analogues is exemplified.
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Affiliation(s)
- Christopher Gartshore
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shinji Tadano
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Prem B Chanda
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anindya Sarkar
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Naidu S Chowdari
- Bristol Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Sanjeev Gangwar
- Bristol Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Qian Zhang
- Bristol Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States
| | - Gregory D Vite
- Bristol Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States.,Bristol Myers Squibb Research & Development, P.O. Box 4000, Princeton, New Jersey 08543 United States
| | - Jelena Momirov
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dale L Boger
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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8
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Ghosh AK, Born JR, Veitschegger AM, Jurica MS. Copper-Catalyzed Stille Cross-Coupling Reaction and Application in the Synthesis of the Spliceostatin Core Structure. J Org Chem 2020; 85:8111-8120. [PMID: 32515594 DOI: 10.1021/acs.joc.0c00976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An efficient palladium-free Stille cross-coupling reaction of allylic bromides and functionalized organostannylfuran using catalytic copper halide has been developed. The coupling reaction was optimized using CuI and low catalyst loading (down to 5 mol %). The reaction was conveniently carried out at ambient temperature in the presence of inorganic base to afford the coupling product in good-to-excellent yields. The utility of this reaction was demonstrated in the synthesis of a furan with sensitive functionalities. A sulfolene moiety was utilized as a masking group for the sensitive diene. Noyori asymmetric reduction, Achmatowicz reaction, and Kishi reduction steps converted sulfolene to a highly substituted tetrahydropyran intermediate used in the synthesis of the highly potent antitumor agents, spliceostatins, and their derivatives.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Joshua R Born
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Anne M Veitschegger
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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9
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Tang C, Okumura M, Zhu Y, Hooper AR, Zhou Y, Lee YH, Sarlah D. Palladium-Catalyzed Dearomative syn-1,4-Carboamination with Grignard Reagents. Angew Chem Int Ed Engl 2019; 58:10245-10249. [PMID: 31090252 PMCID: PMC6640109 DOI: 10.1002/anie.201905021] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 01/03/2023]
Abstract
A protocol for palladium-catalyzed dearomative functionalization of simple, nonactivated arenes with Grignard reagents has been established. This one-pot method features a visible-light-mediated [4+2] cycloaddition between an arene and an arenophile, and subsequent palladium-catalyzed allylic substitution of the resulting cycloadduct with a Grignard reagent. A variety of arenes and Grignard reagents can participate in this process, forming carboaminated products with exclusive syn-1,4-selectivity. Moreover, the dearomatized products are amenable to further elaborations, providing functionalized alicyclic motifs and pharmacophores. For example, naphthalene was converted into sertraline, one of the most prescribed antidepressants, in only four operations. Finally, this process could also be conducted in an enantioselective fashion, as demonstrated with the desymmetrization of naphthalene.
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Affiliation(s)
| | | | - Yunbo Zhu
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Illinois 61801 (USA)
| | - Annie R. Hooper
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Illinois 61801 (USA)
| | - Yu Zhou
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Illinois 61801 (USA)
| | - Yu-Hsuan Lee
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Illinois 61801 (USA)
| | - David Sarlah
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Illinois 61801 (USA)
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10
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Tang C, Okumura M, Zhu Y, Hooper AR, Zhou Y, Lee Y, Sarlah D. Palladium‐Catalyzed Dearomative
syn
‐1,4‐Carboamination with Grignard Reagents. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Conghui Tang
- Roger Adams Laboratory Department of Chemistry University of Illinois Urbana IL 61801 USA
| | - Mikiko Okumura
- Roger Adams Laboratory Department of Chemistry University of Illinois Urbana IL 61801 USA
| | - Yunbo Zhu
- Roger Adams Laboratory Department of Chemistry University of Illinois Urbana IL 61801 USA
| | - Annie R. Hooper
- Roger Adams Laboratory Department of Chemistry University of Illinois Urbana IL 61801 USA
| | - Yu Zhou
- Roger Adams Laboratory Department of Chemistry University of Illinois Urbana IL 61801 USA
| | - Yu‐Hsuan Lee
- Roger Adams Laboratory Department of Chemistry University of Illinois Urbana IL 61801 USA
| | - David Sarlah
- Roger Adams Laboratory Department of Chemistry University of Illinois Urbana IL 61801 USA
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11
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Tonapi SS, Pannu V, Duncan JE, Rosenow M, Helmstetter A, Magee D, Zhang Q, Tinder TT, Richards M, Halbert DD, Famulok M, Spetzler D, Miglarese MR, O'Neill HA, Mayer G. Translocation of a Cell Surface Spliceosomal Complex Induces Alternative Splicing Events and Lymphoma Cell Necrosis. Cell Chem Biol 2019; 26:756-764.e6. [PMID: 30930163 DOI: 10.1016/j.chembiol.2019.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/10/2018] [Accepted: 02/24/2019] [Indexed: 01/08/2023]
Abstract
Spliceosomal dysregulation dramatically affects many cellular processes, notably signal transduction, metabolism, and proliferation, and has led to the concept of targeting intracellular spliceosomal proteins to combat cancer. Here we show that a subset of lymphoma cells displays a spliceosomal complex on their surface, which we term surface spliceosomal complex (SSC). The SSC consists of at least 13 core components and was discovered as the binding target of the non-Hodgkin's lymphoma-specific aptamer C10.36. The aptamer triggers SSC internalization, causing global changes in alternative splicing patterns that eventually lead to necrotic cell death. Our study reveals an exceptional spatial arrangement of a spliceosomal complex and defines it not only as a potential target of anti-cancer drugs, but also suggests that its localization plays a fundamental role in cell survival.
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Affiliation(s)
- Sonal S Tonapi
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Vaishali Pannu
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Janet E Duncan
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Matthew Rosenow
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | | | - Daniel Magee
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Qing Zhang
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Teresa T Tinder
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Melissa Richards
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - David D Halbert
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Michael Famulok
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA; LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Center of Aptamer Research and Development, University of Bonn, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - David Spetzler
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Mark R Miglarese
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | | | - Günter Mayer
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA; LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Center of Aptamer Research and Development, University of Bonn, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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12
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DeNicola AB, Tang Y. Therapeutic approaches to treat human spliceosomal diseases. Curr Opin Biotechnol 2019; 60:72-81. [PMID: 30772756 DOI: 10.1016/j.copbio.2019.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
Mutated RNA splicing machinery drives many human diseases and is a promising therapeutic target for engineering and small molecule therapy. In the case of mutations in individual genes that cause them to be incorrectly spliced, engineered splicing factors can be introduced to correct splicing of these aberrant transcripts and reduce the effects of the disease phenotype. Mutations that occur in certain splicing factor genes themselves have been implicated in many cancers, particularly myelodysplastic syndromes. Small molecules that target splicing factors have been developed as therapies to preferentially induce apoptosis in these cancer cells. Specifically, drugs targeting the splicing factor SF3B1 have led to recent clinical trials. Here, we review the role of alternative splicing in disease, approaches to rescue incorrect splicing using engineered splicing factors, and small molecule splicing inhibitors developed to treat hematological cancers.
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Affiliation(s)
- Anthony B DeNicola
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States.
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
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13
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Bressin RK, Driscoll JL, Wang Y, Koide K. Scalable Preparation of Methylated Ando-Type Horner–Wadsworth–Emmons Reagent. Org Process Res Dev 2019. [DOI: 10.1021/acs.oprd.8b00423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert K. Bressin
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Julia L. Driscoll
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Yanping Wang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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14
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Nicolaou KC, Rhoades D, Kumar SM. Total Syntheses of Thailanstatins A-C, Spliceostatin D, and Analogues Thereof. Stereodivergent Synthesis of Tetrasubstituted Dihydro- and Tetrahydropyrans and Design, Synthesis, Biological Evaluation, and Discovery of Potent Antitumor Agents. J Am Chem Soc 2018; 140:8303-8320. [PMID: 29943984 DOI: 10.1021/jacs.8b04634] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Efficient and selective total syntheses of spliceosome modulating natural products thailanstatins A-C and spliceostatin D are reported. A number of stereoselective methods for the construction of various tetrasubstituted dihydro- and tetrahydropyrans were developed as a prerequisite for the syntheses of these naturally occurring molecules and variations thereof. The pyran-forming reactions utilize a Heck/Saegusa-Ito cascade sequence to generate hydroxy α,β,γ,δ-unsaturated aldehyde precursors followed by a catalyst-controlled oxa-Michael cyclization to furnish tetrasubstituted dihydropyrans with high stereocontrol. Subsequent optimized homogeneous or heterogeneous hydrogenations of these dihydropyran systems afford their tetrahydropyran counterparts, also in a highly stereoselective manner. The synthesized thailanstatins and related analogues were biologically evaluated for their cytotoxic properties, leading to the identification of a number of compounds with exceptionally potent antitumor activities suitable for further development as potential antibody-drug conjugate payloads, single drugs, or drug combinations for cancer therapies. Important structure-activity relationships within the thailanstatin family and structurally related compounds are discussed and are expected to be path-pointing for future studies.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, BioScience Research Collaborative , Rice University , 6100 Main Street , Houston , Texas 77005 , United States
| | - Derek Rhoades
- Department of Chemistry, BioScience Research Collaborative , Rice University , 6100 Main Street , Houston , Texas 77005 , United States
| | - S Mothish Kumar
- Department of Chemistry, BioScience Research Collaborative , Rice University , 6100 Main Street , Houston , Texas 77005 , United States
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Alternative Splicing as a Target for Cancer Treatment. Int J Mol Sci 2018; 19:ijms19020545. [PMID: 29439487 PMCID: PMC5855767 DOI: 10.3390/ijms19020545] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.
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Molecular basis of differential 3' splice site sensitivity to anti-tumor drugs targeting U2 snRNP. Nat Commun 2017; 8:2100. [PMID: 29235465 PMCID: PMC5727392 DOI: 10.1038/s41467-017-02007-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/30/2017] [Indexed: 01/21/2023] Open
Abstract
Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the differential sensitivity of 3′ splice sites to these drugs. Sequences 5′ from the branch point (BP) region strongly influence drug sensitivity, with additional functional BPs reducing, and BP-like sequences allowing, drug responses. Drug-induced retained introns are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs. Drug-induced exon skipping preferentially affects shorter alternatively spliced regions with weaker BPs. Remarkably, structurally similar drugs display both common and differential effects on splicing regulation, SSA generally displaying stronger effects on intron retention, and Sudemycins more acute effects on exon skipping. Collectively, our results illustrate how splicing modulation is exquisitely sensitive to the sequence context of 3′ splice sites and to small structural differences between drugs. Several families of natural compounds target core components of the pre-mRNA splicing machinery and display anti-tumor activity. Here the authors show that particular sequence features can be linked to drug response, and that drugs with very similar chemical structures display substantially different effects on splicing regulation.
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Zhang MG, Lee JY, Gallo RA, Tao W, Tse D, Doddapaneni R, Pelaez D. Therapeutic targeting of oncogenic transcription factors by natural products in eye cancer. Pharmacol Res 2017; 129:365-374. [PMID: 29203441 DOI: 10.1016/j.phrs.2017.11.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/15/2017] [Accepted: 11/30/2017] [Indexed: 02/08/2023]
Abstract
Carcinogenesis has a multifactorial etiology, and the underlying molecular pathogenesis is still not entirely understood, especially for eye cancers. Primary malignant intraocular neoplasms are relatively rare, but delayed detection and inappropriate management contribute to poor outcomes. Conventional treatment, such as orbital exenteration, chemotherapy, or radiotherapy, alone results in high mortality for many of these malignancies. Recent sequential multimodal therapy with a combination of high-dose chemotherapy, followed by appropriate surgery, radiotherapy, and additional adjuvant chemotherapy has helped dramatically improve management. Transcription factors are proteins that regulate gene expression by modulating the synthesis of mRNA. Since transcription is a dominant control point in the production of many proteins, transcription factors represent key regulators for numerous cellular functions, including proliferation, differentiation, and apoptosis, making them compelling targets for drug development. Natural compounds have been studied for their potential to be potent yet safe chemotherapeutic drugs. Since the ancient times, plant-derived bioactive molecules have been used to treat dreadful diseases like cancer, and several refined pharmaceutics have been developed from these compounds. Understanding targeting mechanisms of oncogenic transcription factors by natural products can add to our oncologic management toolbox. This review summarizes the current findings of natural products in targeting specific oncogenic transcription factors in various types of eye cancer.
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Affiliation(s)
- Michelle G Zhang
- Dr Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - John Y Lee
- Dr Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Ryan A Gallo
- Dr Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Wensi Tao
- Dr Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - David Tse
- Dr Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Ravi Doddapaneni
- Dr Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| | - Daniel Pelaez
- Dr Nasser Al-Rashid Orbital Vision Research Center, Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; Department of Biomedical Engineering, University of Miami College of Engineering, Coral Gables, FL, 33146, USA.
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. A Challenging Pie to Splice: Drugging the Spliceosome. Angew Chem Int Ed Engl 2017; 56:12052-12063. [PMID: 28371109 PMCID: PMC6311392 DOI: 10.1002/anie.201701065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 02/05/2023]
Abstract
Since its discovery in 1977, the study of alternative RNA splicing has revealed a plethora of mechanisms that had never before been documented in nature. Understanding these transitions and their outcome at the level of the cell and organism has become one of the great frontiers of modern chemical biology. Until 2007, this field remained in the hands of RNA biologists. However, the recent identification of natural product and synthetic modulators of RNA splicing has opened new access to this field, allowing for the first time a chemical-based interrogation of RNA splicing processes. Simultaneously, we have begun to understand the vital importance of splicing in disease, which offers a new platform for molecular discovery and therapy. As with many natural systems, gaining clear mechanistic detail at the molecular level is key towards understanding the operation of any biological machine. This minireview presents recent lessons learned in this emerging field of RNA splicing chemistry and chemical biology.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - Warren C. Chan
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. Das Spliceosom als Angriffspunkt für Pharmaka. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - Warren C. Chan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
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Thurman M, van Doorn J, Danzer B, Webb TR, Stamm S. Changes in Alternative Splicing as Pharmacodynamic Markers for Sudemycin D6. Biomark Insights 2017; 12:1177271917730557. [PMID: 28932105 PMCID: PMC5598794 DOI: 10.1177/1177271917730557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/08/2017] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE The aim of the study was to define pharmacodynamic markers for sudemycin D6, an experimental cancer drug that changes alternative splicing in human blood. METHODS Blood samples from 12 donors were incubated with sudemycin D6 for up to 24 hours, and at several time points total RNA from lymphocytes was prepared and the pre-messenger RNA (mRNA) splicing patterns were analyzed with reverse transcription-polymerase chain reaction. RESULTS Similar to immortalized cells, blood lymphocytes change alternative splicing due to sudemycin D6 treatment. However, lymphocytes in blood respond slower than immortalized cultured cells. CONCLUSIONS Exon skipping in the DUSP11 and SRRM1 pre-mRNAs are pharmacodynamic markers for sudemycin D6 treatment and show effects beginning at 9 hours after treatment.
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Tripathi R, Lee-Verges E, Higashi M, Gimenez N, Rosich L, Lopez-Guerra M, Colomer D. New drug discovery approaches targeting recurrent mutations in chronic lymphocytic leukemia. Expert Opin Drug Discov 2017; 12:1041-1052. [PMID: 28776453 DOI: 10.1080/17460441.2017.1362387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Next generation sequencing has provided a comprehensive understanding of the mutational landscape in chronic lymphocytic leukemia (CLL), and new drivers have been identified. Some of these drivers could be pharmacologically targeted to choose the most effective personalized therapy in each CLL patient. Areas covered: In this article, the authors uncover the potential role of new targeted therapies against the most recurrent mutations in CLL as well as the recently approved therapies. The authors also provide their expert opinion and give their perspectives for the future. Expert opinion: The development of more personalized therapies is of interest to clinicians as a system to enhance the duration of treatment response and to extend the survival and quality of life of CLL patients. The main challenge, however, will be to translate the preclinical results into the clinics. Therefore, the designing and execution of clinical trials focused on molecular drivers are the need of the hour.
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Affiliation(s)
- Rupal Tripathi
- a Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit , Hospital Clinic, CIBERONC , Barcelona , Spain
| | - Eriong Lee-Verges
- a Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit , Hospital Clinic, CIBERONC , Barcelona , Spain
| | - Morihiro Higashi
- a Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit , Hospital Clinic, CIBERONC , Barcelona , Spain
| | - Neus Gimenez
- a Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit , Hospital Clinic, CIBERONC , Barcelona , Spain
| | - Laia Rosich
- a Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit , Hospital Clinic, CIBERONC , Barcelona , Spain
| | - Monica Lopez-Guerra
- a Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit , Hospital Clinic, CIBERONC , Barcelona , Spain
| | - Dolors Colomer
- a Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hematopathology Unit , Hospital Clinic, CIBERONC , Barcelona , Spain
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