1
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Grams N, Charman M, Halko E, Lauman R, Garcia BA, Weitzman MD. Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production. EMBO J 2024; 43:277-303. [PMID: 38177504 PMCID: PMC10897327 DOI: 10.1038/s44318-023-00021-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
Biomolecular condensates (BMCs) play important roles in diverse biological processes. Many viruses form BMCs which have been implicated in various functions critical for the productive infection of host cells. The adenovirus L1-52/55 kilodalton protein (52K) was recently shown to form viral BMCs that coordinate viral genome packaging and capsid assembly. Although critical for packaging, we do not know how viral condensates are regulated during adenovirus infection. Here we show that phosphorylation of serine residues 28 and 75 within the N-terminal intrinsically disordered region of 52K modulates viral condensates in vitro and in cells, promoting liquid-like properties. Furthermore, we demonstrate that phosphorylation of 52K promotes viral genome packaging and the production of infectious progeny particles. Collectively, our findings provide insights into how viral condensate properties are regulated and maintained in a state conducive to their function in viral progeny production. In addition, our findings have implications for antiviral strategies aimed at targeting the regulation of viral BMCs to limit viral multiplication.
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Affiliation(s)
- Nicholas Grams
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Cell & Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Matthew Charman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Edwin Halko
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Richard Lauman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Weitzman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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2
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Chowdhury I, Dashi G, Keskitalo S. CMGC Kinases in Health and Cancer. Cancers (Basel) 2023; 15:3838. [PMID: 37568654 PMCID: PMC10417348 DOI: 10.3390/cancers15153838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
CMGC kinases, encompassing cyclin-dependent kinases (CDKs), mitogen-activated protein kinases (MAPKs), glycogen synthase kinases (GSKs), and CDC-like kinases (CLKs), play pivotal roles in cellular signaling pathways, including cell cycle regulation, proliferation, differentiation, apoptosis, and gene expression regulation. The dysregulation and aberrant activation of these kinases have been implicated in cancer development and progression, making them attractive therapeutic targets. In recent years, kinase inhibitors targeting CMGC kinases, such as CDK4/6 inhibitors and BRAF/MEK inhibitors, have demonstrated clinical success in treating specific cancer types. However, challenges remain, including resistance to kinase inhibitors, off-target effects, and the need for better patient stratification. This review provides a comprehensive overview of the importance of CMGC kinases in cancer biology, their involvement in cellular signaling pathways, protein-protein interactions, and the current state of kinase inhibitors targeting these kinases. Furthermore, we discuss the challenges and future perspectives in targeting CMGC kinases for cancer therapy, including potential strategies to overcome resistance, the development of more selective inhibitors, and novel therapeutic approaches, such as targeting protein-protein interactions, exploiting synthetic lethality, and the evolution of omics in the study of the human kinome. As our understanding of the molecular mechanisms and protein-protein interactions involving CMGC kinases expands, so too will the opportunities for the development of more selective and effective therapeutic strategies for cancer treatment.
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Affiliation(s)
- Iftekhar Chowdhury
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Giovanna Dashi
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
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3
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Zheng K, Ren Z, Wang Y. Serine-arginine protein kinases and their targets in viral infection and their inhibition. Cell Mol Life Sci 2023; 80:153. [PMID: 37198350 PMCID: PMC10191411 DOI: 10.1007/s00018-023-04808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Accumulating evidence has consolidated the interaction between viral infection and host alternative splicing. Serine-arginine (SR) proteins are a class of highly conserved splicing factors critical for the spliceosome maturation, alternative splicing and RNA metabolism. Serine-arginine protein kinases (SRPKs) are important kinases that specifically phosphorylate SR proteins to regulate their distribution and activities in the central pre-mRNA splicing and other cellular processes. In addition to the predominant SR proteins, other cytoplasmic proteins containing a serine-arginine repeat domain, including viral proteins, have been identified as substrates of SRPKs. Viral infection triggers a myriad of cellular events in the host and it is therefore not surprising that viruses explore SRPKs-mediated phosphorylation as an important regulatory node in virus-host interactions. In this review, we briefly summarize the regulation and biological function of SRPKs, highlighting their involvement in the infection process of several viruses, such as viral replication, transcription and capsid assembly. In addition, we review the structure-function relationships of currently available inhibitors of SRPKs and discuss their putative use as antivirals against well-characterized viruses or newly emerging viruses. We also highlight the viral proteins and cellular substrates targeted by SRPKs as potential antiviral therapeutic candidates.
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Affiliation(s)
- Kai Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518055, China.
| | - Zhe Ren
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
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4
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ElHady AK, El-Gamil DS, Abadi AH, Abdel-Halim M, Engel M. An overview of cdc2-like kinase 1 (Clk1) inhibitors and their therapeutic indications. Med Res Rev 2023; 43:343-398. [PMID: 36262046 DOI: 10.1002/med.21928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/07/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Over the past decade, Clk1 has been identified as a promising target for the treatment of various diseases, in which deregulated alternative splicing plays a role. First small molecules targeting Clk1 are in clinical trials for the treatment of solid cancer, where variants of oncogenic proteins derived from alternative splicing promote tumor progression. Since many infectious pathogens hi-jack the host cell's splicing machinery to ensure efficient replication, further indications in this area are under investigation, such as Influenza A, HIV-1 virus, and Trypanosoma infections, and more will likely be discovered in the future. In addition, Clk1 was found to contribute to the progression of Alzheimer's disease through causing an imbalance of tau splicing products. Interestingly, homozygous Clk1 knockout mice showed a rather mild phenotype, opposed to what might be expected in view of the profound role of Clk1 in alternative splicing. A major drawback of most Clk1 inhibitors is their insufficient selectivity; in particular, Dyrk kinases and haspin were frequently identified as off-targets, besides the other Clk isoforms. Only few inhibitors were shown to be selective over Dyrk1A and haspin, whereas no Clk1 inhibitor so far achieved selectivity over the Clk4 isoform. In this review, we carefully compiled all Clk1 inhibitors from the scientific literature and summarized their structure-activity relationships (SAR). In addition, we critically discuss the available selectivity data and describe the inhibitor's efficacy in cellular models, if reported. Thus, we provide a comprehensive overview on the current state of Clk1 drug discovery and highlight the most promising chemotypes.
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Affiliation(s)
- Ahmed K ElHady
- Department of Organic and Pharmaceutical Chemistry, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Dalia S El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.,Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Matthias Engel
- Department of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
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5
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Discovery of novel 5-methoxybenzothiophene hydrazides as metabolically stable Clk1 inhibitors with high potency and unprecedented Clk1 isoenzyme selectivity. Eur J Med Chem 2023; 247:115019. [PMID: 36580731 DOI: 10.1016/j.ejmech.2022.115019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Clk1 kinase is a key modulator of the pre-mRNA alternative splicing machinery which has been proposed as a promising target for treatment of various tumour types, Duchenne's muscular dystrophy and viral infections such as HIV-1 and influenza. Most reported Clk1 inhibitors showed significant co-inhibition of Clk2 and Clk4 in particular, which limits their usefulness for deciphering the individual roles of the Clk1 isoform in physiology and disease. Herein, we present a new 5-methoxybenzothiophene scaffold, enabling for the first time selective inhibition of Clk1 even among the isoenzymes. The 3,5-difluorophenyl and 3,5-dichlorophenyl derivatives 26a and 27a (Clk1 IC50 = 1.4 and 1.7 nM, respectively) showed unprecedented selectivity factors of 15 and 8 over Clk4, and selectivity factors of 535 and 84 over Clk2. Furthermore, 26a and 27a exhibited good growth inhibitory activity in T24 cancer cells and long metabolic half-lives of almost 1 and 6.4 h, respectively. The overall favorable profile of our new Clk1 inhibitors suggests that they may be used in in vivo disease models or as probes to unravel the physiological or pathogenic roles of the Clk1 isoenzyme.
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6
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Sun M, Jin Y, Zhang Y, Gregorich ZR, Ren J, Ge Y, Guo W. SR Protein Kinases Regulate the Splicing of Cardiomyopathy-Relevant Genes via Phosphorylation of the RSRSP Stretch in RBM20. Genes (Basel) 2022; 13:1526. [PMID: 36140694 PMCID: PMC9498672 DOI: 10.3390/genes13091526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: RNA binding motif 20 (RBM20) regulates mRNA splicing specifically in muscle tissues. Missense mutations in the arginine/serine (RS) domain of RBM20 lead to abnormal gene splicing and have been linked to severe dilated cardiomyopathy (DCM) in human patients and animal models. Interestingly, many of the reported DCM-linked missense mutations in RBM20 are in a highly conserved RSRSP stretch within the RS domain. Recently, it was found that the two Ser residues within this stretch are constitutively phosphorylated, yet the identity of the kinase(s) responsible for phosphorylating these residues, as well as the function of RSRSP phosphorylation, remains unknown. (2) Methods: The ability of three known SR protein kinases (SRPK1, CLK1, and AKT2) to phosphorylate the RBM20 RSRSP stretch and regulate target gene splicing was evaluated by using both in vitro and in vivo approaches. (3) Results: We found that all three kinases phosphorylated S638 and S640 in the RSRSP stretch and regulated RBM20 target gene splicing. While SRPK1 and CLK1 were both capable of directly phosphorylating the RS domain in RBM20, whether AKT2-mediated control of the RS domain phosphorylation is direct or indirect could not be determined. (4) Conclusions: Our results indicate that SR protein kinases regulate the splicing of a cardiomyopathy-relevant gene by modulating phosphorylation of the RSRSP stretch in RBM20. These findings suggest that SR protein kinases may be potential targets for the treatment of RBM20 cardiomyopathy.
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Affiliation(s)
- Mingming Sun
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yanghai Zhang
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachery R Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Ren
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H. Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. J Cell Biol 2022; 221:212888. [PMID: 34854870 PMCID: PMC8647360 DOI: 10.1083/jcb.202104134] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/12/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In eukaryotic nuclei, most genes are transcribed by RNA polymerase II (RNAP2), whose regulation is a key to understanding the genome and cell function. RNAP2 has a long heptapeptide repeat (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), and Ser2 is phosphorylated on an elongation form. To detect RNAP2 Ser2 phosphorylation (RNAP2 Ser2ph) in living cells, we developed a genetically encoded modification-specific intracellular antibody (mintbody) probe. The RNAP2 Ser2ph-mintbody exhibited numerous foci, possibly representing transcription “factories,” and foci were diminished during mitosis and in a Ser2 kinase inhibitor. An in vitro binding assay using phosphopeptides confirmed the mintbody’s specificity. RNAP2 Ser2ph-mintbody foci were colocalized with proteins associated with elongating RNAP2 compared with factors involved in the initiation. These results support the view that mintbody localization represents the sites of RNAP2 Ser2ph in living cells. RNAP2 Ser2ph-mintbody foci showed constrained diffusional motion like chromatin, but they were more mobile than DNA replication domains and p300-enriched foci, suggesting that the elongating RNAP2 complexes are separated from more confined chromatin domains.
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Affiliation(s)
- Satoshi Uchino
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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8
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The Thiazole-5-Carboxamide GPS491 Inhibits HIV-1, Adenovirus, and Coronavirus Replication by Altering RNA Processing/Accumulation. Viruses 2021; 14:v14010060. [PMID: 35062264 PMCID: PMC8779516 DOI: 10.3390/v14010060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Medicinal chemistry optimization of a previously described stilbene inhibitor of HIV-1, 5350150 (2-(2-(5-nitro-2-thienyl)vinyl)quinoline), led to the identification of the thiazole-5-carboxamide derivative (GPS491), which retained potent anti-HIV-1 activity with reduced toxicity. In this report, we demonstrate that the block of HIV-1 replication by GPS491 is accompanied by a drastic inhibition of viral gene expression (IC50 ~ 0.25 µM), and alterations in the production of unspliced, singly spliced, and multiply spliced HIV-1 RNAs. GPS491 also inhibited the replication of adenovirus and multiple coronaviruses. Low µM doses of GPS491 reduced adenovirus infectious yield ~1000 fold, altered virus early gene expression/viral E1A RNA processing, blocked viral DNA amplification, and inhibited late (hexon) gene expression. Loss of replication of multiple coronaviruses (229E, OC43, SARS-CoV2) upon GPS491 addition was associated with the inhibition of viral structural protein expression and the formation of virus particles. Consistent with the observed changes in viral RNA processing, GPS491 treatment induced selective alterations in the accumulation/phosphorylation/function of splicing regulatory SR proteins. Our study establishes that a compound that impacts the activity of cellular factors involved in RNA processing can prevent the replication of several viruses with minimal effect on cell viability.
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9
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Tahtouh T, Durieu E, Villiers B, Bruyère C, Nguyen TL, Fant X, Ahn KH, Khurana L, Deau E, Lindberg MF, Sévère E, Miege F, Roche D, Limanton E, L'Helgoual'ch JM, Burgy G, Guiheneuf S, Herault Y, Kendall DA, Carreaux F, Bazureau JP, Meijer L. Structure-Activity Relationship in the Leucettine Family of Kinase Inhibitors. J Med Chem 2021; 65:1396-1417. [PMID: 34928152 DOI: 10.1021/acs.jmedchem.1c01141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The protein kinase DYRK1A is involved in Alzheimer's disease, Down syndrome, diabetes, viral infections, and leukemia. Leucettines, a family of 2-aminoimidazolin-4-ones derived from the marine sponge alkaloid Leucettamine B, have been developed as pharmacological inhibitors of DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases). We report here on the synthesis and structure-activity relationship (SAR) of 68 Leucettines. Leucettines were tested on 11 purified kinases and in 5 cellular assays: (1) CLK1 pre-mRNA splicing, (2) Threonine-212-Tau phosphorylation, (3) glutamate-induced cell death, (4) autophagy and (5) antagonism of ligand-activated cannabinoid receptor CB1. The Leucettine SAR observed for DYRK1A is essentially identical for CLK1, CLK4, DYRK1B, and DYRK2. DYRK3 and CLK3 are less sensitive to Leucettines. In contrast, the cellular SAR highlights correlations between inhibition of specific kinase targets and some but not all cellular effects. Leucettines deserve further development as potential therapeutics against various diseases on the basis of their molecular targets and cellular effects.
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Affiliation(s)
- Tania Tahtouh
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,CNRS, 'Protein Phosphorylation and Human Disease' Group, Station Biologique De Roscoff, Place G. Teissier, Bp 74, 29682 Roscoff, Bretagne, France.,College Of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Emilie Durieu
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,CNRS, 'Protein Phosphorylation and Human Disease' Group, Station Biologique De Roscoff, Place G. Teissier, Bp 74, 29682 Roscoff, Bretagne, France
| | - Benoît Villiers
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Céline Bruyère
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Thu Lan Nguyen
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,Institut De Génétique Et De Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, Université de Strasbourg, CNRS UMR7104 & INSERM U964, 67400 Illkirch, France.,Laboratory of Molecular & Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, New York 10021-6399, United States
| | - Xavier Fant
- CNRS, 'Protein Phosphorylation and Human Disease' Group, Station Biologique De Roscoff, Place G. Teissier, Bp 74, 29682 Roscoff, Bretagne, France
| | - Kwang H Ahn
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, Connecticut 06269, United States
| | - Leepakshi Khurana
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, Connecticut 06269, United States
| | - Emmanuel Deau
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Mattias F Lindberg
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Elodie Sévère
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Frédéric Miege
- Edelris, Bâtiment Bioserra 1, 60 avenue Rockefeller, 69008 Lyon, France
| | - Didier Roche
- Edelris, Bâtiment Bioserra 1, 60 avenue Rockefeller, 69008 Lyon, France
| | - Emmanuelle Limanton
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Jean-Martial L'Helgoual'ch
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Guillaume Burgy
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France.,Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Solène Guiheneuf
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Yann Herault
- Institut De Génétique Et De Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, Université de Strasbourg, CNRS UMR7104 & INSERM U964, 67400 Illkirch, France
| | - Debra A Kendall
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Storrs, Connecticut 06269, United States
| | - François Carreaux
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Jean-Pierre Bazureau
- Institut des Sciences Chimiques de Rennes ISCR-UMR CNRS 6226, Université de Rennes 1, Campus de Beaulieu, Bât. 10A, CS 74205, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France
| | - Laurent Meijer
- Manros Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, Bretagne, France
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10
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Pastor F, Shkreta L, Chabot B, Durantel D, Salvetti A. Interplay Between CMGC Kinases Targeting SR Proteins and Viral Replication: Splicing and Beyond. Front Microbiol 2021; 12:658721. [PMID: 33854493 PMCID: PMC8040976 DOI: 10.3389/fmicb.2021.658721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/04/2021] [Indexed: 12/27/2022] Open
Abstract
Protein phosphorylation constitutes a major post-translational modification that critically regulates the half-life, intra-cellular distribution, and activity of proteins. Among the large number of kinases that compose the human kinome tree, those targeting RNA-binding proteins, in particular serine/arginine-rich (SR) proteins, play a major role in the regulation of gene expression by controlling constitutive and alternative splicing. In humans, these kinases belong to the CMGC [Cyclin-dependent kinases (CDKs), Mitogen-activated protein kinases (MAPKs), Glycogen synthase kinases (GSKs), and Cdc2-like kinases (CLKs)] group and several studies indicate that they also control viral replication via direct or indirect mechanisms. The aim of this review is to describe known and emerging activities of CMGC kinases that share the common property to phosphorylate SR proteins, as well as their interplay with different families of viruses, in order to advance toward a comprehensive knowledge of their pro- or anti-viral phenotype and better assess possible translational opportunities.
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Affiliation(s)
- Florentin Pastor
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
| | - Lulzim Shkreta
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - David Durantel
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
| | - Anna Salvetti
- International Center for Infectiology Research (CIRI), INSERM U1111, CNRS UMR5308, Université de Lyon (UCBL1), Lyon, France
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11
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Masaki S, Kabuto T, Suzuki K, Kataoka N. Multiple nuclear localization sequences in SRSF4 protein. Genes Cells 2020; 25:327-333. [PMID: 32050040 DOI: 10.1111/gtc.12756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 11/29/2022]
Abstract
SRSF4 is one of the members of serine-/arginine (SR)-rich protein family involved in both constitutive and alternative splicing. SRSF4 is localized in the nucleus with speckled pattern, but its nuclear localization signal was not determined. Here, we have identified nuclear localization signals (NLSs) of SRSF4 by using a pyruvate kinase fusion system. As expected, arginine-/serine (RS)-rich domain of SRSF4 confers nuclear localization activity when it is fused to PK protein. We then further delineated the minimum sequences for nuclear localization in RS domain of SRSF4. Surprisingly, RS-rich region does not always have a nuclear localization activity. In addition, basic amino acid stretches that resemble to classical-type NLSs were identified. These results strongly suggest that SRSF4 protein uses two different nuclear import pathways with multiple NLSs in RS domain.
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Affiliation(s)
- So Masaki
- Laboratory for Malignancy Control Research, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Laboratory of Molecular Medicinal Science, Department of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - Takafumi Kabuto
- Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan
| | - Kenji Suzuki
- Laboratory of Molecular Medicinal Science, Department of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - Naoyuki Kataoka
- Laboratory for Malignancy Control Research, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan.,Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
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12
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Zhu D, Xu S, Deyanat-Yazdi G, Peng SX, Barnes LA, Narla RK, Tran T, Mikolon D, Ning Y, Shi T, Jiang N, Raymon HK, Riggs JR, Boylan JF. Synthetic Lethal Strategy Identifies a Potent and Selective TTK and CLK1/2 Inhibitor for Treatment of Triple-Negative Breast Cancer with a Compromised G 1-S Checkpoint. Mol Cancer Ther 2018; 17:1727-1738. [PMID: 29866747 DOI: 10.1158/1535-7163.mct-17-1084] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/13/2018] [Accepted: 05/08/2018] [Indexed: 11/16/2022]
Abstract
Historically, phenotypic-based drug discovery has yielded a high percentage of novel drugs while uncovering new tumor biology. CC-671 was discovered using a phenotypic screen for compounds that preferentially induced apoptosis in triple-negative breast cancer cell lines while sparing luminal breast cancer cell lines. Detailed in vitro kinase profiling shows CC-671 potently and selectively inhibits two kinases-TTK and CLK2. Cellular mechanism of action studies demonstrate that CC-671 potently inhibits the phosphorylation of KNL1 and SRp75, direct TTK and CLK2 substrates, respectively. Furthermore, CC-671 causes mitotic acceleration and modification of pre-mRNA splicing leading to apoptosis, consistent with cellular TTK and CLK inhibition. Correlative analysis of genomic and potency data against a large panel of breast cancer cell lines identifies breast cancer cells with a dysfunctional G1-S checkpoint as more sensitive to CC-671, suggesting synthetic lethality between G1-S checkpoint and TTK/CLK2 inhibition. Furthermore, significant in vivo CC-671 efficacy was demonstrated in two cell line-derived and one patient tumor-derived xenograft models of triple-negative breast cancer (TNBC) following weekly dosing. These findings are the first to demonstrate the unique inhibitory combination activity of a dual TTK/CLK2 inhibitor that preferably kills TNBC cells and shows synthetic lethality with a compromised G1-S checkpoint in breast cancer cell lines. On the basis of these data, CC-671 was moved forward for clinical development as a potent and selective TTK/CLK2 inhibitor in a subset of patients with TNBC. Mol Cancer Ther; 17(8); 1727-38. ©2018 AACR.
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Affiliation(s)
- Dan Zhu
- Department of Oncology Research, Celgene Corporation, San Diego, California.
| | - Shuichan Xu
- Department of Oncology Research, Celgene Corporation, San Diego, California
| | | | - Sophie X Peng
- Department of Pharmacology, Celgene Corporation, San Diego, California
| | - Leo A Barnes
- Department of Pharmacology, Celgene Corporation, San Diego, California
| | | | - Tam Tran
- Department of Oncology Research, Celgene Corporation, San Diego, California
| | - David Mikolon
- Department of Oncology Research, Celgene Corporation, San Diego, California
| | - Yuhong Ning
- Informatics and Knowledge Utilization Department, Celgene Corporation, San Diego, California
| | - Tao Shi
- Informatics and Knowledge Utilization Department, Celgene Corporation, San Diego, California
| | - Ning Jiang
- Department of Oncology Research, Celgene Corporation, San Diego, California
| | - Heather K Raymon
- Department of Pharmacology, Celgene Corporation, San Diego, California
| | - Jennifer R Riggs
- Department of Chemistry, Celgene Corporation, San Diego, California
| | - John F Boylan
- Department of Oncology Research, Celgene Corporation, San Diego, California
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13
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Riggs JR, Nagy M, Elsner J, Erdman P, Cashion D, Robinson D, Harris R, Huang D, Tehrani L, Deyanat-Yazdi G, Narla RK, Peng X, Tran T, Barnes L, Miller T, Katz J, Tang Y, Chen M, Moghaddam MF, Bahmanyar S, Pagarigan B, Delker S, LeBrun L, Chamberlain PP, Calabrese A, Canan SS, Leftheris K, Zhu D, Boylan JF. The Discovery of a Dual TTK Protein Kinase/CDC2-Like Kinase (CLK2) Inhibitor for the Treatment of Triple Negative Breast Cancer Initiated from a Phenotypic Screen. J Med Chem 2017; 60:8989-9002. [PMID: 28991472 DOI: 10.1021/acs.jmedchem.7b01223] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Triple negative breast cancer (TNBC) remains a serious unmet medical need with discouragingly high relapse rates. We report here the synthesis and structure-activity relationship (SAR) of a novel series of 2,4,5-trisubstituted-7H-pyrrolo[2,3-d]pyrimidines with potent activity against TNBC tumor cell lines. These compounds were discovered from a TNBC phenotypic screen and possess a unique dual inhibition profile targeting TTK (mitotic exit) and CLK2 (mRNA splicing). Design and optimization, driven with a TNBC tumor cell assay, identified potent and selective compounds with favorable in vitro and in vivo activity profiles and good iv PK properties. This cell-based driven SAR produced compounds with strong single agent in vivo efficacy in multiple TNBC xenograft models without significant body weight loss. These data supported the nomination of CC-671 into IND-enabling studies as a single agent TNBC therapy.
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Affiliation(s)
- Jennifer R Riggs
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Mark Nagy
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Jan Elsner
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Paul Erdman
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Dan Cashion
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Dale Robinson
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Roy Harris
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Dehua Huang
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Lida Tehrani
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Gordafaried Deyanat-Yazdi
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Rama Krishna Narla
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Xiaohui Peng
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Tam Tran
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Leo Barnes
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Terra Miller
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Jason Katz
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Yang Tang
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Ming Chen
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Mehran F Moghaddam
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Sogole Bahmanyar
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Barbra Pagarigan
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Silvia Delker
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Laurie LeBrun
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Philip P Chamberlain
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Andrew Calabrese
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Stacie S Canan
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Katerina Leftheris
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - Dan Zhu
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
| | - John F Boylan
- Celgene Corporation , 10300 Campus Pointe Drive, Suite 100, San Diego, California 92121, United States
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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15
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Sako Y, Ninomiya K, Okuno Y, Toyomoto M, Nishida A, Koike Y, Ohe K, Kii I, Yoshida S, Hashimoto N, Hosoya T, Matsuo M, Hagiwara M. Development of an orally available inhibitor of CLK1 for skipping a mutated dystrophin exon in Duchenne muscular dystrophy. Sci Rep 2017; 7:46126. [PMID: 28555643 PMCID: PMC5448077 DOI: 10.1038/srep46126] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 03/13/2017] [Indexed: 12/27/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal progressive muscle-wasting disease. Various attempts are underway to convert severe DMD to a milder phenotype by modulating the splicing of the dystrophin gene and restoring its expression. In our previous study, we reported TG003, an inhibitor of CDC2-like kinase 1 (CLK1), as a splice-modifying compound for exon-skipping therapy; however, its metabolically unstable feature hinders clinical application. Here, we show an orally available inhibitor of CLK1, named TG693, which promoted the skipping of the endogenous mutated exon 31 in DMD patient-derived cells and increased the production of the functional exon 31-skipped dystrophin protein. Oral administration of TG693 to mice inhibited the phosphorylation of serine/arginine-rich proteins, which are the substrates of CLK1, and modulated pre-mRNA splicing in the skeletal muscle. Thus, TG693 is a splicing modulator for the mutated exon 31 of the dystrophin gene in vivo, possibly possessing therapeutic potential for DMD patients.
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Affiliation(s)
- Yukiya Sako
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kensuke Ninomiya
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yukiko Okuno
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masayasu Toyomoto
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsushi Nishida
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Yuka Koike
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Ohe
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Isao Kii
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naohiro Hashimoto
- Department of Regenerative Medicine, National Center for Geriatrics and Gerontology, Oobu, Japan
| | - Takamitsu Hosoya
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masafumi Matsuo
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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16
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Suppression of Adenovirus Replication by Cardiotonic Steroids. J Virol 2017; 91:JVI.01623-16. [PMID: 27881644 DOI: 10.1128/jvi.01623-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
The dependence of adenovirus on the host pre-RNA splicing machinery for expression of its complete genome potentially makes it vulnerable to modulators of RNA splicing, such as digoxin and digitoxin. Both drugs reduced the yields of four human adenoviruses (HAdV-A31, -B35, and -C5 and a species D conjunctivitis isolate) by at least 2 to 3 logs by affecting one or more steps needed for genome replication. Immediate early E1A protein levels are unaffected by the drugs, but synthesis of the delayed protein E4orf6 and the major late capsid protein hexon is compromised. Quantitative reverse transcription-PCR (qRT-PCR) analyses revealed that both drugs altered E1A RNA splicing (favoring the production of 13S over 12S RNA) early in infection and partially blocked the transition from 12S and 13S to 9S RNA at late stages of virus replication. Expression of multiple late viral protein mRNAs was lost in the presence of either drug, consistent with the observed block in viral DNA replication. The antiviral effect was dependent on the continued presence of the drug and was rapidly reversible. RIDK34, a derivative of convallotoxin, although having more potent antiviral activity, did not show an improved selectivity index. All three drugs reduced metabolic activity to some degree without evidence of cell death. By blocking adenovirus replication at one or more steps beyond the onset of E1A expression and prior to genome replication, digoxin and digitoxin show potential as antiviral agents for treatment of serious adenovirus infections. Furthermore, understanding the mechanism(s) by which digoxin and digitoxin inhibit adenovirus replication will guide the development of novel antiviral therapies. IMPORTANCE Despite human adenoviruses being a common and, in some instances, life-threating pathogen in humans, there are few well-tolerated therapies. In this report, we demonstrate that two cardiotonic steroids already in use in humans, digoxin and digitoxin, are potent inhibitors of multiple adenovirus species. A synthetic derivative of the cardiotonic steroid convallotoxin was even more potent than digoxin and digitoxin when tested with HAdV-C5. These drugs alter the cascade of adenovirus gene expression, acting after initiation of early gene expression to block viral DNA replication and synthesis of viral structural proteins. These findings validate a novel approach to treating adenovirus infections through the modulation of host cell processes.
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17
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Nishida A, Oda A, Takeuchi A, Lee T, Awano H, Hashimoto N, Takeshima Y, Matsuo M. Staurosporine allows dystrophin expression by skipping of nonsense-encoding exon. Brain Dev 2016; 38:738-45. [PMID: 27021413 DOI: 10.1016/j.braindev.2016.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 03/13/2016] [Accepted: 03/17/2016] [Indexed: 01/16/2023]
Abstract
BACKGROUND Antisense oligonucleotides that induce exon skipping have been nominated as the most plausible treatment method for dystrophin expression in dystrophin-deficient Duchenne muscular dystrophy. Considering this therapeutic efficiency, small chemical compounds that can enable exon skipping have been highly awaited. In our previous report, a small chemical kinase inhibitor, TG003, was shown to enhance dystrophin expression by enhancing exon skipping. PURPOSE Staurosporine (STS), a small chemical broad kinase inhibitor, was examined for enhanced skipping of a nonsense-encoding dystrophin exon. METHODS STS was added to culture medium of HeLa cells transfected with minigenes expressing wild-type or mutated exon 31 with c.4303G>T (p.Glu1435X), and the resulting mRNAs were analyzed by RT-PCR amplification. Dystrophin mRNA and protein were analyzed in muscle cells treated with STS by RT-PCR and western blotting, respectively. RESULTS STS did not alter splicing of the wild-type minigene. In the mutated minigene, STS increased the exon 31-skipped product. A combination of STS and TG003 did not significantly increase the exon 31-skipped product. STS enhanced skipping of exon 4 of the CDC-like kinase 1 gene, whereas TG003 suppressed it. Two STS analogs with selective kinase inhibitory activity did not enhance the mutated exon 31 skipping. When immortalized muscle cells with c.4303G>T in the dystrophin gene were treated with STS, skipping of the mutated exon 31 and dystrophin expression was enhanced. CONCLUSIONS STS, a broad kinase inhibitor, was shown to enhance skipping of the mutated exon 31 and dystrophin expression, but selective kinase inhibitors did not.
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Affiliation(s)
- Atsushi Nishida
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Japan; Biopharmaceutical Innovation Research Department, Research Institute, Research Division, JCR Pharmaceuticals Co. Ltd., Japan
| | - Ayaka Oda
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Japan; Department of Clinical Pharmacology, Kobe Pharmaceutical University, Japan
| | - Atsuko Takeuchi
- Department of Clinical Pharmacology, Kobe Pharmaceutical University, Japan
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Japan
| | - Naohiro Hashimoto
- Department of Regenerative Medicine, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, Japan
| | | | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Japan.
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18
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Nuclear protein kinase CLK1 uses a non-traditional docking mechanism to select physiological substrates. Biochem J 2015; 472:329-38. [PMID: 26443864 DOI: 10.1042/bj20150903] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/06/2015] [Indexed: 01/22/2023]
Abstract
Phosphorylation-dependent cell communication requires enzymes that specifically recognize key proteins in a sea of similar, competing substrates. The protein kinases achieve this goal by utilizing docking grooves in the kinase domain or heterologous protein adaptors to reduce 'off pathway' targeting. We now provide evidence that the nuclear protein kinase CLK1 (cell division cycle2-like kinase 1) important for splicing regulation departs from these classic paradigms by using a novel self-association mechanism. The disordered N-terminus of CLK1 induces oligomerization, a necessary event for targeting its physiological substrates the SR protein (splicing factor containing a C-terminal RS domain) family of splicing factors. Increasing the CLK1 concentration enhances phosphorylation of the splicing regulator SRSF1 (SR protein splicing factor 1) compared with the general substrate myelin basic protein (MBP). In contrast, removal of the N-terminus or dilution of CLK1 induces monomer formation and reverses this specificity. CLK1 self-association also occurs in the nucleus, is induced by the N-terminus and is important for localization of the kinase in sub-nuclear compartments known as speckles. These findings present a new picture of substrate recognition for a protein kinase in which an intrinsically disordered domain is used to capture physiological targets with similar disordered domains in a large oligomeric complex while discriminating against non-physiological targets.
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Sakuma M, Iida K, Hagiwara M. Deciphering targeting rules of splicing modulator compounds: case of TG003. BMC Mol Biol 2015; 16:16. [PMID: 26400733 PMCID: PMC4580995 DOI: 10.1186/s12867-015-0044-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired effect of genetic mutations. However, the knowledge and tools to understand factors contributing to splicing modulator compound sensitivity have been lacking. Our goal was to establish a method to characterize sequence features found in compound sensitive exons. Results Here we developed a comparative transcriptomic approach to explore features that make an exon sensitive to a chemical compound. In this study, we chose TG003, a potential drug for Duchenne muscular dystrophy, and performed RNA-sequencing on samples from human and mouse skeletal muscle cells, with and without TG003 treatments. We compared TG003 responsiveness between homologous exon pairs and identified 21 pairs in which human exons were skip-enhanced but not mouse exons. We compared the sequence features; splice site scores, number of splicing factor binding sites, and properties of branch sequence and polypyrimidine tracts, and found that polypyrimidine tracts were stronger (longer stretches and richer content of consecutive polypyrimidine) in the mouse TG003 insensitive exons. We also compared the features between TG003 skip-enhanced and insensitive exons within the species, and discovered that human TG003 skip-enhanced exons were shorter and had less splicing factor binding sites than the group of human TG003 insensitive exons. Mouse insensitive exons homologous to human TG003 skip-enhanced exons shared these properties. Our results suggested that these features are prerequisites for TG003 skip-enhanced exons and weak polypyrimidine tracts are defining features, which were supported by a decision tree analysis on all cassette exons in human. Conclusions In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0044-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maki Sakuma
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan. .,Medical Research Support Center, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
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20
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Splicing Regulators and Their Roles in Cancer Biology and Therapy. BIOMED RESEARCH INTERNATIONAL 2015; 2015:150514. [PMID: 26273588 PMCID: PMC4529883 DOI: 10.1155/2015/150514] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 03/10/2015] [Accepted: 04/01/2015] [Indexed: 12/17/2022]
Abstract
Alternative splicing allows cells to expand the encoding potential of their genomes. In this elegant mechanism, a single gene can yield protein isoforms with even antagonistic functions depending on the cellular physiological context. Alterations in splicing regulatory factors activity in cancer cells, however, can generate an abnormal protein expression pattern that promotes growth, survival, and other processes, which are relevant to tumor biology. In this review, we discuss dysregulated alternative splicing events and regulatory factors that impact pathways related to cancer. The SR proteins and their regulatory kinases SRPKs and CLKs have been frequently found altered in tumors and are examined in more detail. Finally, perspectives that support splicing machinery as target for the development of novel anticancer therapies are discussed.
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21
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Conserved proline-directed phosphorylation regulates SR protein conformation and splicing function. Biochem J 2015; 466:311-22. [PMID: 25529026 DOI: 10.1042/bj20141373] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The alternative splicing of human genes is dependent on SR proteins, a family of essential splicing factors whose name derives from a signature C-terminal domain rich in arginine-serine dipeptide repeats (RS domains). Although the SRPKs (SR-specific protein kinases) phosphorylate these repeats, RS domains also contain prolines with flanking serines that are phosphorylated by a second family of protein kinases known as the CLKs (Cdc2-like kinases). The role of specific serine-proline phosphorylation within the RS domain has been difficult to assign since CLKs also phosphorylate arginine-serine dipeptides and, thus, display overlapping residue specificities with the SRPKs. In the present study, we address the effects of discrete serine-proline phosphorylation on the conformation and cellular function of the SR protein SRSF1 (SR protein splicing factor 1). Using chemical tagging and dephosphorylation experiments, we show that modification of serine-proline dipeptides broadly amplifies the conformational ensemble of SRSF1. The induction of these new structural forms triggers SRSF1 mobilization in the nucleus and alters its binding mechanism to an exonic splicing enhancer in precursor mRNA. These physical events correlate with changes in the alternative splicing of over 100 human genes based on a global splicing assay. Overall, these studies draw a direct causal relationship between a specific type of chemical modification in an SR protein and the regulation of alternative gene splicing programmes.
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Boutz PL, Bhutkar A, Sharp PA. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev 2015; 29:63-80. [PMID: 25561496 PMCID: PMC4281565 DOI: 10.1101/gad.247361.114] [Citation(s) in RCA: 275] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts. Boutz et al. identified thousands of these “detained” introns (DIs) in human and mouse cell lines as well as the adult mouse liver. Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs, altering transcript pools of >300 genes. Srsf4 regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as “detained” introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs—including those in Mdm4, a negative regulator of p53—was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression.
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Affiliation(s)
- Paul L Boutz
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Arjun Bhutkar
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Phillip A Sharp
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Schmitt C, Miralinaghi P, Mariano M, Hartmann RW, Engel M. Hydroxybenzothiophene Ketones Are Efficient Pre-mRNA Splicing Modulators Due to Dual Inhibition of Dyrk1A and Clk1/4. ACS Med Chem Lett 2014; 5:963-7. [PMID: 25221649 DOI: 10.1021/ml500059y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/14/2014] [Indexed: 12/20/2022] Open
Abstract
Dysregulated usage of pre-mRNA splicing sites contributes to the progression of cancer, neurodegenerative diseases, and viral infections. Serine/arginine-rich (SR) proteins play major roles in the splice site recognition and are largely regulated by phosphorylation. This provides an option for the pharmacological correction of aberrant splicing by inhibiting the relevant kinases. Cdc2-like kinases (Clks) and dual specificity tyrosine phosphorylation-regulated kinases (Dyrks) were both reported to phosphorylate numerous SR proteins in vitro and in vivo. In this study, we describe the discovery of new selective dual Clk/Dyrk1A/1B inhibitors, which are able to modulate alternative pre-mRNA splicing of model gene transcripts in cells with submicromolar potencies. The optimization process yielded a dual Clk and Dyrk inhibitor with exceptionally high ligand efficiency. Our results suggested that dual inhibition of both Clk1 and Dyrk1A increased the efficacy of pre-mRNA splicing modulation.
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Affiliation(s)
- Christian Schmitt
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
| | - Parisa Miralinaghi
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
| | - Marica Mariano
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
- Department
of Drug Design and Optimization, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Campus C2.3, D-66123 Saarbrücken, Germany
| | - Matthias Engel
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
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24
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Fant X, Durieu E, Chicanne G, Payrastre B, Sbrissa D, Shisheva A, Limanton E, Carreaux F, Bazureau JP, Meijer L. cdc-like/dual-specificity tyrosine phosphorylation-regulated kinases inhibitor leucettine L41 induces mTOR-dependent autophagy: implication for Alzheimer's disease. Mol Pharmacol 2014; 85:441-50. [PMID: 24366666 PMCID: PMC6067634 DOI: 10.1124/mol.113.090837] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/23/2013] [Indexed: 12/26/2022] Open
Abstract
Leucettines, a family of pharmacological inhibitors of dual-specificity tyrosine phosphorylation regulated kinases and cdc-like kinases (CLKs), are currently under investigation for their potential therapeutic application to Down syndrome and Alzheimer's disease. We here report that leucettine L41 triggers bona fide autophagy in osteosarcoma U-2 OS cells and immortalized mouse hippocampal HT22 cells, characterized by microtubule-associated protein light chain 3 membrane translocation and foci formation. Leucettine L41-triggered autophagy requires the Unc-51-like kinase and is sensitive to the phosphatidylinositol 3-kinase (PI3K) inhibitors wortmannin and 3-methyladenine, suggesting that it acts through the mammalian target of rapamycin (mTOR)/PI3K-dependent pathway. Leucettine L41 does not act by modifying the autophagic flux of vesicles. Leucettine L41-induced autophagy correlates best with inhibition of CLKs. Leucettine L41 modestly inhibited phosphatidylinositol-3-phosphate 5-kinase, FYVE domain-containing activity as tested both in vitro and in vivo, which may also contribute to autophagy induction. Altogether these results demonstrate that leucettines can activate the autophagic mTOR/PI3K pathway, a characteristic that may turn advantageous in the context of Alzheimer's disease treatment.
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Affiliation(s)
- Xavier Fant
- Centre National de la Recherche Scientifique (CNRS), USR3151, "Protein Phosphorylation and Human Disease," Station Biologique, Roscoff cedex, France (X.F., E.D.); Institut National de la Santé et de la Recherche Médicale/Université Paul Sabatier Unité Mixte de Recherche (UMR) 1048, "Production et fonctions plaquettaires: signalisation et phosphoinositides" group, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Toulouse cedex, France (G.C., B.P.); Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan (D.S., A.S.); Laboratoire Sciences Chimiques de Rennes, UMR CNRS 6226, Groupe Ingénierie Chimique et Molécules pour le Vivant (ICMV), Université de Rennes, Campus de Beaulieu, Rennes cedex, France (E.L., F.C., J.-P.B.); and ManRos Therapeutics, Perharidy Research Center, Roscoff, Bretagne, France (L.M.)
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25
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Coombs TC, Tanega C, Shen M, Wang JL, Auld DS, Gerritz SW, Schoenen FJ, Thomas CJ, Aubé J. Small-molecule pyrimidine inhibitors of the cdc2-like (Clk) and dual specificity tyrosine phosphorylation-regulated (Dyrk) kinases: development of chemical probe ML315. Bioorg Med Chem Lett 2013; 23:3654-61. [PMID: 23642479 PMCID: PMC3664191 DOI: 10.1016/j.bmcl.2013.02.096] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/21/2013] [Indexed: 01/17/2023]
Abstract
Substituted pyrimidine inhibitors of the Clk and Dyrk kinases have been developed, exploring structure-activity relationships around four different chemotypes. The most potent compounds have low-nanomolar inhibitory activity against Clk1, Clk2, Clk4, Dyrk1A and Dyrk1B. Kinome scans with 442 kinases using agents representing three of the chemotypes show these inhibitors to be highly selective for the Clk and Dyrk families. Further off-target pharmacological evaluation with ML315, the most selective agent, supports this conclusion.
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Affiliation(s)
- Thomas C Coombs
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, KS 66047, USA
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26
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Partitioning RS domain phosphorylation in an SR protein through the CLK and SRPK protein kinases. J Mol Biol 2013; 425:2894-909. [PMID: 23707382 DOI: 10.1016/j.jmb.2013.05.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/20/2013] [Indexed: 11/21/2022]
Abstract
SR proteins are essential splicing factors whose biological function is regulated through phosphorylation of their C-terminal RS domains. Prior studies have shown that cytoplasmic-nuclear translocalization of the SR protein SRSF1 is regulated by multisite phosphorylation of a long Arg-Ser repeat in the N-terminus of the RS domain while subnuclear localization is controlled by phosphorylation of a shorter Arg-Ser repeat along with several Ser-Pro dipeptides in the C-terminus of the RS domain. To better understand how these two kinases partition Arg-Ser versus Ser-Pro specificities, we monitored the phosphorylation of SRSF1 by CLK1 and SRPK1. Although SRPK1 initially binds at the center of the RS domain phosphorylating in an orderly, N-terminal direction, CLK1 makes widespread contacts in the RS domain and generates multiple enzyme-substrate complexes that induce a random addition mechanism. While SRPK1 rapidly phosphorylates N-terminal serines, SRPK1 and CLK1 display similar activities toward Arg-Ser repeats in the C-terminus, suggesting that these kinases may not separate function in a strict linear manner along the RS domain. CLK1 induces a unique gel shift in SRSF1 that is not the result of enhanced Arg-Ser phosphorylation but rather is the direct result of the phosphorylation of several Ser-Pro dipeptides. These prolines are important for binding and phosphorylation of the SR protein by CLK1 but not for the SRPK1-dependent reaction. The data establish a new view of SR protein regulation in which SRPK1 and CLK1 partition activities based on Ser-Pro versus Arg-Ser placement rather than on N- and C-terminal preferences along the RS domain.
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27
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Regulation of splicing by SR proteins and SR protein-specific kinases. Chromosoma 2013; 122:191-207. [PMID: 23525660 DOI: 10.1007/s00412-013-0407-z] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 12/21/2022]
Abstract
Genomic sequencing reveals similar but limited numbers of protein-coding genes in different genomes, which begs the question of how organismal diversities are generated. Alternative pre-mRNA splicing, a widespread phenomenon in higher eukaryotic genomes, is thought to provide a mechanism to increase the complexity of the proteome and introduce additional layers for regulating gene expression in different cell types and during development. Among a large number of factors implicated in the splicing regulation are the SR protein family of splicing factors and SR protein-specific kinases. Here, we summarize the rules for SR proteins to function as splicing regulators, which depend on where they bind in exons versus intronic regions, on alternative exons versus flanking competing exons, and on cooperative as well as competitive binding between different SR protein family members on many of those locations. We review the importance of cycles of SR protein phosphorylation/dephosphorylation in the splicing reaction with emphasis on the recent molecular insight into the role of SR protein phosphorylation in early steps of spliceosome assembly. Finally, we highlight recent discoveries of SR protein-specific kinases in transducing growth signals to regulate alternative splicing in the nucleus and the connection of both SR proteins and SR protein kinases to human diseases, particularly cancer.
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28
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Liu Y, Conaway L, Rutherford Bethard J, Al-Ayoubi AM, Thompson Bradley A, Zheng H, Weed SA, Eblen ST. Phosphorylation of the alternative mRNA splicing factor 45 (SPF45) by Clk1 regulates its splice site utilization, cell migration and invasion. Nucleic Acids Res 2013; 41:4949-62. [PMID: 23519612 PMCID: PMC3643583 DOI: 10.1093/nar/gkt170] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alternative mRNA splicing is a mechanism to regulate protein isoform expression and is regulated by alternative splicing factors. The alternative splicing factor 45 (SPF45) is overexpressed in cancer, although few biological effects of SPF45 are known, and few splicing targets have been identified. We previously showed that Extracellular Regulated Kinase 2 (ERK2) phosphorylation of SPF45 regulates cell proliferation and adhesion to fibronectin. In this work, we show that Cdc2-like kinase 1 (Clk1) phosphorylates SPF45 on eight serine residues. Clk1 expression enhanced, whereas Clk1 inhibition reduced, SPF45-induced exon 6 exclusion from Fas mRNA. Mutational analysis of the Clk1 phosphorylation sites on SPF45 showed both positive and negative regulation of splicing, with a net effect of inhibiting SPF45-induced exon 6 exclusion, correlating with reduced Fas mRNA binding. However, Clk1 enhanced SPF45 protein expression, but not mRNA expression, whereas inhibition of Clk1 increased SPF45 degradation through a proteasome-dependent pathway. Overexpression of SPF45 or a phospho-mimetic mutant, but not a phospho-inhibitory mutant, stimulated ovarian cancer cell migration and invasion, correlating with increased fibronectin expression, ERK activation and enhanced splicing and phosphorylation of full-length cortactin. Our results demonstrate for the first time that SPF45 overexpression enhances cell migration and invasion, dependent on biochemical regulation by Clk1.
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Affiliation(s)
- Yuying Liu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave, Charleston, SC 29425, USA
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29
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Tahtouh T, Elkins JM, Filippakopoulos P, Soundararajan M, Burgy G, Durieu E, Cochet C, Schmid RS, Lo DC, Delhommel F, Oberholzer AE, Pearl LH, Carreaux F, Bazureau JP, Knapp S, Meijer L. Selectivity, cocrystal structures, and neuroprotective properties of leucettines, a family of protein kinase inhibitors derived from the marine sponge alkaloid leucettamine B. J Med Chem 2012; 55:9312-30. [PMID: 22998443 DOI: 10.1021/jm301034u] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases) are implicated in the onset and development of Alzheimer's disease and Down syndrome. The marine sponge alkaloid leucettamine B was recently identified as an inhibitor of DYRKs/CLKs. Synthesis of analogues (leucettines) led to an optimized product, leucettine L41. Leucettines were cocrystallized with DYRK1A, DYRK2, CLK3, PIM1, and GSK-3β. The selectivity of L41 was studied by activity and interaction assays of recombinant kinases and affinity chromatography and competition affinity assays. These approaches revealed unexpected potential secondary targets such as CK2, SLK, and the lipid kinase PIKfyve/Vac14/Fig4. L41 displayed neuroprotective effects on glutamate-induced HT22 cell death. L41 also reduced amyloid precursor protein-induced cell death in cultured rat brain slices. The unusual multitarget selectivity of leucettines may account for their neuroprotective effects. This family of kinase inhibitors deserves further optimization as potential therapeutics against neurodegenerative diseases such as Alzheimer's disease.
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Affiliation(s)
- Tania Tahtouh
- CNRS, "Protein Phosphorylation & Human Disease" Group, Station Biologique, 29680 Roscoff, Bretagne, France
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30
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Ogawa Y, Hagiwara M. Challenges to congenital genetic disorders with “RNA-targeting” chemical compounds. Pharmacol Ther 2012; 134:298-305. [DOI: 10.1016/j.pharmthera.2012.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 01/24/2012] [Indexed: 11/16/2022]
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31
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Establishment of a Monitoring System to Detect Inhibition of mRNA Processing. Biosci Biotechnol Biochem 2012; 76:1248-51. [DOI: 10.1271/bbb.120226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Chemical treatment enhances skipping of a mutated exon in the dystrophin gene. Nat Commun 2011; 2:308. [PMID: 21556062 PMCID: PMC3113229 DOI: 10.1038/ncomms1306] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 04/11/2011] [Indexed: 12/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by a loss of the dystrophin protein. Control of dystrophin mRNA splicing to convert severe DMD to a milder phenotype is attracting much attention. Here we report a dystrophinopathy patient who has a point mutation in exon 31 of the dystrophin gene. Although the mutation generates a stop codon, a small amount of internally deleted, but functional, dystrophin protein is produced in the patient cells. An analysis of the mRNA reveals that the mutation promotes exon skipping and restores the open reading frame of dystrophin. Presumably, the mutation disrupts an exonic splicing enhancer and creates an exonic splicing silencer. Therefore, we searched for small chemicals that enhance exon skipping, and found that TG003 promotes the skipping of exon 31 in the endogenous dystrophin gene in a dose-dependent manner and increases the production of the dystrophin protein in the patient's cells. Duchenne muscular dystrophy is caused by a loss of the dystrophin gene, and control of dystrophin mRNA splicing could aid treatment of the disease. Nishida et al. show that a small molecule promotes skipping of exon 31 and increases production of a functional dystrophin protein in a patient.
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33
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Ninomiya K, Kataoka N, Hagiwara M. Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor. ACTA ACUST UNITED AC 2011; 195:27-40. [PMID: 21949414 PMCID: PMC3187705 DOI: 10.1083/jcb.201107093] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A nuclear pool of partially spliced Clk1/4 pre-mRNAs matures in response to stress and induces SR protein phosphorylation and activation. It has been assumed that premessenger ribonucleic acids (RNAs; pre-mRNAs) are spliced cotranscriptionally in the process of gene expression. However, in this paper, we report that splicing of Clk1/4 mRNAs is suspended in tissues and cultured cells and that intermediate forms retaining specific introns are abundantly pooled in the nucleus. Administration of the Cdc2-like kinase–specific inhibitor TG003 increased the level of Clk1/4 mature mRNAs by promoting splicing of the intron-retaining RNAs. Under stress conditions, splicing of general pre-mRNAs was inhibited by dephosphorylation of SR splicing factors, but exposure to stresses, such as heat shock and osmotic stress, promoted the maturation of Clk1/4 mRNAs. Clk1/4 proteins translated after heat shock catalyzed rephosphorylation of SR proteins, especially SRSF4 and SRSF10. These findings suggest that Clk1/4 expression induced by stress-responsive splicing serves to maintain the phosphorylation state of SR proteins.
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Affiliation(s)
- Kensuke Ninomiya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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34
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Debdab M, Carreaux F, Renault S, Soundararajan M, Fedorov O, Filippakopoulos P, Lozach O, Babault L, Tahtouh T, Baratte B, Ogawa Y, Hagiwara M, Eisenreich A, Rauch U, Knapp S, Meijer L, Bazureau JP. Leucettines, a class of potent inhibitors of cdc2-like kinases and dual specificity, tyrosine phosphorylation regulated kinases derived from the marine sponge leucettamine B: modulation of alternative pre-RNA splicing. J Med Chem 2011; 54:4172-86. [PMID: 21615147 DOI: 10.1021/jm200274d] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We here report on the synthesis, optimization, and biological characterization of leucettines, a family of kinase inhibitors derived from the marine sponge leucettamine B. Stepwise synthesis of analogues starting from the natural structure, guided by activity testing on eight purified kinases, led to highly potent inhibitors of CLKs and DYRKs, two families of kinases involved in alternative pre-mRNA splicing and Alzheimer's disease/Down syndrome. Leucettine L41 was cocrystallized with CLK3. It interacts with key residues located within the ATP-binding pocket of the kinase. Leucettine L41 inhibits the phosphorylation of serine/arginine-rich proteins (SRp), a family of proteins regulating pre-RNA splicing. Indeed leucettine L41 was demonstrated to modulate alternative pre-mRNA splicing, in a cell-based reporting system. Leucettines should be further explored as pharmacological tools to study and modulate pre-RNA splicing. Leucettines may also be investigated as potential therapeutic drugs in Alzheimer's disease (AD) and in diseases involving abnormal pre-mRNA splicing.
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Affiliation(s)
- Mansour Debdab
- Université de Rennes 1, Sciences Chimiques de Rennes, UMR CNRS 6226, Groupe Ingénierie Chimique & Molécules pour le Vivant (ICMV), Bât. 10A, Campus de Beaulieu, Avenue du Général Leclerc, CS 74205, 35042 Rennes cedex, France
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35
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Wong R, Balachandran A, Mao AY, Dobson W, Gray-Owen S, Cochrane A. Differential effect of CLK SR Kinases on HIV-1 gene expression: potential novel targets for therapy. Retrovirology 2011; 8:47. [PMID: 21682887 PMCID: PMC3148977 DOI: 10.1186/1742-4690-8-47] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 06/17/2011] [Indexed: 12/03/2022] Open
Abstract
Background RNA processing plays a critical role in the replication of HIV-1, regulated in part through the action of host SR proteins. To explore the impact of modulating SR protein activity on virus replication, the effect of increasing or inhibiting the activity of the Cdc2-like kinase (CLK) family of SR protein kinases on HIV-1 expression and RNA processing was examined. Results Despite their high homology, increasing individual CLK expression had distinct effects on HIV-1, CLK1 enhancing Gag production while CLK2 inhibited the virus. Parallel studies on the anti-HIV-1 activity of CLK inhibitors revealed a similar discrepant effect on HIV-1 expression. TG003, an inhibitor of CLK1, 2 and 4, had no effect on viral Gag synthesis while chlorhexidine, a CLK2, 3 and 4 inhibitor, blocked virus production. Chlorhexidine treatment altered viral RNA processing, decreasing levels of unspliced and single spliced viral RNAs, and reduced Rev accumulation. Subsequent experiments in the context of HIV-1 replication in PBMCs confirmed the capacity of chlorhexidine to suppress virus replication. Conclusions Together, these findings establish that HIV-1 RNA processing can be targeted to suppress virus replication as demonstrated by manipulating individual CLK function and identified chlorhexidine as a lead compound in the development of novel anti-viral therapies.
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Affiliation(s)
- Raymond Wong
- Dept. of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
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36
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Rosenthal AS, Tanega C, Shen M, Mott BT, Bougie JM, Nguyen DT, Misteli T, Auld DS, Maloney DJ, Thomas CJ. Potent and selective small molecule inhibitors of specific isoforms of Cdc2-like kinases (Clk) and dual specificity tyrosine-phosphorylation-regulated kinases (Dyrk). Bioorg Med Chem Lett 2011; 21:3152-8. [PMID: 21450467 PMCID: PMC3085634 DOI: 10.1016/j.bmcl.2011.02.114] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 02/24/2011] [Accepted: 02/28/2011] [Indexed: 11/22/2022]
Abstract
Continued examination of substituted 6-arylquinazolin-4-amines as Clk4 inhibitors resulted in selective inhibitors of Clk1, Clk4, Dyrk1A and Dyrk1B. Several of the most potent inhibitors were validated as being highly selective within a comprehensive kinome scan.
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Affiliation(s)
- Andrew S. Rosenthal
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Cordelle Tanega
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Min Shen
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Bryan T. Mott
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - James M. Bougie
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Dac-Trung Nguyen
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, NIH, 41 Library Drive, Bethesda, MD 20892 USA
| | - Douglas S. Auld
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - David J. Maloney
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Craig J. Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
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37
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Zheng ZM. Viral oncogenes, noncoding RNAs, and RNA splicing in human tumor viruses. Int J Biol Sci 2010; 6:730-55. [PMID: 21152115 PMCID: PMC2999850 DOI: 10.7150/ijbs.6.730] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 11/27/2010] [Indexed: 12/13/2022] Open
Abstract
Viral oncogenes are responsible for oncogenesis resulting from persistent virus infection. Although different human tumor viruses express different viral oncogenes and induce different tumors, their oncoproteins often target similar sets of cellular tumor suppressors or signal pathways to immortalize and/or transform infected cells. Expression of the viral E6 and E7 oncogenes in papillomavirus, E1A and E1B oncogenes in adenovirus, large T and small t antigen in polyomavirus, and Tax oncogene in HTLV-1 are regulated by alternative RNA splicing. However, this regulation is only partially understood. DNA tumor viruses also encode noncoding RNAs, including viral microRNAs, that disturb normal cell functions. Among the determined viral microRNA precursors, EBV encodes 25 from two major clusters (BART and BHRF1), KSHV encodes 12 from a latent region, human polyomavirus MCV produce only one microRNA from the late region antisense to early transcripts, but HPVs appears to produce no viral microRNAs.
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Affiliation(s)
- Zhi-Ming Zheng
- Tumor Virus RNA Biology Laboratory, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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38
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Ricciardi S, Kilstrup-Nielsen C, Bienvenu T, Jacquette A, Landsberger N, Broccoli V. CDKL5 influences RNA splicing activity by its association to the nuclear speckle molecular machinery. Hum Mol Genet 2009; 18:4590-602. [PMID: 19740913 DOI: 10.1093/hmg/ddp426] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in the human X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been shown to cause severe neurodevelopmental disorders including infantile spasms, encephalopathy, West-syndrome and an early-onset variant of Rett syndrome. CDKL5 is a serine/threonine kinase whose involvement in Rett syndrome can be inferred by its ability to directly bind and mediate phosphorylation of MeCP2. However, it remains to be elucidated how CDKL5 exerts its function. Here, we report that CDKL5 localizes to specific nuclear foci referred to as nuclear speckles in both cell lines and tissues. These sub-nuclear structures are traditionally considered as storage/modification sites of pre-mRNA splicing factors. Interestingly, we provide evidence that CDKL5 regulates the dynamic behaviour of nuclear speckles. Indeed, CDKL5 overexpression leads to nuclear speckle disassembly, and this event is strictly dependent on its kinase activity. Conversely, its down-regulation affects nuclear speckle morphology leading to abnormally large and uneven speckles. Similar results were obtained for primary adult fibroblasts isolated from CDKL5-mutated patients. Altogether, these findings indicate that CDKL5 controls nuclear speckle morphology probably by regulating the phosphorylation state of splicing regulatory proteins. Nuclear speckles are dynamic sites that can continuously supply splicing factors to active transcription sites, where splicing occurs. Notably, we proved that CDKL5 influences alternative splicing, at least as proved in heterologous minigene assays. In conclusion, we provide evidence that CDKL5 is involved indirectly in pre-mRNA processing, by controlling splicing factor dynamics. These findings identify a biological process whose disregulation might affect neuronal maturation and activity in CDKL5-related disorders.
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Affiliation(s)
- Sara Ricciardi
- Division of Neuroscience, San Raffaele Rett Research Center, San Raffaele Scientific Institute, Milan 20132, Italy
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39
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Rennel ES, Harper SJ, Bates DO. Therapeutic potential of manipulating VEGF splice isoforms in oncology. Future Oncol 2009; 5:703-12. [PMID: 19519209 DOI: 10.2217/fon.09.33] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Anti-angiogenic therapies currently revolve around targeting vascular endothelial growth factor-A (VEGF-A) or its receptors. These therapies are effective to some degree, but have low response rates and poor side-effect profiles. Part of these problems is likely to be due to their lack of specificity between pro- and anti-angiogenic isoforms, and their nonspecific effects on proactive, pleiotropic survival and maintenance roles of VEGF-A in endothelial and other cell types. An alternative approach, and one which has recently been shown to be effective in animal models of neovascularization in the eye, is to target the mechanisms by which the cell generates pro-angiogenic splice forms of VEGF-A, its receptors and, co-incidentally, by targeting the upstream processes, other oncogenes that have antagonistic splice isoforms. The concept here is to target the splicing mechanisms that control splice site choice in the VEGF-A mRNA. Recent evidence on the pharmacological possibilities of such splice factors is described.
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Affiliation(s)
- Emma S Rennel
- Microvascular Research Laboratories, Department of Physiology and Pharmacology, School of Veterinary Sciences, University of Bristol, Bristol, UK.
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