1
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Pohorilets I, Beard JP, Driscoll JL, Schmitz JC, Koide K. Synthesis and antiproliferative activity of a tetrahydrofuran analog of FR901464. Bioorg Med Chem Lett 2024; 104:129739. [PMID: 38599298 DOI: 10.1016/j.bmcl.2024.129739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/03/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
Abstract
FR901464 is a natural product that exhibits antiproliferative activity at single-digit nanomolar concentrations in cancer cells. Its tetrahydropyran-spiroepoxide covalently binds the spliceosome. Through our medicinal chemistry campaign, we serendipitously discovered that a bromoetherification formed a tetrahydrofuran. The tetrahydrofuran analog was three orders of magnitude less potent than the corresponding tetrahydropyran analogs. This study shows the significance of the tetrahydropyran ring that presents the epoxide toward the spliceosome.
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Affiliation(s)
- Ivanna Pohorilets
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States
| | - Jacob P Beard
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States
| | - Julia L Driscoll
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States
| | - John C Schmitz
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine 5150 Centre Avenue, Pittsburgh, PA 15232, United States; Cancer Therapeutics Program, UPMC Hillman Cancer Center 5117 Centre Ave, Pittsburgh, PA 15232, United States
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States; Cancer Therapeutics Program, UPMC Hillman Cancer Center 5117 Centre Ave, Pittsburgh, PA 15232, United States.
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2
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Aya F, Lanuza-Gracia P, González-Pérez A, Bonnal S, Mancini E, López-Bigas N, Arance A, Valcárcel J. Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma. Cell Rep 2024; 43:114048. [PMID: 38614086 DOI: 10.1016/j.celrep.2024.114048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/06/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024] Open
Abstract
Resistance to MAPK inhibitors (MAPKi), the main cause of relapse in BRAF-mutant melanoma, is associated with the production of alternative BRAF mRNA isoforms (altBRAFs) in up to 30% of patients receiving BRAF inhibitor monotherapy. These altBRAFs have been described as being generated by alternative pre-mRNA splicing, and splicing modulation has been proposed as a therapeutic strategy to overcome resistance. In contrast, we report that altBRAFs are generated through genomic deletions. Using different in vitro models of altBRAF-mediated melanoma resistance, we demonstrate the production of altBRAFs exclusively from the BRAF V600E allele, correlating with corresponding genomic deletions. Genomic deletions are also detected in tumor samples from melanoma and breast cancer patients expressing altBRAFs. Along with the identification of altBRAFs in BRAF wild-type and in MAPKi-naive melanoma samples, our results represent a major shift in our understanding of mechanisms leading to the generation of BRAF transcripts variants associated with resistance in melanoma.
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Affiliation(s)
- Francisco Aya
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pablo Lanuza-Gracia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria López-Bigas
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ana Arance
- Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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3
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Beard J, Bressin RK, Markaj PL, Schmitz JC, Koide K. Synthesis and Conformational Analysis of FR901464-Based RNA Splicing Modulators and Their Synergism in Drug-Resistant Cancers. J Med Chem 2023; 66:14497-14512. [PMID: 37870431 PMCID: PMC10641826 DOI: 10.1021/acs.jmedchem.3c00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 10/24/2023]
Abstract
FR901464 is a cytotoxic natural product that binds splicing factor 3B subunit 1 (SF3B1) and PHD finger protein 5A (PHF5A), the components of the human spliceosome. The amide-containing tetrahydropyran ring binds SF3B1, and it remains unclear how the substituents on the ring contribute to the binding. Here, we synthesized meayamycin D, an analogue of FR901464, and three additional analogues to probe the conformation through methyl scanning. We discovered that the amide-containing tetrahydropyran ring assumes only one of the two possible chair conformations and that methylation of the nitrogen distorts the chair form, dramatically reducing cytotoxicity. Meayamycin D induced alternative splicing of MCL-1, showed strong synergism with venetoclax in drug-resistant lung cancer cells, and was cancer-specific over normal cells. Meayamycin D incorporates an alkyl ether and shows a long half-life in mouse plasma. The characteristics of meayamycin D may provide an approach to designing other bioactive L-shaped molecules.
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Affiliation(s)
- Jacob
P. Beard
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Robert K. Bressin
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Paulo L. Markaj
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - John C. Schmitz
- Division
of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine, 5150 Centre Avenue, Pittsburgh, Pennsylvania 15232, United States
- Cancer
Therapeutics Program, UPMC Hillman Cancer
Center, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15232, United States
| | - Kazunori Koide
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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López-Oreja I, Gohr A, Playa-Albinyana H, Giró A, Arenas F, Higashi M, Tripathi R, López-Guerra M, Irimia M, Aymerich M, Valcárcel J, Bonnal S, Colomer D. SF3B1 mutation-mediated sensitization to H3B-8800 splicing inhibitor in chronic lymphocytic leukemia. Life Sci Alliance 2023; 6:e202301955. [PMID: 37562845 PMCID: PMC10415613 DOI: 10.26508/lsa.202301955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Splicing factor 3B subunit 1 (SF3B1) is involved in pre-mRNA branch site recognition and is the target of antitumor-splicing inhibitors. Mutations in SF3B1 are observed in 15% of patients with chronic lymphocytic leukemia (CLL) and are associated with poor prognosis, but their pathogenic mechanisms remain poorly understood. Using deep RNA-sequencing data from 298 CLL tumor samples and isogenic SF3B1 WT and K700E-mutated CLL cell lines, we characterize targets and pre-mRNA sequence features associated with the selection of cryptic 3' splice sites upon SF3B1 mutation, including an event in the MAP3K7 gene relevant for activation of NF-κB signaling. Using the H3B-8800 splicing modulator, we show, for the first time in CLL, cytotoxic effects in vitro in primary CLL samples and in SF3B1-mutated isogenic CLL cell lines, accompanied by major splicing changes and delayed leukemic infiltration in a CLL xenotransplant mouse model. H3B-8800 displayed preferential lethality towards SF3B1-mutated cells and synergism with the BCL2 inhibitor venetoclax, supporting the potential use of SF3B1 inhibitors as a novel therapeutic strategy in CLL.
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Affiliation(s)
- Irene López-Oreja
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - André Gohr
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Fabian Arenas
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Morihiro Higashi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Rupal Tripathi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Mònica López-Guerra
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
- Universitat Barcelona, Barcelona, Spain
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5
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Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023; 24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
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Affiliation(s)
- Malgorzata Ewa Rogalska
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Vivori
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- The Francis Crick Institute, London, UK
| | - Juan Valcárcel
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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6
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Liu M, Guo J, Jia R. Emerging roles of alternative RNA splicing in oral squamous cell carcinoma. Front Oncol 2022; 12:1019750. [PMID: 36505770 PMCID: PMC9732560 DOI: 10.3389/fonc.2022.1019750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Alternative RNA splicing (ARS) is an essential and tightly regulated cellular process of post-transcriptional regulation of pre-mRNA. It produces multiple isoforms and may encode proteins with different or even opposite functions. The dysregulated ARS of pre-mRNA contributes to the development of many cancer types, including oral squamous cell carcinoma (OSCC), and may serve as a biomarker for the diagnosis and prognosis of OSCC and an attractive therapeutic target. ARS is mainly regulated by splicing factors, whose expression is also often dysregulated in OSCC and involved in tumorigenesis. This review focuses on the expression and roles of splicing factors in OSCC, the alternative RNA splicing events associated with OSCC, and recent advances in therapeutic approaches that target ARS.
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Affiliation(s)
- Miaomiao Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,RNA Institute, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
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7
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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He X, Zhang J, Guo Y, Yang X, Huang Y, Hao D. LncRNA MIAT Promotes Spinal Cord Injury Recovery in Rats by Regulating RBFOX2-Mediated Alternative Splicing of MCL-1. Mol Neurobiol 2022. [PMID: 35641779 DOI: 10.1007/s12035-022-02896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/21/2022] [Indexed: 10/18/2022]
Abstract
LncRNA myocardial infarction-associated transcript (MIAT) alleviates acute spinal cord injury (ASCI)-induced neuronal cell apoptosis, but the specific mechanism of it involved in regulating SCI progression needs further exploration. Here, a SCI rat model was established, followed by administration with adenovirus-mediated MIAT overexpression vector (Ad-MIAT) alone or together with Ad-RBFOX2 (RNA binding fox-1 homolog 2). The data indicated that MIAT overexpression promoted motor function recovery, improved morphology of injured tissues, and restrained neuron loss and cell apoptosis in SCI rats. Then, PC-12 cells were treated with H2O2 to induce cell injury. And highly expressed MIAT suppressed H2O2-caused decrease in cell viability and increase in cell apoptosis. MIAT stabilized RBFOX2 protein expression by binding to RBFOX2, thereby promoting RBFOX2-induced upregulation of anti-apoptotic MCL-1L (myeloid cell leukemia sequence 1) and reduction of pro-apoptotic MCL-1S. And silencing RBFOX2 in vitro blocked the inhibitory effect of MIAT on cell apoptosis. Moreover, MCL-1-specific steric-blocking oligonucleotides (SBOs) were used to transfer the MCL-1 pre-mRNA splicing pattern from MCL-1L to MCL-1S. SBOs reversed the protection effect of RBFOX2 overexpression on H2O2-induced cell injury. Furthermore, overexpression of MCL-1L instead of MCL-1S facilitated autophagy activation in H2O2-stimulated cells. Interestingly, co-overexpression of MIAT and RBFOX2 had a better promoting effect on SCI recovery. In conclusion, MIAT mitigated SCI by promoting RBFOX2-mediated alternative splicing of MCL-1. Our findings might provide a promising therapeutic target for SCI.
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Sulkshane P, Teni T. Myeloid cell leukemia-1: a formidable barrier to anticancer therapeutics and the quest of targeting it. Exploration of Targeted Anti-tumor Therapy 2022; 3:278-296. [PMID: 36045907 PMCID: PMC9400788 DOI: 10.37349/etat.2022.00083] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/16/2022] [Indexed: 11/22/2022] Open
Abstract
The antiapoptotic B cell lymphoma-2 (Bcl-2) family members are apical regulators of the intrinsic pathway of apoptosis that orchestrate mitochondrial outer membrane permeabilization (MOMP) through interactions with their proapoptotic counterparts. Overexpression of antiapoptotic Bcl-2 family proteins has been linked to therapy resistance and poor prognosis in diverse cancers. Among the antiapoptotic Bcl-2 family members, predominant overexpression of the prosurvival myeloid cell leukemia-1 (Mcl-1) has been reported in a myriad of hematological malignancies and solid tumors, contributing to therapy resistance and poor outcomes, thus making it a potential druggable target. The unique structure of Mcl-1 and its complex regulatory mechanism makes it an adaptive prosurvival switch that ensures tumor cell survival despite therapeutic intervention. This review focusses on diverse mechanisms adopted by tumor cells to maintain sustained elevated levels of Mcl-1 and how high Mcl-1 levels contribute to resistance in conventional as well as targeted therapies. Moreover, recent developments in the Mcl-1-targeted therapeutics and the underlying challenges and considerations in designing novel Mcl-1 inhibitors are also discussed.
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Affiliation(s)
- Prasad Sulkshane
- Glickman Laboratory, Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Tanuja Teni
- Teni Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Mumbai 400094, India
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10
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Kumar D, Kashyap MK, Yu Z, Spaanderman I, Villa R, Kipps TJ, La Clair JJ, Burkart MD, Castro JE. Modulation of RNA splicing associated with Wnt signaling pathway using FD-895 and pladienolide B. Aging (Albany NY) 2022; 14:2081-2100. [PMID: 35230971 PMCID: PMC8954975 DOI: 10.18632/aging.203924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Alterations in RNA splicing are associated with different malignancies, including leukemia, lymphoma, and solid tumors. The RNA splicing modulators such as FD-895 and pladienolide B have been investigated in different malignancies to target/modulate spliceosome for therapeutic purpose. Different cell lines were screened using an RNA splicing modulator to test in vitro cytotoxicity and the ability to modulate RNA splicing capability via induction of intron retention (using RT-PCR and qPCR). The Cignal Finder Reporter Array evaluated [pathways affected by the splice modulators in HeLa cells. Further, the candidates associated with the pathways were validated at protein level using western blot assay, and gene-gene interaction studies were carried out using GeneMANIA. We show that FD-895 and pladienolide B induces higher apoptosis levels than conventional chemotherapy in different solid tumors. In addition, both agents modulate Wnt signaling pathways and mRNA splicing. Specifically, FD-895 and pladienolide B significantly downregulates Wnt signaling pathway-associated transcripts (GSK3β and LRP5) and both transcript and proteins including LEF1, CCND1, LRP6, and pLRP6 at the transcript, total protein, and protein phosphorylation's levels. These results indicate FD-895 and pladienolide B inhibit Wnt signaling by decreasing LRP6 phosphorylation and modulating mRNA splicing through induction of intron retention in solid tumors.
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Affiliation(s)
- Deepak Kumar
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- ThermoFisher Scientific, Carlsbad, CA 92008, USA
| | - Manoj K. Kashyap
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Zhe Yu
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Ide Spaanderman
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Januario E. Castro
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Hematology-Oncology Division, Mayo Clinic, Phoenix, AZ 85054, USA
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11
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Chhipi-Shrestha JK, Schneider-Poetsch T, Suzuki T, Mito M, Khan K, Dohmae N, Iwasaki S, Yoshida M. Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns. Cell Chem Biol 2022; 29:259-275.e10. [PMID: 34520743 PMCID: PMC8857039 DOI: 10.1016/j.chembiol.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/10/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022]
Abstract
Chemical splicing modulators that bind to the spliceosome have provided an attractive avenue for cancer treatment. Splicing modulators induce accumulation and subsequent translation of a subset of intron-retained mRNAs. However, the biological effect of proteins containing translated intron sequences remains unclear. Here, we identify a number of truncated proteins generated upon treatment with the splicing modulator spliceostatin A (SSA) via genome-wide ribosome profiling and bio-orthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry. A subset of these truncated proteins has intrinsically disordered regions, forms insoluble cellular condensates, and triggers the proteotoxic stress response through c-Jun N-terminal kinase (JNK) phosphorylation, thereby inhibiting the mTORC1 pathway. In turn, this reduces global translation. These findings indicate that creating an overburden of condensate-prone proteins derived from introns represses translation and prevents further production of harmful truncated proteins. This mechanism appears to contribute to the antiproliferative and proapoptotic activity of splicing modulators.
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Affiliation(s)
- Jagat K. Chhipi-Shrestha
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Khalid Khan
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Wako, Saitama 351-0198, Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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12
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Reviejo M, Soto M, Lozano E, Asensio M, Martínez-Augustin O, Sánchez de Medina F, Marin JJG. Impact of alternative splicing on mechanisms of resistance to anticancer drugs. Biochem Pharmacol 2021; 193:114810. [PMID: 34673012 DOI: 10.1016/j.bcp.2021.114810] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
A shared characteristic of many tumors is the lack of response to anticancer drugs. Multiple mechanisms of pharmacoresistance (MPRs) are involved in permitting cancer cells to overcome the effect of these agents. Pharmacoresistance can be primary (intrinsic) or secondary (acquired), i.e., triggered or enhanced in response to the treatment. Moreover, MPRs usually result in the lack of sensitivity to several agents, which accounts for diverse multidrug-resistant (MDR) phenotypes. MPRs are based on the dynamic expression of more than one hundred genes, constituting the so-called resistome. Alternative splicing (AS) during pre-mRNA maturation results in changes affecting proteins involved in the resistome. The resulting splicing variants (SVs) reduce the efficacy of anticancer drugs by lowering the intracellular levels of active agents, altering molecular targets, enhancing both DNA repair ability and defensive mechanism of tumors, inducing changes in the balance between pro-survival and pro-apoptosis signals, modifying interactions with the tumor microenvironment, and favoring malignant phenotypic transitions. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the impact of AS on MPR in cancer cells.
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13
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Blijlevens M, Li J, van Beusechem VW. Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:5110. [PMID: 34065983 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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14
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Nicolaou KC, Rekula SR, Kumar SM, Podilapu AR, Matuszak RP, Jung PM, Lam LT, Phillips AC, Lyssikatos J, Munneke S, Gu C, Sarvaiya H, Sandoval J, Hammond M, Aujay M, Purcell JW, Reilly RM, Gavrilyuk J. Design, Synthesis, and Biological Investigation of Thailanstatin A and Spliceostatin D Analogues Containing Tetrahydropyran, Tetrahydrooxazine, and Fluorinated Structural Motifs. J Org Chem 2021; 86:2499-2521. [PMID: 33417458 DOI: 10.1021/acs.joc.0c02643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thailanstatin A and spliceostatin D, two naturally occurring molecules endowed with potent antitumor activities by virtue of their ability to bind and inhibit the function of the spliceosome, and their natural siblings and designed analogues, constitute an appealing family of compounds for further evaluation and optimization as potential drug candidates for cancer therapies. In this article, the design, synthesis, and biological investigation of a number of novel thailanstatin A analogues, including some accommodating 1,1-difluorocyclopropyl and tetrahydrooxazine structural motifs within their structures, are described. Important findings from these studies paving the way for further investigations include the identification of several highly potent compounds for advancement as payloads for antibody-drug conjugates (ADCs) as potential targeted cancer therapies and/or small molecule drugs, either alone or in combination with other anticancer agents.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Santhosh Reddy Rekula
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - S Mothish Kumar
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ananda Rao Podilapu
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ryan P Matuszak
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Paul M Jung
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Lloyd T Lam
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Andrew C Phillips
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Joseph Lyssikatos
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Stefan Munneke
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Christine Gu
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Hetal Sarvaiya
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Joseph Sandoval
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Mikhail Hammond
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Monette Aujay
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - James W Purcell
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Regina M Reilly
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Julia Gavrilyuk
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
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15
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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16
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Abstract
RNA-binding proteins (RBPs) are critical effectors of gene expression, and as such their malfunction underlies the origin of many diseases. RBPs can recognize hundreds of transcripts and form extensive regulatory networks that help to maintain cell homeostasis. System-wide unbiased identification of RBPs has increased the number of recognized RBPs into the four-digit range and revealed new paradigms: from the prevalence of structurally disordered RNA-binding regions with roles in the formation of membraneless organelles to unsuspected and potentially pervasive connections between intermediary metabolism and RNA regulation. Together with an increasingly detailed understanding of molecular mechanisms of RBP function, these insights are facilitating the development of new therapies to treat malignancies. Here, we provide an overview of RBPs involved in human genetic disorders, both Mendelian and somatic, and discuss emerging aspects in the field with emphasis on molecular mechanisms of disease and therapeutic interventions.
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Affiliation(s)
- Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain. .,University Pompeu Fabra (UPF), Barcelona, Spain.
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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17
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Zhang D, Meng F. A Comprehensive Overview of Structure-Activity Relationships of Small-Molecule Splicing Modulators Targeting SF3B1 as Anticancer Agents. ChemMedChem 2020; 15:2098-2120. [PMID: 33037739 DOI: 10.1002/cmdc.202000642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/19/2020] [Indexed: 02/06/2023]
Abstract
The pre-mRNA splicing factor SF3B1 shows recurrent mutations among hematologic malignancies and some solid tumors. In 2007, the identification of two cytotoxic natural products, which showed splicing inhibition by binding to SF3b, prompted the development of small-molecule splicing modulators of SF3B1 as therapeutics for cancer. Recent studies suggested that spliceosome-mutant cells are preferentially sensitive to pharmacologic splicing modulation; therefore, exploring the clinical utility of splicing modulator therapies in patients with spliceosome-mutant hematologic malignancies who have failed current therapies is greatly needed, as these patients have few treatment options. H3B-8800 had unique pharmacological activity and exhibited favorable data in phase I clinical trials to treat patients with advanced myeloid malignancies, indicating that further clinical trials are promising. The most established small-molecule modulators of SF3B1 can be categorized into three classes: the bicycles, the monopyranes, and the 12-membered macrolides. This review provides a comprehensive overview of the structure-activity relationships of small-molecule SF3B1 modulators, with a detailed analysis of interactions between modulators and protein binding pocket. The future strategy for splicing modulators development is also discussed.
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Affiliation(s)
- Datong Zhang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, P. R. China
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, 306 Huiren Road, Tianjin, 300301, P. R. China
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18
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Li Y, Gao X, Wei C, Guo R, Xu H, Bai Z, Zhou J, Zhu J, Wang W, Wu Y, Li J, Zhang Z, Xie X. Modification of Mcl-1 alternative splicing induces apoptosis and suppresses tumor proliferation in gastric cancer. Aging (Albany NY) 2020; 12:19293-19315. [PMID: 33052877 PMCID: PMC7732305 DOI: 10.18632/aging.103766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/07/2020] [Indexed: 01/24/2023]
Abstract
Splicing dysregulation, which leads to apoptosis resistance, has been recognized as a major hallmark for tumorigenesis and cancer progression. Targeting alternative splicing by either increasing pro-apoptotic proteins or inhibiting anti-apoptotic proteins in tumor cells may be an effective approach for gastric cancer (GC) therapy. However, the role of modulation of alternative splicing in GC remains poorly understood. In this study, to the best of our knowledge, the unbalanced expression of the myeloid cell leukemia-1 (Mcl-1) splicing variants, Mcl-1L and Mcl-1S, was identified in GC patients for the first time. Increasing anti-apoptotic Mcl-1L and decreasing pro-apoptotic Mcl-1S expression levels were correlated with tumor proliferation and poor survival. In vitro data showed that a shift in splicing from Mcl-1L to Mcl-1S induced by treatment with Mcl-1-specific steric-blocking oligonucleotides (SBOs) efficiently decreased Mcl-1L expression, increased Mcl-1S expression, and accelerated tumor cell apoptosis in a dose-dependent manner. Additionally, mouse xenotransplant models confirmed that modification of Mcl-1 alternative splicing increased tumor cell death and suppressed tumor proliferation. This study demonstrated that the modification of Mcl-1 splicing might stimulate the pro-apoptotic factor and inhibit the anti-apoptotic protein to induce significant apoptosis. Thus, this finding provided a strategy for cancer therapy, according to which SBOs could be used to change the Mcl-1 splicing pattern, thereby inducing apoptosis.
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Affiliation(s)
- Yonghong Li
- Key Laboratory of Preclinical Study for New Drug of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Xiaoling Gao
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Chaojun Wei
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Rui Guo
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Hui Xu
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Zhongtian Bai
- The Second Department of General Surgery, Lanzhou University First Hospital, Lanzhou 730000, China
| | - Jianye Zhou
- Key Lab of Stomatology of State Ethnic Affairs Commission, Northwest Minzu University, Lanzhou 730030, China
| | - Jun Zhu
- Pathology Department, Lanzhou University First Hospital, Lanzhou 730000, China
| | - Wanxia Wang
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Yu Wu
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Jingzhe Li
- Oncology Department, The First Hospital of Lanzhou, Lanzhou 730050, China
| | - Zhongliang Zhang
- Oncology Department, The First Hospital of Lanzhou, Lanzhou 730050, China
| | - Xiaodong Xie
- Key Laboratory of Preclinical Study for New Drug of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
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19
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Sciarrillo R, Wojtuszkiewicz A, Assaraf YG, Jansen G, Kaspers GJL, Giovannetti E, Cloos J. The role of alternative splicing in cancer: From oncogenesis to drug resistance. Drug Resist Updat 2020; 53:100728. [PMID: 33070093 DOI: 10.1016/j.drup.2020.100728] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
Alternative splicing is a tightly regulated process whereby non-coding sequences of pre-mRNA are removed and protein-coding segments are assembled in diverse combinations, ultimately giving rise to proteins with distinct or even opposing functions. In the past decade, whole genome/transcriptome sequencing studies revealed the high complexity of splicing regulation, which occurs co-transcriptionally and is influenced by chromatin status and mRNA modifications. Consequently, splicing profiles of both healthy and malignant cells display high diversity and alternative splicing was shown to be widely deregulated in multiple cancer types. In particular, mutations in pre-mRNA regulatory sequences, splicing regulators and chromatin modifiers, as well as differential expression of splicing factors are important contributors to cancer pathogenesis. It has become clear that these aberrations contribute to many facets of cancer, including oncogenic transformation, cancer progression, response to anticancer drug treatment as well as resistance to therapy. In this respect, alternative splicing was shown to perturb the expression a broad spectrum of relevant genes involved in drug uptake/metabolism (i.e. SLC29A1, dCK, FPGS, and TP), activation of nuclear receptor pathways (i.e. GR, AR), regulation of apoptosis (i.e. MCL1, BCL-X, and FAS) and modulation of response to immunotherapy (CD19). Furthermore, aberrant splicing constitutes an important source of novel cancer biomarkers and the spliceosome machinery represents an attractive target for a novel and rapidly expanding class of therapeutic agents. Small molecule inhibitors targeting SF3B1 or splice factor kinases were highly cytotoxic against a wide range of cancer models, including drug-resistant cells. Importantly, these effects are enhanced in specific cancer subsets, such as splicing factor-mutated and c-MYC-driven tumors. Furthermore, pre-clinical studies report synergistic effects of spliceosome modulators in combination with conventional antitumor agents. These strategies based on the use of low dose splicing modulators could shift the therapeutic window towards decreased toxicity in healthy tissues. Here we provide an extensive overview of the latest findings in the field of regulation of splicing in cancer, including molecular mechanisms by which cancer cells harness alternative splicing to drive oncogenesis and evade anticancer drug treatment as well as splicing-based vulnerabilities that can provide novel treatment opportunities. Furthermore, we discuss current challenges arising from genome-wide detection and prediction methods of aberrant splicing, as well as unravelling functional relevance of the plethora of cancer-related splicing alterations.
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Affiliation(s)
- Rocco Sciarrillo
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Anna Wojtuszkiewicz
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Gerrit Jansen
- Amsterdam Immunology and Rheumatology Center, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Gertjan J L Kaspers
- Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Fondazione Pisana per la Scienza, Pisa, Italy
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands.
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20
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Liu T, Wu Z, He Y, Xiao Y, Xia C. Single and dual target inhibitors based on Bcl-2: Promising anti-tumor agents for cancer therapy. Eur J Med Chem 2020; 201:112446. [PMID: 32563811 DOI: 10.1016/j.ejmech.2020.112446] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023]
Abstract
B-cell lymphoma-2 (Bcl-2) proteins family is an essential checkpoint in apoptosis. Extensive evidences suggested that overexpression of anti-apoptotic Bcl-2 proteins can be observed in multiple cancer cell lines and primary tumor biopsy samples, which is an important reason for tumor cells to evade apoptosis and further acquire drug resistance for chemotherapy. Hence, down-regulation of anti-apoptotic Bcl-2 proteins is effective for the treatment of cancers. In view that Bcl-2 inhibitors and some other anti-tumor agents, such as HDAC inhibitors and Mdm2 inhibitors, exert synergy effects in tumor cells, it is pointed out that dual-targeting therapies based on these targets are regarded as rational strategies to enhance the effectiveness of single target agents for cancer treatment. This review briefly introduces the apoptosis, the structure of Bcl-2 family proteins, and focuses on the current status and recent advances of Bcl-2 inhibitors and the corresponding SARs of them. Moreover, we discuss the synergisms between Bcl-2 and other anti-tumor targets, and summarize the current dual-target agents.
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21
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Bonnal SC, López-Oreja I, Valcárcel J. Roles and mechanisms of alternative splicing in cancer - implications for care. Nat Rev Clin Oncol 2020; 17:457-74. [PMID: 32303702 DOI: 10.1038/s41571-020-0350-x] [Citation(s) in RCA: 332] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
Removal of introns from messenger RNA precursors (pre-mRNA splicing) is an essential step for the expression of most eukaryotic genes. Alternative splicing enables the regulated generation of multiple mRNA and protein products from a single gene. Cancer cells have general as well as cancer type-specific and subtype-specific alterations in the splicing process that can have prognostic value and contribute to every hallmark of cancer progression, including cancer immune responses. These splicing alterations are often linked to the occurrence of cancer driver mutations in genes encoding either core components or regulators of the splicing machinery. Of therapeutic relevance, the transcriptomic landscape of cancer cells makes them particularly vulnerable to pharmacological inhibition of splicing. Small-molecule splicing modulators are currently in clinical trials and, in addition to splice site-switching antisense oligonucleotides, offer the promise of novel and personalized approaches to cancer treatment.
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22
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Rahhal R, Seto E. Emerging roles of histone modifications and HDACs in RNA splicing. Nucleic Acids Res 2019; 47:4911-4926. [PMID: 31162605 PMCID: PMC6547430 DOI: 10.1093/nar/gkz292] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Histone modifications and RNA splicing, two seemingly unrelated gene regulatory processes, greatly increase proteome diversity and profoundly influence normal as well as pathological eukaryotic cellular functions. Like many histone modifying enzymes, histone deacetylases (HDACs) play critical roles in governing cellular behaviors and are indispensable in numerous biological processes. While the association between RNA splicing and histone modifications is beginning to be recognized, a lack of knowledge exists regarding the role of HDACs in splicing. Recent studies however, reveal that HDACs interact with spliceosomal and ribonucleoprotein complexes, actively control the acetylation states of splicing-associated histone marks and splicing factors, and thereby unexpectedly could modulate splicing. Here, we review the role of histone/protein modifications and HDACs in RNA splicing and discuss the convergence of two parallel fields, which supports the argument that HDACs, and perhaps most histone modifying enzymes, are much more versatile and far more complicated than their initially proposed functions. Analogously, an HDAC-RNA splicing connection suggests that splicing is regulated by additional upstream factors and pathways yet to be defined or not fully characterized. Some human diseases share common underlying causes of aberrant HDACs and dysregulated RNA splicing and, thus, further support the potential link between HDACs and RNA splicing.
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Affiliation(s)
- Raneen Rahhal
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
| | - Edward Seto
- George Washington Cancer Center, Department of Biochemistry & Molecular Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC 20037, USA
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23
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Pearson JM, Tan SF, Sharma A, Annageldiyev C, Fox TE, Abad JL, Fabrias G, Desai D, Amin S, Wang HG, Cabot MC, Claxton DF, Kester M, Feith DJ, Loughran TP. Ceramide Analogue SACLAC Modulates Sphingolipid Levels and MCL-1 Splicing to Induce Apoptosis in Acute Myeloid Leukemia. Mol Cancer Res 2019; 18:352-363. [PMID: 31744877 DOI: 10.1158/1541-7786.mcr-19-0619] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a disease characterized by uncontrolled proliferation of immature myeloid cells in the blood and bone marrow. The 5-year survival rate is approximately 25%, and recent therapeutic developments have yielded little survival benefit. Therefore, there is an urgent need to identify novel therapeutic targets. We previously demonstrated that acid ceramidase (ASAH1, referred to as AC) is upregulated in AML and high AC activity correlates with poor patient survival. Here, we characterized a novel AC inhibitor, SACLAC, that significantly reduced the viability of AML cells with an EC50 of approximately 3 μmol/L across 30 human AML cell lines. Treatment of AML cell lines with SACLAC effectively blocked AC activity and induced a decrease in sphingosine 1-phosphate and a 2.5-fold increase in total ceramide levels. Mechanistically, we showed that SACLAC treatment led to reduced levels of splicing factor SF3B1 and alternative MCL-1 mRNA splicing in multiple human AML cell lines. This increased proapoptotic MCL-1S levels and contributed to SACLAC-induced apoptosis in AML cells. The apoptotic effects of SACLAC were attenuated by SF3B1 or MCL-1 overexpression and by selective knockdown of MCL-1S. Furthermore, AC knockdown and exogenous C16-ceramide supplementation induced similar changes in SF3B1 level and MCL-1S/L ratio. Finally, we demonstrated that SACLAC treatment leads to a 37% to 75% reduction in leukemic burden in two human AML xenograft mouse models. IMPLICATIONS: These data further emphasize AC as a therapeutic target in AML and define SACLAC as a potent inhibitor to be further optimized for future clinical development.
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Affiliation(s)
- Jennifer M Pearson
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia
| | - Arati Sharma
- Penn State Cancer Institute, Hershey, Pennsylvania.,Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | | | - Todd E Fox
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia
| | - Jose Luis Abad
- Department of Biological Chemistry, Networking Biomedical Research Centre on Liver and Digestive Diseases (CIBER-EHD), Institute for Advanced Chemistry of Catalonia, Spanish National Research Council (IQAC-CSIC), Barcelona, Spain
| | - Gemma Fabrias
- Department of Biological Chemistry, Networking Biomedical Research Centre on Liver and Digestive Diseases (CIBER-EHD), Institute for Advanced Chemistry of Catalonia, Spanish National Research Council (IQAC-CSIC), Barcelona, Spain
| | - Dhimant Desai
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Shantu Amin
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Hong-Gang Wang
- Penn State Cancer Institute, Hershey, Pennsylvania.,Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania
| | - Myles C Cabot
- Department of Biochemistry and Molecular Biology, East Carolina Diabetes and Obesity Institute, Brody School of Medicine, East Carolina University, Greenville, North Carolina
| | | | - Mark Kester
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania.,University of Virginia Cancer Center, Charlottesville, Virginia
| | - David J Feith
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia.,University of Virginia Cancer Center, Charlottesville, Virginia
| | - Thomas P Loughran
- Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia. .,University of Virginia Cancer Center, Charlottesville, Virginia
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Koedoot E, Wolters L, van de Water B, Dévédec SEL. Splicing regulatory factors in breast cancer hallmarks and disease progression. Oncotarget 2019; 10:6021-37. [PMID: 31666932 DOI: 10.18632/oncotarget.27215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
By regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing events to fulfill their requirements in order to develop, progress and metastasize. However, there has been less attention for the role of the complex catalyzing the complicated multistep splicing reaction: the spliceosome. The spliceosome consists of multiple sub-complexes in total comprising 244 proteins or splice factors and 5 associated RNA molecules. Here we discuss the role of splice factors in the oncogenic processes tumors cells need to fulfill their oncogenic properties (the so-called the hallmarks of cancer). Despite the fact that splice factors have been investigated only recently, they seem to play a prominent role in already five hallmarks of cancer: angiogenesis, resisting cell death, sustaining proliferation, deregulating cellular energetics and invasion and metastasis formation by affecting major signaling pathways such as epithelial-to-mesenchymal transition, the Warburg effect, DNA damage response and hormone receptor dependent proliferation. Moreover, we could relate expression of representative genes of four other hallmarks (enabling replicative mortality, genomic instability, avoiding immune destruction and evading growth suppression) to splice factor levels in human breast cancer tumors, suggesting that also these hallmarks could be regulated by splice factors. Since many splice factors are involved in multiple hallmarks of cancer, inhibiting splice factors might provide a new layer of oncogenic control and a powerful method to combat breast cancer progression.
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25
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Vivet-Noguer R, Tarin M, Roman-Roman S, Alsafadi S. Emerging Therapeutic Opportunities Based on Current Knowledge of Uveal Melanoma Biology. Cancers (Basel) 2019; 11:E1019. [PMID: 31330784 DOI: 10.3390/cancers11071019] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Uveal Melanoma (UM) is a rare and malignant intraocular tumor with dismal prognosis. Despite the efficient control of the primary tumor by radiation or surgery, up to 50% of patients subsequently develop metastasis, mainly in the liver. Once the tumor has spread from the eye, the treatment is challenging and the median survival is only nine months. UM represents an intriguing model of oncogenesis that is characterized by a relatively homogeneous histopathological architecture and a low burden of genetic alterations, in contrast to other melanomas. UM is driven by recurrent activating mutations in Gαq pathway, which are associated with a second mutation in BRCA1 associated protein 1 (BAP1), splicing factor 3b subunit 1 (SF3B1), or eukaryotic translation initiation factor 1A X-linked (EIF1AX), occurring in an almost mutually exclusive manner. The monosomy of chromosome 3 is also a recurrent feature that is associated with high metastatic risk. These events driving UM oncogenesis have been thoroughly investigated over the last decade. However, no efficient related therapeutic strategies are yet available and the metastatic disease remains mostly incurable. Here, we review current knowledge regarding the molecular biology and the genetics of uveal melanoma and highlight the related therapeutic applications and perspectives.
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26
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Warren CFA, Wong-Brown MW, Bowden NA. BCL-2 family isoforms in apoptosis and cancer. Cell Death Dis 2019; 10:177. [PMID: 30792387 DOI: 10.1038/s41419-019-1407-6] [Citation(s) in RCA: 342] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/17/2018] [Accepted: 01/29/2019] [Indexed: 12/17/2022]
Abstract
The BCl-2 family has long been identified for its role in apoptosis. Following the initial discovery of BCL-2 in the context of B-cell lymphoma in the 1980s, a number of homologous proteins have since been identified. The members of the Bcl-2 family are designated as such due to their BCL-2 homology (BH) domains and involvement in apoptosis regulation. The BH domains facilitate the family members’ interactions with each other and can indicate pro- or anti-apoptotic function. Traditionally, these proteins are categorised into one of the three subfamilies; anti-apoptotic, BH3-only (pro-apoptotic), and pore-forming or ‘executioner’ (pro-apoptotic) proteins. Each of the BH3-only or anti-apoptotic proteins has a distinct pattern of activation, localisation and response to cell death or survival stimuli. All of these can vary across cell or stress types, or developmental stage, and this can cause the delineation of the roles of BCL-2 family members. Added to this complexity is the presence of relatively uncharacterised isoforms of many of the BCL-2 family members. There is a gap in our knowledge regarding the function of BCL-2 family isoforms. BH domain status is not always predictive or indicative of protein function, and several other important sequences, which can contribute to apoptotic activity have been identified. While therapeutic strategies targeting the BCL-2 family are constantly under development, it is imperative that we understand the molecules, which we are attempting to target. This review, discusses our current knowledge of anti-apoptotic BCL-2 family isoforms. With significant improvements in the potential for splicing therapies, it is important that we begin to understand the distinctions of the BCL-2 family, not limited to just the mechanisms of apoptosis control, but in their roles outside of apoptosis.
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27
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Blijlevens M, van der Meulen-Muileman IH, de Menezes RX, Smit EF, van Beusechem VW. High-throughput RNAi screening reveals cancer-selective lethal targets in the RNA spliceosome. Oncogene 2019; 38:4142-53. [PMID: 30705407 DOI: 10.1038/s41388-019-0711-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/21/2018] [Accepted: 01/16/2019] [Indexed: 12/23/2022]
Abstract
Novel therapeutic strategies for non-small-cell lung cancer (NSCLC) are urgently needed. RNA splicing, orchestrated by the spliceosome, is deregulated in many forms of cancer, including NSCLC. Here, we performed high-throughput screening with a small interfering RNA library targeting all annotated human spliceosome proteins to identify cancer-selective lethal targets in the RNA splicing machinery. Silencing of several spliceosome proteins reduced cell viability in a panel of NSCLC cell lines, but not in non-malignant lung fibroblasts and epithelial cells. Interestingly, the cancer-selective lethal target set comprised all seven Sm proteins that, together with small nuclear RNA, form the core structure of most spliceosome subunits. Interfering with Sm protein expression induced apoptosis in NSCLC cells, but not in non-malignant cells. In silico analysis revealed that Sm proteins are frequently upregulated in NSCLC. For several Sm proteins, increased expression showed a positive correlation with disease severity. Together, our results suggest that the Sm proteins represent particularly useful novel targets for selective treatment of NSCLC.
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Aird D, Teng T, Huang CL, Pazolli E, Banka D, Cheung-Ong K, Eifert C, Furman C, Wu ZJ, Seiler M, Buonamici S, Fekkes P, Karr C, Palacino J, Park E, Smith PG, Yu L, Mizui Y, Warmuth M, Chicas A, Corson L, Zhu P. Sensitivity to splicing modulation of BCL2 family genes defines cancer therapeutic strategies for splicing modulators. Nat Commun 2019; 10:137. [PMID: 30635584 DOI: 10.1038/s41467-018-08150-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/18/2018] [Indexed: 11/24/2022] Open
Abstract
Dysregulation of RNA splicing by spliceosome mutations or in cancer genes is increasingly recognized as a hallmark of cancer. Small molecule splicing modulators have been introduced into clinical trials to treat solid tumors or leukemia bearing recurrent spliceosome mutations. Nevertheless, further investigation of the molecular mechanisms that may enlighten therapeutic strategies for splicing modulators is highly desired. Here, using unbiased functional approaches, we report that the sensitivity to splicing modulation of the anti-apoptotic BCL2 family genes is a key mechanism underlying preferential cytotoxicity induced by the SF3b-targeting splicing modulator E7107. While BCL2A1, BCL2L2 and MCL1 are prone to splicing perturbation, BCL2L1 exhibits resistance to E7107-induced splicing modulation. Consequently, E7107 selectively induces apoptosis in BCL2A1-dependent melanoma cells and MCL1-dependent NSCLC cells. Furthermore, combination of BCLxL (BCL2L1-encoded) inhibitors and E7107 remarkably enhances cytotoxicity in cancer cells. These findings inform mechanism-based approaches to the future clinical development of splicing modulators in cancer treatment. Small molecule modulators of RNA splicing have therapeutic potential in tumours bearing spliceosome mutations. Here, the authors identify BCL2 genes have differential sensitivities to SF3b-targeting splicing modulators and combination of SF3b-targeting splicing modulators and BCLxL inhibition induces synergistic cytotoxicity in cancer cells.
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29
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Yamano T, Kubo S, Yano A, Kominato T, Tanaka S, Ikeda M, Tomita N. Splicing modulator FR901464 is a potential agent for colorectal cancer in combination therapy. Oncotarget 2019; 10:352-367. [PMID: 30719229 PMCID: PMC6349454 DOI: 10.18632/oncotarget.26564] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 12/29/2018] [Indexed: 12/22/2022] Open
Abstract
FR901464 (FR) was first described as an anticancer drug and later identified as a modulator of splicing factor 3B subunit 1 (SF3B1). Although the effectiveness of splicing modulators has been investigated in colorectal cancer (CRC) cells, their usefulness in animal experiments has not been confirmed. The association of SF3B1 with CRC progression and the influence of FR on transcriptional activity in CRC has not been fully elucidated. FR showed strong cytotoxicity against CRC cell lines, SF3B1-mutated cancer cell lines, and human fibroblasts with IC50 values less than 1 ng/ml. FR-resistant clones derived from HCT116, DLD1, Lovo, and CT26 cells showed IC50 values greater than 100 ng/ml. SF3B1 sequencing demonstrated low frequencies of SF3B1 mutations in CRC and mutations in codon 1074 of exon 22 in all FR-resistant clones. Unlike hematological malignancies, SF3B1 expression was not associated with CRC progression. Although FR showed significant growth inhibition in a xenograft model of RKO cells, severe toxicity was also induced. These data indicated CRC might be a suitable target of FR unless toxicity occurs. Microarray analysis and real-time quantitative PCR demonstrated downregulation of genes associated with Fanconi anemia (BRCA1 and BRCA2) and 28 driver oncogenes. These data suggested combination treatment of FR with other anticancer drugs whose sensitivity is associated with genes affected by FR treatment. Combination treatment with PARP1 inhibitor olaparib, whose sensitivity was enhanced by BRCA 1/2 deficiency, showed synergistic effects in CRC cells. Our data indicates the potential of FR in combination therapy rather than monotherapy for CRC treatment.
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Affiliation(s)
- Tomoki Yamano
- Division of Lower Gastrointestinal Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Shuji Kubo
- Laboratory of Molecular and Genetic Therapeutics, Institute for Advanced Medical Sciences, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Aya Yano
- Division of Lower Gastrointestinal Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Tomoko Kominato
- Division of Lower Gastrointestinal Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Shino Tanaka
- Division of Lower Gastrointestinal Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Masataka Ikeda
- Division of Lower Gastrointestinal Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Naohiro Tomita
- Division of Lower Gastrointestinal Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
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Abstract
Breast cancer is known to be a heterogeneous disease driven by a large repertoire of molecular abnormalities, which contribute to its diverse clinical behaviour. Despite the success of targeted therapy approaches for breast cancer patient management, there is still a lack of the molecular understanding of aggressive forms of the disease and clinical management of these patients remains difficult. The advent of high-throughput sequencing technologies has paved the way for a more complete understanding of the molecular make-up of the breast cancer genome. As such, it is becoming apparent that disruption of canonical splicing within breast cancer governs its clinical progression. In this review, we discuss the role of dysregulation of spliceosomal component genes and associated factors in the progression of breast cancer, their role in therapy resistance and the use of quantitative isoform expression as potential prognostic and predictive biomarkers with a particular focus on oestrogen receptor-positive breast cancer.
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Affiliation(s)
- Abigail Read
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
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31
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Hepburn LA, McHugh A, Fernandes K, Boag G, Proby CM, Leigh IM, Saville MK. Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-46. [PMID: 29796170 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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32
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Martinez-Montiel N, Rosas-Murrieta NH, Anaya Ruiz M, Monjaraz-Guzman E, Martinez-Contreras R. Alternative Splicing as a Target for Cancer Treatment. Int J Mol Sci 2018; 19:E545. [PMID: 29439487 DOI: 10.3390/ijms19020545] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.
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33
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Wong ACH, Rasko JEJ, Wong JJL. We skip to work: alternative splicing in normal and malignant myelopoiesis. Leukemia 2018; 32:1081-1093. [DOI: 10.1038/s41375-018-0021-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/14/2017] [Accepted: 12/22/2017] [Indexed: 12/15/2022]
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Vigevani L, Gohr A, Webb T, Irimia M, Valcárcel J. Molecular basis of differential 3' splice site sensitivity to anti-tumor drugs targeting U2 snRNP. Nat Commun 2017; 8:2100. [PMID: 29235465 DOI: 10.1038/s41467-017-02007-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/30/2017] [Indexed: 01/21/2023] Open
Abstract
Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the differential sensitivity of 3′ splice sites to these drugs. Sequences 5′ from the branch point (BP) region strongly influence drug sensitivity, with additional functional BPs reducing, and BP-like sequences allowing, drug responses. Drug-induced retained introns are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs. Drug-induced exon skipping preferentially affects shorter alternatively spliced regions with weaker BPs. Remarkably, structurally similar drugs display both common and differential effects on splicing regulation, SSA generally displaying stronger effects on intron retention, and Sudemycins more acute effects on exon skipping. Collectively, our results illustrate how splicing modulation is exquisitely sensitive to the sequence context of 3′ splice sites and to small structural differences between drugs. Several families of natural compounds target core components of the pre-mRNA splicing machinery and display anti-tumor activity. Here the authors show that particular sequence features can be linked to drug response, and that drugs with very similar chemical structures display substantially different effects on splicing regulation.
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Zöllner SK, Selvanathan SP, Graham GT, Commins RMT, Hong SH, Moseley E, Parks S, Haladyna JN, Erkizan HV, Dirksen U, Hogarty MD, Üren A, Toretsky JA. Inhibition of the oncogenic fusion protein EWS-FLI1 causes G 2-M cell cycle arrest and enhanced vincristine sensitivity in Ewing's sarcoma. Sci Signal 2017; 10:10/499/eaam8429. [PMID: 28974650 DOI: 10.1126/scisignal.aam8429] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ewing's sarcoma (ES) is a rare and highly malignant cancer that grows in the bones or surrounding tissues mostly affecting adolescents and young adults. A chimeric fusion between the RNA binding protein EWS and the ETS family transcription factor FLI1 (EWS-FLI1), which is generated from a chromosomal translocation, is implicated in driving most ES cases by modulation of transcription and alternative splicing. The small-molecule YK-4-279 inhibits EWS-FLI1 function and induces apoptosis in ES cells. We aimed to identify both the underlying mechanism of the drug and potential combination therapies that might enhance its antitumor activity. We tested 69 anticancer drugs in combination with YK-4-279 and found that vinca alkaloids exhibited synergy with YK-4-279 in five ES cell lines. The combination of YK-4-279 and vincristine reduced tumor burden and increased survival in mice bearing ES xenografts. We determined that independent drug-induced events converged to cause this synergistic therapeutic effect. YK-4-279 rapidly induced G2-M arrest, increased the abundance of cyclin B1, and decreased EWS-FLI1-mediated generation of microtubule-associated proteins, which rendered cells more susceptible to microtubule depolymerization by vincristine. YK-4-279 reduced the expression of the EWS-FLI1 target gene encoding the ubiquitin ligase UBE2C, which, in part, contributed to the increase in cyclin B1. YK-4-279 also increased the abundance of proapoptotic isoforms of MCL1 and BCL2, presumably through inhibition of alternative splicing by EWS-FLI1, thus promoting cell death in response to vincristine. Thus, a combination of vincristine and YK-4-279 might be therapeutically effective in ES patients.
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Affiliation(s)
- Stefan K Zöllner
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA.,Department of Pediatric Hematology and Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149 Münster, Germany
| | - Saravana P Selvanathan
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Garrett T Graham
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Ryan M T Commins
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Sung Hyeok Hong
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Eric Moseley
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Sydney Parks
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Jessica N Haladyna
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Hayriye V Erkizan
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Uta Dirksen
- Department of Pediatric Hematology and Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149 Münster, Germany
| | - Michael D Hogarty
- Division of Oncology, Children's Hospital of Philadelphia, Colket Translational Research Building, Room 3020, 3501 Civic Center Boulevard, Philadelphia, PA 19014, USA
| | - Aykut Üren
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - Jeffrey A Toretsky
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA.
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36
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. A Challenging Pie to Splice: Drugging the Spliceosome. Angew Chem Int Ed Engl 2017; 56:12052-12063. [PMID: 28371109 PMCID: PMC6311392 DOI: 10.1002/anie.201701065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 02/05/2023]
Abstract
Since its discovery in 1977, the study of alternative RNA splicing has revealed a plethora of mechanisms that had never before been documented in nature. Understanding these transitions and their outcome at the level of the cell and organism has become one of the great frontiers of modern chemical biology. Until 2007, this field remained in the hands of RNA biologists. However, the recent identification of natural product and synthetic modulators of RNA splicing has opened new access to this field, allowing for the first time a chemical-based interrogation of RNA splicing processes. Simultaneously, we have begun to understand the vital importance of splicing in disease, which offers a new platform for molecular discovery and therapy. As with many natural systems, gaining clear mechanistic detail at the molecular level is key towards understanding the operation of any biological machine. This minireview presents recent lessons learned in this emerging field of RNA splicing chemistry and chemical biology.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - Warren C. Chan
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. Das Spliceosom als Angriffspunkt für Pharmaka. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - Warren C. Chan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
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Pawellek A, Ryder U, Tammsalu T, King LJ, Kreinin H, Ly T, Hay RT, Hartley RC, Lamond AI. Characterisation of the biflavonoid hinokiflavone as a pre-mRNA splicing modulator that inhibits SENP. eLife 2017; 6:27402. [PMID: 28884683 PMCID: PMC5619949 DOI: 10.7554/elife.27402] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 09/06/2017] [Indexed: 12/17/2022] Open
Abstract
We have identified the plant biflavonoid hinokiflavone as an inhibitor of splicing in vitro and modulator of alternative splicing in cells. Chemical synthesis confirms hinokiflavone is the active molecule. Hinokiflavone inhibits splicing in vitro by blocking spliceosome assembly, preventing formation of the B complex. Cells treated with hinokiflavone show altered subnuclear organization specifically of splicing factors required for A complex formation, which relocalize together with SUMO1 and SUMO2 into enlarged nuclear speckles containing polyadenylated RNA. Hinokiflavone increases protein SUMOylation levels, both in in vitro splicing reactions and in cells. Hinokiflavone also inhibited a purified, E. coli expressed SUMO protease, SENP1, in vitro, indicating the increase in SUMOylated proteins results primarily from inhibition of de-SUMOylation. Using a quantitative proteomics assay we identified many SUMO2 sites whose levels increased in cells following hinokiflavone treatment, with the major targets including six proteins that are components of the U2 snRNP and required for A complex formation.
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Affiliation(s)
- Andrea Pawellek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ursula Ryder
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Triin Tammsalu
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Lewis J King
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Helmi Kreinin
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Tony Ly
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Richard C Hartley
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Pham D, Koide K. Discoveries, target identifications, and biological applications of natural products that inhibit splicing factor 3B subunit 1. Nat Prod Rep 2017; 33:637-47. [PMID: 26812544 DOI: 10.1039/c5np00110b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Covering: 1992 to 2015The natural products FR901464, pladienolide, and herboxidiene were discovered as activators of reporter gene systems. Unexpectedly, these compounds target neither transcription nor translation; rather, they target splicing factor 3B subunit 1 of the spliceosome, causing changes in splicing patterns. All of them showed anticancer activity in a low nanomolar range. Since their discovery, these molecules have been used in a variety of biological applications.
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Affiliation(s)
- Dianne Pham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA.
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40
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Teng T, Tsai JH, Puyang X, Seiler M, Peng S, Prajapati S, Aird D, Buonamici S, Caleb B, Chan B, Corson L, Feala J, Fekkes P, Gerard B, Karr C, Korpal M, Liu X, T Lowe J, Mizui Y, Palacino J, Park E, Smith PG, Subramanian V, Wu ZJ, Zou J, Yu L, Chicas A, Warmuth M, Larsen N, Zhu P. Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex. Nat Commun 2017; 8:15522. [PMID: 28541300 DOI: 10.1038/ncomms15522] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/05/2017] [Indexed: 01/28/2023] Open
Abstract
Pladienolide, herboxidiene and spliceostatin have been identified as splicing modulators that target SF3B1 in the SF3b subcomplex. Here we report that PHF5A, another component of this subcomplex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074 and SF3B1-V1078 confer resistance to these modulators, suggesting a common interaction site. RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but inhibits the global action of splicing modulators. Moreover, PHF5A-Y36C alters splicing modulator-induced intron-retention/exon-skipping profile, which correlates with the differential GC content between adjacent introns and exons. We determine the crystal structure of human PHF5A demonstrating that Y36 is located on a highly conserved surface. Analysis of the cryo-EM spliceosome Bact complex shows that the resistance mutations cluster in a pocket surrounding the branch point adenosine, suggesting a competitive mode of action. Collectively, we propose that PHF5A–SF3B1 forms a central node for binding to these splicing modulators. A number of natural occurring small-molecule splicing modulators are known. Here, the authors combine chemogenomic, structural and biochemical methods and show that these compounds also target the spliceosome-associated protein PHF5A and propose a potential modulator binding site in the PHF5A–SF3B1 complex.
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Makowski K, Vigevani L, Albericio F, Valcárcel J, Álvarez M. Sudemycin K: A Synthetic Antitumor Splicing Inhibitor Variant with Improved Activity and Versatile Chemistry. ACS Chem Biol 2017; 12:163-173. [PMID: 28103691 DOI: 10.1021/acschembio.6b00562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Important links exist between the process of pre-mRNA splicing and cancer, as illustrated by the frequent mutation of splicing factors in tumors and the emergence of various families of antitumor drugs that target components of the splicing machinery, notably SF3B1, a protein subunit of spliceosomal U2 small nuclear ribonucleoprotein particle (snRNP). Sudemycins are synthetic compounds that harbor a pharmacophore common to various classes of splicing inhibitors. Here, we describe the synthesis and functional characterization of novel sudemycin analogues that functionally probe key chemical groups within this pharmacophore. Our results confirm the importance of a conjugated diene group and in addition reveal significant spatial flexibility in this region of the molecule. Sudemycin K, a derivative that replaces the pharmacophore's oxycarbonyl by an amide group, displays improved potency as an inhibitor of cancer cell proliferation, as a regulator of alternative splicing in cultured cells and as an inhibitor of in vitro spliceosome assembly. Sudemycin K displays higher stability, likely related to the replacement of the oxycarbonyl group, which can be a substrate of esterases, by an amide group. The activity and special reactivity of sudemycin K can pave the way to the synthesis and evaluation of a variety of novel sudemycin derivatives.
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Affiliation(s)
- Kamil Makowski
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
| | - Luisa Vigevani
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr.
Aiguader 88, 08003 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
- Department
of Organic Chemistry, Faculty of Chemistry, University of Barcelona, Martí Franqués 1, 08028 Barcelona,Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Juan Valcárcel
- Centre
for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr.
Aiguader 88, 08003 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Mercedes Álvarez
- Institute for Research in Biomedicine (IRB-Barcelona), Baldiri i Reixac 10, 08028, Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
- Laboratory
of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, Joan XXIII s/n, 08028 Barcelona, Spain
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42
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Kumar D, Kashyap MK, La Clair JJ, Villa R, Spaanderman I, Chien S, Rassenti LZ, Kipps TJ, Burkart MD, Castro JE. Selectivity in Small Molecule Splicing Modulation. ACS Chem Biol 2016; 11:2716-2723. [PMID: 27499047 DOI: 10.1021/acschembio.6b00399] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dysregulation of RNA splicing is a molecular hallmark of disease, including different and often complex cancers. While gaining recognition as a target for therapeutic discovery, understanding the complex mechanisms guiding RNA splicing remains a challenge for chemical biology. The discovery of small molecule splicing modulators has recently enabled an evaluation of the mechanisms of aberrant splicing. We now report on three unique features within the selectivity of splicing modulators. First, we provide evidence that structural modifications within a splicing modulator can alter the splicing of introns in specific genes differently. These studies indicate that structure activity relationships not only have an effect on splicing activity but also include specificity for specific introns within different genes. Second, we find that these splicing modulators also target the mRNAs encoding components of the spliceosome itself. Remarkably, this effect includes the genes for the SF3B complex, a target of pladienolide B and related splicing modulators. Finally, we report on the first observation of a temporal phenomenon associated with small molecule splicing modulation. Combined, these three observations provide an important new perspective for the exploration of splicing modulation in terms of both future medicinal chemistry programs as well as understanding the key facets underlying its timing.
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Affiliation(s)
- Deepak Kumar
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Manoj K Kashyap
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Ide Spaanderman
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Stephen Chien
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
| | - Laura Z Rassenti
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Thomas J Kipps
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California , San Diego, La Jolla, California 92093-0358, United States
| | - Januario E Castro
- The Moores Cancer Center, University of California San Diego , La Jolla, California 92093, United States
- CLL Research Consortium, and Department of Medicine, University of California , San Diego, La Jolla, California 92093-0358, United States
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Abstract
The advent of next-generation sequencing technologies has unveiled a new window into the heterogeneity of acute myeloid leukemia (AML). In particular, recurrent mutations in spliceosome machinery and genome-wide aberrant splicing events have been recognized as a prominent component of this disease. This review will focus on how these factors influence drug resistance through altered splicing of tumor suppressor and oncogenes and dysregulation of the apoptotic signaling network. A better understanding of these factors in disease progression is necessary to design appropriate therapeutic strategies recognizing specific alternatively spliced or mutated oncogenic targets.
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Affiliation(s)
- Rosalia de Necochea-Campion
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Geoffrey P Shouse
- Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA
| | - Qi Zhou
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Saied Mirshahidi
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chien-Shing Chen
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA. .,Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA.
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44
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Xargay-Torrent S, López-Guerra M, Rosich L, Montraveta A, Roldán J, Rodríguez V, Villamor N, Aymerich M, Lagisetti C, Webb TR, López-Otín C, Campo E, Colomer D. The splicing modulator sudemycin induces a specific antitumor response and cooperates with ibrutinib in chronic lymphocytic leukemia. Oncotarget 2016; 6:22734-49. [PMID: 26068951 PMCID: PMC4673195 DOI: 10.18632/oncotarget.4212] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 05/26/2015] [Indexed: 12/20/2022] Open
Abstract
Mutations or deregulated expression of the components of the spliceosome can influence the splicing pattern of several genes and contribute to the development of tumors. In this context, we report that the spliceosome modulator sudemycin induces selective cytotoxicity in primary chronic lymphocytic leukemia (CLL) cells when compared with healthy lymphocytes and tumor cells from other B-lymphoid malignancies, with a slight bias for CLL cases with mutations in spliceosome-RNA processing machinery. Consistently, sudemycin exhibits considerable antitumor activity in NOD/SCID/IL2Rγ−/− (NSG) mice engrafted with primary cells from CLL patients. The antileukemic effect of sudemycin involves the splicing modulation of several target genes important for tumor survival, both in SF3B1-mutated and -unmutated cases. Thus, the apoptosis induced by this compound is related to the alternative splicing switch of MCL1 toward its proapoptotic isoform. Sudemycin also functionally disturbs NF-κB pathway in parallel with the induction of a spliced RELA variant that loses its DNA binding domain. Importantly, we show an enhanced antitumor effect of sudemycin in combination with ibrutinib that might be related to the modulation of the alternative splicing of the inhibitor of Btk (IBTK). In conclusion, we provide first evidence that the spliceosome is a relevant therapeutic target in CLL, supporting the use of splicing modulators alone or in combination with ibrutinib as a promising approach for the treatment of CLL patients.
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Affiliation(s)
- Sílvia Xargay-Torrent
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica López-Guerra
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laia Rosich
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Arnau Montraveta
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jocabed Roldán
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Vanina Rodríguez
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Neus Villamor
- Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marta Aymerich
- Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Chandraiah Lagisetti
- Center for Chemical Biology, Biosciences Division, SRI International, Menlo Park, California, USA
| | - Thomas R Webb
- Center for Chemical Biology, Biosciences Division, SRI International, Menlo Park, California, USA
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo - IUOPA, Oviedo, Spain
| | - Elias Campo
- Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Dolors Colomer
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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45
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Effenberger KA, Urabe VK, Jurica MS. Modulating splicing with small molecular inhibitors of the spliceosome. Wiley Interdiscip Rev RNA 2016; 8. [PMID: 27440103 DOI: 10.1002/wrna.1381] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 06/06/2016] [Accepted: 06/28/2016] [Indexed: 12/23/2022]
Abstract
Small molecule inhibitors that target components of the spliceosome have great potential as tools to probe splicing mechanism and dissect splicing regulatory networks in cells. These compounds also hold promise as drug leads for diseases in which splicing regulation plays a critical role, including many cancers. Because the spliceosome is a complicated and dynamic macromolecular machine comprised of many RNA and protein components, a variety of compounds that interfere with different aspects of spliceosome assembly is needed to probe its function. By screening chemical libraries with high-throughput splicing assays, several labs have added to the collection of splicing inhibitors, although the mechanistic insight into splicing yielded from the initial compound hits is somewhat limited so far. In contrast, SF3B1 inhibitors stand out as a great example of what can be accomplished with small molecule tools. This group of compounds were first discovered as natural products that are cytotoxic to cancer cells, and then later shown to target the core spliceosome protein SF3B1. The inhibitors have since been used to uncover details of SF3B1 mechanism in the spliceosome and its impact on gene expression in cells. Continuing structure activity relationship analysis of the compounds is also making progress in identifying chemical features key to their function, which is critical in understanding the mechanism of SF3B1 inhibition. The knowledge is also important for the design of analogs with new and useful features for both splicing researchers and clinicians hoping to exploit splicing as pressure point to target in cancer therapy. WIREs RNA 2017, 8:e1381. doi: 10.1002/wrna.1381 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kerstin A Effenberger
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | - Veronica K Urabe
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
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46
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Abstract
Small-molecule splice modulators have recently been recognized for their clinical potential for diverse cancers. This, combined with their use as tools to study the importance of splice-regulated events and their association with disease, continues to fuel the discovery of new splice modulators. One of the key challenges found in the current class of materials arises from their instability, where rapid metabolic degradation can lead to off-target responses. We now describe the preparation of bench-stable splice modulators by adapting carbohydrate motifs as a central scaffold to provide rapid access to potent splice modulators.
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Affiliation(s)
- Sachin Dhar
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Brian León
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Justin C Hammons
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Zhe Yu
- Moores Cancer Center, University of California-San Diego , La Jolla, California 92093-0358, United States
| | - Manoj K Kashyap
- Moores Cancer Center, University of California-San Diego , La Jolla, California 92093-0358, United States
| | - Januario E Castro
- Moores Cancer Center, University of California-San Diego , La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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47
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Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is often stated as a mark of transcriptionally active promoters. However, closer study of the positioning of H3K4me3 shows the mark locating primarily after the first exon at the 5′ splice site and overlapping with a CpG island in mammalian cells. There are several enzyme complexes that are involved in the placement of the H3K4me3 mark, including multiple protein complexes containing SETD1A, SETD1B, and MLL1 enzymes (writers). CXXC1, which is associated with SETD1A and SETD1B, target these enzymes to unmethylated CpG islands. Lysine demethylases (KDM5 family members, erasers) demethylate H3K4me3. The H3K4me3 mark is recognized by several proteins (readers), including lysine acetyltransferase complexes, chromatin remodelers, and RNA bound proteins involved in pre-mRNA splicing. Interestingly, attenuation of H3K4me3 impacts pre-mRNA splicing, and inhibition of pre-mRNA splicing attenuates H3K4me3.
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Affiliation(s)
- James R. Davie
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Wayne Xu
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Genevieve P. Delcuve
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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48
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Larrayoz M, Blakemore SJ, Dobson RC, Blunt MD, Rose-Zerilli MJ, Walewska R, Duncombe A, Oscier D, Koide K, Forconi F, Packham G, Yoshida M, Cragg MS, Strefford JC, Steele AJ. The SF3B1 inhibitor spliceostatin A (SSA) elicits apoptosis in chronic lymphocytic leukaemia cells through downregulation of Mcl-1. Leukemia 2016; 30:351-60. [PMID: 26488112 DOI: 10.1038/leu.2015.286] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 09/03/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022]
Abstract
The pro-survival Bcl-2 family member Mcl-1 is expressed in chronic lymphocytic leukaemia (CLL), with high expression correlated with progressive disease. The spliceosome inhibitor spliceostatin A (SSA) is known to regulate Mcl-1 and so here we assessed the ability of SSA to elicit apoptosis in CLL. SSA induced apoptosis of CLL cells at low nanomolar concentrations in a dose- and time-dependent manner, but independently of SF3B1 mutational status, IGHV status and CD38 or ZAP70 expression. However, normal B and T cells were less sensitive than CLL cells (P=0.006 and P<0.001, respectively). SSA altered the splicing of anti-apoptotic MCL-1(L) to MCL-1(s) in CLL cells coincident with induction of apoptosis. Overexpression studies in Ramos cells suggested that Mcl-1 was important for SSA-induced killing since its expression inversely correlated with apoptosis (P=0.001). IL4 and CD40L, present in patient lymph nodes, are known to protect tumour cells from apoptosis and significantly inhibited SSA, ABT-263 and ABT-199 induced killing following administration to CLL cells (P=0.008). However, by combining SSA with the Bcl-2/Bcl-x(L) antagonists ABT-263 or ABT-199, we were able to overcome this pro-survival effect. We conclude that SSA combined with Bcl-2/Bcl-x(L) antagonists may have therapeutic utility for CLL.
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Kashyap MK, Kumar D, Villa R, La Clair JJ, Benner C, Sasik R, Jones H, Ghia EM, Rassenti LZ, Kipps TJ, Burkart MD, Castro JE. Targeting the spliceosome in chronic lymphocytic leukemia with the macrolides FD-895 and pladienolide-B. Haematologica 2015; 100:945-54. [PMID: 25862704 PMCID: PMC4486229 DOI: 10.3324/haematol.2014.122069] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/02/2015] [Indexed: 02/05/2023] Open
Abstract
RNA splicing plays a fundamental role in human biology. Its relevance in cancer is rapidly emerging as demonstrated by spliceosome mutations that determine the prognosis of patients with hematologic malignancies. We report studies using FD-895 and pladienolide-B in primary leukemia cells derived from patients with chronic lymphocytic leukemia and leukemia-lymphoma cell lines. We found that FD-895 and pladienolide-B induce an early pattern of mRNA intron retention - spliceosome modulation. This process was associated with apoptosis preferentially in cancer cells as compared to normal lymphocytes. The pro-apoptotic activity of these compounds was observed regardless of poor prognostic factors such as Del(17p), TP53 or SF3B1 mutations and was able to overcome the protective effect of culture conditions that resemble the tumor microenvironment. In addition, the activity of these compounds was observed not only in vitro but also in vivo using the A20 lymphoma murine model. Overall, these findings give evidence for the first time that spliceosome modulation is a valid target in chronic lymphocytic leukemia and provide an additional rationale for the development of spliceosome modulators for cancer therapy.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Cell Line, Tumor
- Epoxy Compounds/pharmacology
- Gene Expression
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Macrolides/pharmacology
- Mice
- Mice, Inbred BALB C
- Mutation
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- RNA Splicing/drug effects
- RNA Splicing Factors
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Spliceosomes/drug effects
- Survival Analysis
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Manoj K Kashyap
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Deepak Kumar
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Chris Benner
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roman Sasik
- Center for Computational Biology, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Harrison Jones
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Emanuela M Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA CLL Research Consortium, and Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA CLL Research Consortium, and Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Januario E Castro
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA CLL Research Consortium, and Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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Wojtuszkiewicz A, Assaraf YG, Maas MJP, Kaspers GJL, Jansen G, Cloos J. Pre-mRNA splicing in cancer: the relevance in oncogenesis, treatment and drug resistance. Expert Opin Drug Metab Toxicol 2014; 11:673-89. [PMID: 25495223 DOI: 10.1517/17425255.2015.993316] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Aberrant pre-mRNA splicing in cancer is emerging as an important determinant of oncogenesis, response to treatment and anticancer drug resistance. At the same time, the spliceosome has become a target for a novel class of pre-clinical chemotherapeutics with a potential future application in cancer treatment. Taken together, these findings offer novel opportunities for the enhancement of the efficacy of cancer therapy. AREAS COVERED This review presents a comprehensive overview of the molecular mechanisms involved in splicing and current developments regarding splicing aberrations in relation to several aspects of cancer formation and therapy. Identified mutations in the various components of the spliceosome and their implications for cancer prognosis are delineated. Moreover, the contribution of abnormal splicing patterns as well as deregulated splicing factors to chemoresistance is discussed, along with novel splicing-based therapeutic approaches. EXPERT OPINION Significant progress has been made in deciphering the role of splicing factors in cancer including carcinogenesis and drug resistance. Splicing-based prognostic tools as well as therapeutic options hold great potential towards improvements in cancer therapy. However, gaining more in-depth molecular insight into the consequences of mutations in various components of the splicing machinery as well as of cellular effects of spliceosome inhibition is a prerequisite to establish the role of splicing in tumor progression and treatment options, respectively.
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Affiliation(s)
- Anna Wojtuszkiewicz
- VU University Medical Center, Department of Pediatric Oncology/Hematology , Amsterdam , The Netherlands
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