Literature DB >> 33689684

A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex.

Rakesh Chatrikhi1, Callen F Feeney1, Mary J Pulvino1, Georgios Alachouzos2, Andrew J MacRae3, Zackary Falls4, Sumit Rai5, William W Brennessel2, Jermaine L Jenkins1, Matthew J Walter6, Timothy A Graubert5, Ram Samudrala4, Melissa S Jurica3, Alison J Frontier2, Clara L Kielkopf7.   

Abstract

Dysregulated pre-mRNA splicing is an emerging Achilles heel of cancers and myelodysplasias. To expand the currently limited portfolio of small-molecule drug leads, we screened for chemical modulators of the U2AF complex, which nucleates spliceosome assembly and is mutated in myelodysplasias. A hit compound specifically enhances RNA binding by a U2AF2 subunit. Remarkably, the compound inhibits splicing of representative substrates and stalls spliceosome assembly at the stage of U2AF function. Computational docking, together with structure-guided mutagenesis, indicates that the compound bridges the tandem U2AF2 RNA recognition motifs via hydrophobic and electrostatic moieties. Cells expressing a cancer-associated U2AF1 mutant are preferentially killed by treatment with the compound. Altogether, our results highlight the potential of trapping early spliceosome assembly as an effective pharmacological means to manipulate pre-mRNA splicing. By extension, we suggest that stabilizing assembly intermediates may offer a useful approach for small-molecule inhibition of macromolecular machines.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  S34F mutant; U2AF(35); U2AF(65); U2AF1; myelodysplastic syndrome; ribonucleoprotein targeting; spliceosome inhibition; splicing factor mutation; therapeutic strategy

Mesh:

Substances:

Year:  2021        PMID: 33689684      PMCID: PMC8380659          DOI: 10.1016/j.chembiol.2021.02.007

Source DB:  PubMed          Journal:  Cell Chem Biol        ISSN: 2451-9448            Impact factor:   9.039


  71 in total

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Authors:  Melissa S Jurica; Lawrence J Licklider; Steven R Gygi; Nikolaus Grigorieff; Melissa J Moore
Journal:  RNA       Date:  2002-04       Impact factor: 4.942

3.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.

Authors:  Qun Pan; Ofer Shai; Leo J Lee; Brendan J Frey; Benjamin J Blencowe
Journal:  Nat Genet       Date:  2008-11-02       Impact factor: 38.330

4.  Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability.

Authors:  Brenton R Paolella; William J Gibson; Laura M Urbanski; John A Alberta; Travis I Zack; Pratiti Bandopadhayay; Caitlin A Nichols; Pankaj K Agarwalla; Meredith S Brown; Rebecca Lamothe; Yong Yu; Peter S Choi; Esther A Obeng; Dirk Heckl; Guo Wei; Belinda Wang; Aviad Tsherniak; Francisca Vazquez; Barbara A Weir; David E Root; Glenn S Cowley; Sara J Buhrlage; Charles D Stiles; Benjamin L Ebert; William C Hahn; Robin Reed; Rameen Beroukhim
Journal:  Elife       Date:  2017-02-08       Impact factor: 8.140

5.  Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing.

Authors:  Debanjana Maji; Eliezra Glasser; Steven Henderson; Justin Galardi; Mary J Pulvino; Jermaine L Jenkins; Clara L Kielkopf
Journal:  J Biol Chem       Date:  2020-10-05       Impact factor: 5.157

6.  Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes.

Authors:  Timothy A Graubert; Dong Shen; Li Ding; Theresa Okeyo-Owuor; Cara L Lunn; Jin Shao; Kilannin Krysiak; Christopher C Harris; Daniel C Koboldt; David E Larson; Michael D McLellan; David J Dooling; Rachel M Abbott; Robert S Fulton; Heather Schmidt; Joelle Kalicki-Veizer; Michelle O'Laughlin; Marcus Grillot; Jack Baty; Sharon Heath; John L Frater; Talat Nasim; Daniel C Link; Michael H Tomasson; Peter Westervelt; John F DiPersio; Elaine R Mardis; Timothy J Ley; Richard K Wilson; Matthew J Walter
Journal:  Nat Genet       Date:  2011-12-11       Impact factor: 38.330

7.  Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.

Authors:  Kathi Zarnack; Julian König; Mojca Tajnik; Iñigo Martincorena; Sebastian Eustermann; Isabelle Stévant; Alejandro Reyes; Simon Anders; Nicholas M Luscombe; Jernej Ule
Journal:  Cell       Date:  2013-01-31       Impact factor: 41.582

8.  Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins.

Authors:  Stanley Chun-Wei Lee; Heidi Dvinge; Eunhee Kim; Hana Cho; Jean-Baptiste Micol; Young Rock Chung; Benjamin H Durham; Akihide Yoshimi; Young Joon Kim; Michael Thomas; Camille Lobry; Chun-Wei Chen; Alessandro Pastore; Justin Taylor; Xujun Wang; Andrei Krivtsov; Scott A Armstrong; James Palacino; Silvia Buonamici; Peter G Smith; Robert K Bradley; Omar Abdel-Wahab
Journal:  Nat Med       Date:  2016-05-02       Impact factor: 53.440

9.  Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers.

Authors:  Manaswini Sivaramakrishnan; Kathleen D McCarthy; Sébastien Campagne; Sylwia Huber; Sonja Meier; Angélique Augustin; Tobias Heckel; Hélène Meistermann; Melanie N Hug; Pascale Birrer; Ahmed Moursy; Sarah Khawaja; Roland Schmucki; Nikos Berntenis; Nicolas Giroud; Sabrina Golling; Manuel Tzouros; Balazs Banfai; Gonzalo Duran-Pacheco; Jens Lamerz; Ying Hsiu Liu; Thomas Luebbers; Hasane Ratni; Martin Ebeling; Antoine Cléry; Sergey Paushkin; Adrian R Krainer; Frédéric H-T Allain; Friedrich Metzger
Journal:  Nat Commun       Date:  2017-11-14       Impact factor: 14.919

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  2 in total

Review 1.  Dysregulation and therapeutic targeting of RNA splicing in cancer.

Authors:  Robert F Stanley; Omar Abdel-Wahab
Journal:  Nat Cancer       Date:  2022-05-27

2.  Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies.

Authors:  Giulia Biancon; Poorval Joshi; Joshua T Zimmer; Torben Hunck; Yimeng Gao; Mark D Lessard; Edward Courchaine; Andrew E S Barentine; Martin Machyna; Valentina Botti; Ashley Qin; Rana Gbyli; Amisha Patel; Yuanbin Song; Lea Kiefer; Gabriella Viero; Nils Neuenkirchen; Haifan Lin; Joerg Bewersdorf; Matthew D Simon; Karla M Neugebauer; Toma Tebaldi; Stephanie Halene
Journal:  Mol Cell       Date:  2022-03-17       Impact factor: 19.328

  2 in total

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