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Anglada-Girotto M, Ciampi L, Bonnal S, Head SA, Miravet-Verde S, Serrano L. In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications. Nat Commun 2024; 15:7039. [PMID: 39147755 PMCID: PMC11327330 DOI: 10.1038/s41467-024-51380-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/06/2024] [Indexed: 08/17/2024] Open
Abstract
Alternative splicing is crucial for cancer progression and can be targeted pharmacologically, yet identifying driver exons genome-wide remains challenging. We propose identifying such exons by associating statistically gene-level cancer dependencies from knockdown viability screens with splicing profiles and gene expression. Our models predict the effects of splicing perturbations on cell proliferation from transcriptomic data, enabling in silico RNA screening and prioritizing targets for splicing-based therapies. We identified 1,073 exons impacting cell proliferation, many from genes not previously linked to cancer. Experimental validation confirms their influence on proliferation, especially in highly proliferative cancer cell lines. Integrating pharmacological screens with splicing dependencies highlights the potential driver exons affecting drug sensitivity. Our models also allow predicting treatment outcomes from tumor transcriptomes, suggesting applications in precision oncology. This study presents an approach to identifying cancer driver exon and their therapeutic potential, emphasizing alternative splicing as a cancer target.
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Affiliation(s)
- Miquel Anglada-Girotto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sarah A Head
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland.
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain.
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2
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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] [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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3
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Wu L, Wang D. The "Janus-like" RNA-editing machinery in innate antiviral immunity. CURRENT TRENDS IN IMMUNOLOGY 2022; 23:23-32. [PMID: 36398055 PMCID: PMC9668064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Our innate immune systems are evolved to provide the first line of immune defense against microbial infections. A key effector component is the adenosine deaminase acting on the RNA-1 (ADAR-1)/interferon (IFN) pathway of the innate cytoplasmic immunity that mounts rapid responses to many viral pathogens. As an RNA-editing enzyme, ADAR-1 targets viral RNA intermediates in the cytoplasmic compartment to interfere with the infection. However, ADAR-1 may also edit characteristic RNA structures of certain host genes, notably, the 5-hydroxytryptamine (serotonin) receptor 2C (5-HT2CR). Dysfunction of 5-HT2CR has been linked to the pathology of several human mental conditions, such as Schizophrenia, anxiety, bipolar disorder, major depression, and the mental illnesses of substance use disorders (SUD). Thus, the ADAR-1-mediated RNA editing may be either beneficial or harmful; these effects need to be tightly modulated to sustain innate antiviral immunity while restricting undesired off-target self-reactivity. In this communication, we discuss ideas and tools to identify the orphan drug candidates, including small molecules and biologics that may serve as effective modulators of the ADAR-1/IFN innate immunity and are thereby promising for use in treating or preventing SUD- and/or viral infection-associated mental illnesses.
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4
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Sahin I, George A, Seyhan AA. Therapeutic Targeting of Alternative RNA Splicing in Gastrointestinal Malignancies and Other Cancers. Int J Mol Sci 2021; 22:11790. [PMID: 34769221 PMCID: PMC8583749 DOI: 10.3390/ijms222111790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/22/2022] Open
Abstract
Recent comprehensive genomic studies including single-cell RNA sequencing and characterization have revealed multiple processes by which protein-coding and noncoding RNA processing are dysregulated in many cancers. More specifically, the abnormal regulation of mRNA and precursor mRNA (pre-mRNA) processing, which includes the removal of introns by splicing, is frequently altered in tumors, producing multiple different isoforms and diversifying protein expression. These alterations in RNA processing result in numerous cancer-specific mRNAs and pathogenically spliced events that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumor suppressor genes. Abnormally spliced pre-mRNAs are also associated with resistance to cancer treatment, and certain cancers are highly sensitive to the pharmacological inhibition of splicing. The discovery of these alterations in RNA processing has not only provided new insights into cancer pathogenesis but identified novel therapeutic vulnerabilities and therapeutic opportunities in targeting these aberrations in various ways (e.g., small molecules, splice-switching oligonucleotides (SSOs), and protein therapies) to modulate alternative RNA splicing or other RNA processing and modification mechanisms. Some of these strategies are currently progressing toward clinical development or are already in clinical trials. Additionally, tumor-specific neoantigens produced from these pathogenically spliced events and other abnormal RNA processes provide a potentially extensive source of tumor-specific therapeutic antigens (TAs) for targeted cancer immunotherapy. Moreover, a better understanding of the molecular mechanisms associated with aberrant RNA processes and the biological impact they play might provide insights into cancer initiation, progression, and metastasis. Our goal is to highlight key alternative RNA splicing and processing mechanisms and their roles in cancer pathophysiology as well as emerging therapeutic alternative splicing targets in cancer, particularly in gastrointestinal (GI) malignancies.
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Affiliation(s)
- Ilyas Sahin
- Division of Hematology Oncology, Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL 32610, USA;
| | - Andrew George
- Department of Chemistry, Brown University, Providence, RI 02912, USA;
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA
| | - Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI 02912, USA
- Cancer Center at Brown University, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
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5
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Total Syntheses of Pladienolide-Derived Spliceosome Modulators. Molecules 2021; 26:molecules26195938. [PMID: 34641481 PMCID: PMC8512135 DOI: 10.3390/molecules26195938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022] Open
Abstract
Pladienolides, an emerging class of naturally occurring spliceosome modulators, exhibit interesting structural features, such as highly substituted 12-membered macrocycles and epoxide-containing diene side chains. The potential of pladienolides as anti-cancer agents is confirmed by H3B-8800, a synthetic analog of this natural product class, which is currently under Phase I clinical trials. Since its isolation in 2004 and the first total synthesis in 2007, a dozen total syntheses and synthetic approaches toward the pladienolide class have been reported to date. This review focuses on the eight completed total syntheses of naturally occurring pladienolides or their synthetic analogs, in addition to a synthetic approach to the main framework of the natural product.
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6
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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7
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Cretu C, Gee P, Liu X, Agrawal A, Nguyen TV, Ghosh AK, Cook A, Jurica M, Larsen NA, Pena V. Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Nat Commun 2021; 12:4491. [PMID: 34301950 PMCID: PMC8302644 DOI: 10.1038/s41467-021-24741-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/27/2022] Open
Abstract
Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)—a complex chaperoning the selection of branch and 3′ splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept. Chemical modulation of intron selection has emerged as a route for cancer therapy. Here, structures of the U2 snRNP’s SF3B module and of prespliceosome- both in complexes with splicing modulators- provide insight into the mechanisms of intron recognition and branch site inactivation.
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Affiliation(s)
- Constantin Cretu
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.,Cluster of Excellence Multiscale Bioimaging (MBExC), Universitätsmedizin Göttingen, Göttingen, Germany
| | | | - Xiang Liu
- H3 Biomedicine, Inc, Cambridge, MA, USA
| | | | | | - Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Melissa Jurica
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | | | - Vladimir Pena
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.
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8
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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9
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Yang JY, Huo YM, Yang MW, Shen Y, Liu DJ, Fu XL, Tao LY, He RZ, Zhang JF, Hua R, Jiang SH, Sun YW, Liu W. SF3B1 mutation in pancreatic cancer contributes to aerobic glycolysis and tumor growth through a PP2A-c-Myc axis. Mol Oncol 2021; 15:3076-3090. [PMID: 33932092 PMCID: PMC8564647 DOI: 10.1002/1878-0261.12970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/17/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
Hot spot gene mutations in splicing factor 3b subunit 1 (SF3B1) are observed in many types of cancer and create abundant aberrant mRNA splicing, which is profoundly implicated in tumorigenesis. Here, we identified that the SF3B1 K700E (SF3B1K700E) mutation is strongly associated with tumor growth in pancreatic ductal adenocarcinoma (PDAC). Knockdown of SF3B1 significantly retarded cell proliferation and tumor growth in a cell line (Panc05.04) with the SF3B1K700E mutation. However, SF3B1 knockdown had no notable effect on cell proliferation in two cell lines (BxPC3 and AsPC1) carrying wild‐type SF3B1. Ectopic expression of SF3B1K700E but not SF3B1WT in SF3B1‐knockout Panc05.04 cells largely restored the inhibitory role induced by SF3B1 knockdown. Introduction of the SF3B1K700E mutation in BxPC3 and AsPC1 cells also boosted cell proliferation. Gene set enrichment analysis demonstrated a close correlation between SF3B1 mutation and aerobic glycolysis. Functional analyses showed that the SF3B1K700E mutation promoted tumor glycolysis, as evidenced by glucose consumption, lactate release, and extracellular acidification rate. Mechanistically, the SF3B1 mutation promoted the aberrant splicing of PPP2R5A and led to the activation of the glycolytic regulator c‐Myc via post‐translational regulation. Pharmacological activation of PP2A with FTY‐720 markedly compromised the growth advantage induced by the SF3B1K700E mutation in vitro and in vivo. Taken together, our data suggest a novel function for SF3B1 mutation in the Warburg effect, and this finding may offer a potential therapeutic strategy against PDAC with the SF3B1K700E mutation.
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Affiliation(s)
- Jian-Yu Yang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan-Miao Huo
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min-Wei Yang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Shen
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - De-Jun Liu
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Liang Fu
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ling-Ye Tao
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Zhe He
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Feng Zhang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Hua
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Ren Ji Hospital, Shanghai Jiao Tong University, China
| | - Yong-Wei Sun
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Liu
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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10
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Rouf Banday A, Onabajo OO, Lin SHY, Obajemu A, Vargas JM, Delviks-Frankenberry KA, Lamy P, Bayanjargal A, Zettelmeyer C, Florez-Vargas O, Pathak VK, Dyrskjøt L, Prokunina-Olsson L. Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity. Commun Biol 2021; 4:386. [PMID: 33753867 PMCID: PMC7985488 DOI: 10.1038/s42003-021-01844-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
APOBEC3A (A3A) and APOBEC3B (A3B) enzymes drive APOBEC-mediated mutagenesis. Identification of factors affecting the activity of these enzymes could help modulate mutagenesis and associated clinical outcomes. Here, we show that canonical and alternatively spliced A3A and A3B isoforms produce corresponding mutagenic and non-mutagenic enzymes. Increased expression of the mutagenic A3B isoform predicted shorter progression-free survival in bladder cancer. We demonstrate that the production of mutagenic vs. non-mutagenic A3B protein isoforms was considerably affected by inclusion/skipping of exon 5 in A3B. Furthermore, exon 5 skipping, resulting in lower levels of mutagenic A3B enzyme, could be increased in vitro. Specifically, we showed the effects of treatment with an SF3B1 inhibitor affecting spliceosome interaction with a branch point site in intron 4, or with splice-switching oligonucleotides targeting exon 5 of A3B. Our results underscore the clinical role of A3B and implicate alternative splicing of A3B as a mechanism that could be targeted to restrict APOBEC-mediated mutagenesis.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Seraph Han-Yin Lin
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adeola Obajemu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ariunaa Bayanjargal
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara Zettelmeyer
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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11
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Molecular Targeted Therapy in Myelodysplastic Syndromes: New Options for Tailored Treatments. Cancers (Basel) 2021; 13:cancers13040784. [PMID: 33668555 PMCID: PMC7917605 DOI: 10.3390/cancers13040784] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Myelodysplastic syndromes (MDS) are a group of diseases in which bone marrow stem cells acquire genetic alterations and can initiate leukemia, blocking the production of mature blood cells. It is of crucial importance to identify those genetic abnormalities because some of them can be the targeted. To date only very few drugs are approved for patients manifesting this group of disorders and there is an urgent need to develop new effective therapies. This review gives an overview of the genetic of MDS and the therapeutic options available and in clinical experimentation. Abstract Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, progressive cytopenias and increased risk of transformation to acute myeloid leukemia. The improved understanding of the underlying biology and genetics of MDS has led to better disease and risk classification, paving the way for novel therapeutic opportunities. Indeed, we now have a vast pipeline of targeted agents under pre-clinical and clinical development, potentially able to modify the natural history of the diverse disease spectrum of MDS. Here, we review the latest therapeutic approaches (investigational and approved agents) for MDS treatment. A deep insight will be given to molecularly targeted therapies by reviewing new agents for individualized precision medicine.
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12
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Kim Guisbert KS, Mossiah I, Guisbert E. Titration of SF3B1 Activity Reveals Distinct Effects on the Transcriptome and Cell Physiology. Int J Mol Sci 2020; 21:ijms21249641. [PMID: 33348896 PMCID: PMC7766730 DOI: 10.3390/ijms21249641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/16/2022] Open
Abstract
SF3B1 is a core component of the U2 spliceosome that is frequently mutated in cancer. We have previously shown that titrating the activity of SF3B1, using the inhibitor pladienolide B (PB), affects distinct steps of the heat shock response (HSR). Here, we identify other genes that are sensitive to different levels of SF3B1 (5 vs. 100 nM PB) using RNA sequencing. Significant changes to mRNA splicing were identified at both low PB and high PB concentrations. Changes in expression were also identified in the absence of alternative splicing, suggesting that SF3B1 influences other gene expression pathways. Surprisingly, gene expression changes identified in low PB are not predictive of changes in high PB. Specific pathways were identified with differential sensitivity to PB concentration, including nonsense-mediated decay and protein-folding homeostasis, both of which were validated using independent reporter constructs. Strikingly, cells exposed to low PB displayed enhanced protein-folding capacity relative to untreated cells. These data reveal that the transcriptome is exquisitely sensitive to SF3B1 and suggests that the activity of SF3B1 is finely regulated to coordinate mRNA splicing, gene expression and cellular physiology.
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Zhang D, Meng F. A Comprehensive Overview of Structure-Activity Relationships of Small-Molecule Splicing Modulators Targeting SF3B1 as Anticancer Agents. ChemMedChem 2020; 15:2098-2120. [PMID: 33037739 DOI: 10.1002/cmdc.202000642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/19/2020] [Indexed: 02/06/2023]
Abstract
The pre-mRNA splicing factor SF3B1 shows recurrent mutations among hematologic malignancies and some solid tumors. In 2007, the identification of two cytotoxic natural products, which showed splicing inhibition by binding to SF3b, prompted the development of small-molecule splicing modulators of SF3B1 as therapeutics for cancer. Recent studies suggested that spliceosome-mutant cells are preferentially sensitive to pharmacologic splicing modulation; therefore, exploring the clinical utility of splicing modulator therapies in patients with spliceosome-mutant hematologic malignancies who have failed current therapies is greatly needed, as these patients have few treatment options. H3B-8800 had unique pharmacological activity and exhibited favorable data in phase I clinical trials to treat patients with advanced myeloid malignancies, indicating that further clinical trials are promising. The most established small-molecule modulators of SF3B1 can be categorized into three classes: the bicycles, the monopyranes, and the 12-membered macrolides. This review provides a comprehensive overview of the structure-activity relationships of small-molecule SF3B1 modulators, with a detailed analysis of interactions between modulators and protein binding pocket. The future strategy for splicing modulators development is also discussed.
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Affiliation(s)
- Datong Zhang
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, P. R. China
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, 306 Huiren Road, Tianjin, 300301, P. R. China
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14
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The biological function and clinical significance of SF3B1 mutations in cancer. Biomark Res 2020; 8:38. [PMID: 32905346 PMCID: PMC7469106 DOI: 10.1186/s40364-020-00220-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
Spliceosome mutations have become the most interesting mutations detected in human cancer in recent years. The spliceosome, a large, dynamic multimegadalton small nuclear ribonucleoprotein composed of small nuclear RNAs associated with proteins, is responsible for removing introns from precursor mRNA (premRNA) and generating mature, spliced mRNAs. SF3B1 is the largest subunit of the spliceosome factor 3b (SF3B) complex, which is a core component of spliceosomes. Recurrent somatic mutations in SF3B1 have been detected in human cancers, including hematological malignancies and solid tumors, and indicated to be related to patient prognosis. This review summarizes the research progress of SF3B1 mutations in cancer, including SF3B1 mutations in the HEAT domain, the multiple roles and aberrant splicing events of SF3B1 mutations in the pathogenesis of tumors, and changes in mutated cancer cells regarding sensitivity to SF3B small-molecule inhibitors. In addition, the potential of SF3B1 or its mutations to serve as biomarkers or therapeutic targets in cancer is discussed. The accumulated knowledge about SF3B1 mutations in cancer provides critical insight into the integral role the SF3B1 protein plays in mRNA splicing and suggests new targets for anticancer therapy.
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15
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Silencing Core Spliceosome Sm Gene Expression Induces a Cytotoxic Splicing Switch in the Proteasome Subunit Beta 3 mRNA in Non-Small Cell Lung Cancer Cells. Int J Mol Sci 2020; 21:ijms21124192. [PMID: 32545483 PMCID: PMC7349683 DOI: 10.3390/ijms21124192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
The core spliceosomal Sm proteins were recently proposed as cancer-selective lethal targets in non-small cell lung cancer (NSCLC). In contrast, the loss of the commonly mutated cancer target SF3B1 appeared to be toxic to non-malignant cells as well. In the current study, the transcriptomes of A549 NSCLC cells, in which SF3B1 or SNRPD3 was silenced, were compared using RNA sequencing. The skipping of exon 4 of the proteasomal subunit beta type-3 (PSMB3) mRNA, resulting in a shorter PSMB3-S variant, occurred only after silencing SNRPD3. This observation was extended to the other six Sm genes. Remarkably, the alternative splicing of PSMB3 mRNA upon Sm gene silencing was not observed in non-malignant IMR-90 lung fibroblasts. Furthermore, PSMB3 was found to be overexpressed in NSCLC clinical samples and PSMB3 expression correlated with Sm gene expression. Moreover, a high PSMB3 expression corresponds to worse survival in patients with lung adenocarcinomas. Finally, silencing the canonical full-length PSMB3-L, but not the shorter PSMB3-S variant, was cytotoxic and was accompanied by a decrease in proteasomal activity. Together, silencing Sm genes, but not SF3B1, causes a cytotoxic alternative splicing switch in the PSMB3 mRNA in NSCLC cells only.
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16
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Rahman MA, Nasrin F, Bhattacharjee S, Nandi S. Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine. Cancers (Basel) 2020; 12:cancers12061381. [PMID: 32481522 PMCID: PMC7352608 DOI: 10.3390/cancers12061381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.
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17
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Roles and mechanisms of alternative splicing in cancer - implications for care. Nat Rev Clin Oncol 2020; 17:457-474. [PMID: 32303702 DOI: 10.1038/s41571-020-0350-x] [Citation(s) in RCA: 379] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [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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18
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Taylor J, Lee SC. Mutations in spliceosome genes and therapeutic opportunities in myeloid malignancies. Genes Chromosomes Cancer 2019; 58:889-902. [PMID: 31334570 PMCID: PMC6852509 DOI: 10.1002/gcc.22784] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of RNA splicing more than 40 years ago, our comprehension of the molecular events orchestrating constitutive and alternative splicing has greatly improved. Dysregulation of pre-mRNA splicing has been observed in many human diseases including neurodegenerative diseases and cancer. The recent identification of frequent somatic mutations in core components of the spliceosome in myeloid malignancies and functional analysis using model systems has advanced our knowledge of how splicing alterations contribute to disease pathogenesis. In this review, we summarize our current understanding on the mechanisms of how mutant splicing factors impact splicing and the resulting functional and pathophysiological consequences. We also review recent advances to develop novel therapeutic approaches targeting splicing catalysis and splicing regulatory proteins, and discuss emerging technologies using oligonucleotide-based therapies to modulate pathogenically spliced isoforms.
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Affiliation(s)
- Justin Taylor
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkNew York
- Leukemia Service, Department of MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew York
| | - Stanley C. Lee
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkNew York
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19
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Visconte V, O. Nakashima M, J. Rogers H. Mutations in Splicing Factor Genes in Myeloid Malignancies: Significance and Impact on Clinical Features. Cancers (Basel) 2019; 11:E1844. [PMID: 31766606 PMCID: PMC6966670 DOI: 10.3390/cancers11121844] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 11/16/2022] Open
Abstract
Components of the pre-messenger RNA splicing machinery are frequently mutated in myeloid malignancies. Mutations in LUC7L2, PRPF8, SF3B1, SRSF2, U2AF1, and ZRSR2 genes occur at various frequencies ranging between 40% and 85% in different subtypes of myelodysplastic syndrome (MDS) and 5% and 10% of acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPNs). In some instances, splicing factor (SF) mutations have provided diagnostic utility and information on clinical outcomes as exemplified by SF3B1 mutations associated with increased ring sideroblasts (RS) in MDS-RS or MDS/MPN-RS with thrombocytosis. SF3B1 mutations are associated with better survival outcomes, while SRSF2 mutations are associated with a shorter survival time and increased AML progression, and U2AF1 mutations with a lower remission rate and shorter survival time. Beside the presence of mutations, transcriptomics technologies have shown that one third of genes in AML patients are differentially expressed, leading to altered transcript stability, interruption of protein function, and improper translation compared to those of healthy individuals. The detection of SF mutations demonstrates the importance of splicing abnormalities in the hematopoiesis of MDS and AML patients given the fact that abnormal splicing regulates the function of several transcriptional factors (PU.1, RUNX1, etc.) crucial in hematopoietic function. This review provides a summary of the significance of the most frequently mutated SF genes in myeloid malignancies and an update on novel targeted therapies in experimental and clinical trial stages.
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Affiliation(s)
- Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Megan O. Nakashima
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Heesun J. Rogers
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH 44195, USA;
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20
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Nussbacher JK, Tabet R, Yeo GW, Lagier-Tourenne C. Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions. Neuron 2019; 102:294-320. [PMID: 30998900 DOI: 10.1016/j.neuron.2019.03.014] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 01/24/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
RNA binding proteins are critical to the maintenance of the transcriptome via controlled regulation of RNA processing and transport. Alterations of these proteins impact multiple steps of the RNA life cycle resulting in various molecular phenotypes such as aberrant RNA splicing, transport, and stability. Disruption of RNA binding proteins and widespread RNA processing defects are increasingly recognized as critical determinants of neurological diseases. Here, we describe distinct mechanisms by which the homeostasis of RNA binding proteins is compromised in neurological disorders through their reduced expression level, increased propensity to aggregate or sequestration by abnormal RNAs. These mechanisms all converge toward altered neuronal function highlighting the susceptibility of neurons to deleterious changes in RNA expression and the central role of RNA binding proteins in preserving neuronal integrity. Emerging therapeutic approaches to mitigate or reverse alterations of RNA binding proteins in neurological diseases are discussed.
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Affiliation(s)
- Julia K Nussbacher
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Ricardos Tabet
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA.
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21
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Desterro J, Bak-Gordon P, Carmo-Fonseca M. Targeting mRNA processing as an anticancer strategy. Nat Rev Drug Discov 2019; 19:112-129. [PMID: 31554928 DOI: 10.1038/s41573-019-0042-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2019] [Indexed: 12/19/2022]
Abstract
Discoveries in the past decade have highlighted the potential of mRNA as a therapeutic target for cancer. Specifically, RNA sequencing revealed that, in addition to gene mutations, alterations in mRNA can contribute to the initiation and progression of cancer. Indeed, precursor mRNA processing, which includes the removal of introns by splicing and the formation of 3' ends by cleavage and polyadenylation, is frequently altered in tumours. These alterations result in numerous cancer-specific mRNAs that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumour-suppressor genes. Abnormally spliced and polyadenylated mRNAs are also associated with resistance to cancer treatment and, unexpectedly, certain cancers are highly sensitive to the pharmacological inhibition of splicing. This Review summarizes recent progress in our understanding of how splicing and polyadenylation are altered in cancer and highlights how this knowledge has been translated for drug discovery, resulting in the production of small molecules and oligonucleotides that modulate the spliceosome and are in clinical trials for the treatment of cancer.
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Affiliation(s)
- Joana Desterro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Português de Oncologia de Lisboa, Serviço de Hematologia, Lisboa, Portugal
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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22
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Ohashi R, Schraml P, Batavia A, Angori S, Simmler P, Rupp N, Ajioka Y, Oliva E, Moch H. Allele Loss and Reduced Expression of CYCLOPS Genes is a Characteristic Feature of Chromophobe Renal Cell Carcinoma. Transl Oncol 2019; 12:1131-1137. [PMID: 31200327 PMCID: PMC6563336 DOI: 10.1016/j.tranon.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes have been recently identified as the most enriched class of copy-number associated gene dependencies in human cancer. These genes are cell essential and render tumor cells highly sensitive to the expression of the remaining copy. Chromophobe renal cell carcinoma (chRCC) is characterized by frequent chromosomal deletions, but the relevance of CYCLOPS genes in this tumor subtype is unclear. We found 39 (31%) of 124 recently published candidate CYCLOPS genes (B. Paolella et al., eLife 2017;6:e23268) located on 7 autosomes that are frequently lost in chRCC. GISTIC and RNA-seq data obtained from the TCGA-KICH database showed that 62% of these CYCLOPS genes had significantly lower expression levels in samples with deletion of the respective gene. As copy number (CN) loss of the CYCLOPS gene SF3B1 (Splicing factor 3B subunit 1) has been recently reported in 71% chRCC, we explored the relevance of SF3B1 CN alteration and SF3B1 expression in a set of chRCC and additional oncocytic renal neoplasms. The frequency of SF3B1 CN loss (65%) was similar to that obtained from the TCGA-KICH database and correlated significantly with both lower SF3B1 mRNA (P < .05) and protein expression (P < .001). Other tumor subtypes with oncocytic cytoplasm had normal SF3B1 CN and displayed strong SF3B1 protein expression. These results suggest that CN loss of CYCLOPS genes is a characteristic feature in chRCC. Since many CYCLOPS genes code for components of proteasomes and transcriptional regulation, their alteration could make chRCC vulnerable to targeted drugs.
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Affiliation(s)
- Riuko Ohashi
- Histopathology Core Facility, 1-757 Asahimachi-dori, Niigata University Faculty of Medicine, Chuo-ku, 951-8510 Niigata, Japan; Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Aashil Batavia
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Silvia Angori
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Patrik Simmler
- Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Niels Rupp
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Yoichi Ajioka
- Histopathology Core Facility, 1-757 Asahimachi-dori, Niigata University Faculty of Medicine, Chuo-ku, 951-8510 Niigata, Japan; Division of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, 757 Ichibancho, Asahimachi-dori, Chuo Ward, 951-8510 Niigata, Japan.
| | - Esther Oliva
- Department of Pathology, Warren Building, 55 Fruit Street, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Holger Moch
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Wu HY, Peng ZG, He RQ, Luo B, Ma J, Hu XH, Dang YW, Chen G, Pan SL. Prognostic index of aberrant mRNA splicing profiling acts as a predictive indicator for hepatocellular carcinoma based on TCGA SpliceSeq data. Int J Oncol 2019; 55:425-438. [PMID: 31268164 PMCID: PMC6615926 DOI: 10.3892/ijo.2019.4834] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing in tumor cells may be used as a molecular marker for the differential diagnosis of certain tumor types and assessment of prognosis. The aim of the present study was to investigate the associations among alternative splicing events, splicing factors, and the survival of patients with hepatocellular carcinoma (HCC). The alternative splicing event profiles of 371 patients with HCC were downloaded from The Cancer Genome Atlas (TCGA) SpliceSeq data, and the percent-splice-in value for each splicing event was calculated. The association between alternative splicing events and overall survival was evaluated. The most significant prognosis-related splicing events were used to build up a prognostic index (PI). A total of 3,082 survival-associated alternative splicing events were detected in HCC. The final PI based on all of the most significant candidate alternative splicing events exhibited better performance in distinguishing good or poor survival in patients compared to the PI based on a single type of splicing event. Receiver operating characteristic curves confirmed the high efficiency of the PI in predicting the survival of HCC patients, with an area under the curve of 0.914. The overexpression of 32 prognosis-related splicing factor genes could also predict poor prognosis in patients with HCC. In conclusion, the constructed computational prognostic model based on HCC-specific alternative splicing events may be used as a molecular marker for the prognosis of HCC.
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Affiliation(s)
- Hua-Yu Wu
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhi-Gang Peng
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Bin Luo
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jie Ma
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiao-Hua Hu
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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25
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Chen MX, Wijethunge BDIK, Zhou SM, Yang JF, Dai L, Wang SS, Chen C, Fu LJ, Zhang J, Hao GF, Yang GF. Chemical Modulation of Alternative Splicing for Molecular-Target Identification by Potential Genetic Control in Agrochemical Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5072-5084. [PMID: 30986354 DOI: 10.1021/acs.jafc.9b02086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Alternative splicing (AS), the process of removing introns from pre-mRNA and the rearrangement of exons to produce several types of mature transcripts, is a remarkable step preceding protein synthesis. In particular, it has now been conclusively shown that up to ∼95% of genes are alternatively spliced to generate a complex and diverse proteome in eukaryotic organisms. Consequently, AS is one of the determinants of the functional repertoire of cells. Many studies have revealed that AS in plants can be regulated by cell type, developmental stage, environmental stress, and the circadian clock. Moreover, increasing amounts of evidence reveal that chemical compounds can affect various steps during splicing to induce major effects on plant physiology. Hence, the chemical modulation of AS can serve as a good strategy for molecular-target identification in attempts to potentially control plant genetics. However, the kind of mechanisms involved in the chemical modulation of AS that can be used in agrochemical research remain largely unknown. This review introduces recent studies describing the specific roles AS plays in plant adaptation to environmental stressors and in the regulation of development. We also discuss recent advances in small molecules that induce alterations of AS and the possibility of using this strategy in agrochemical-target identification, giving a new direction for potential genetic control in agrochemical research.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education; Research and Development Center for Fine Chemicals , Guizhou University , Guiyang 550025 , PR China
- Division of Gastroenterology , Shenzhen Children's Hospital , Shenzhen 518038 , PR China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology , Chinese Academy of Sciences , Shenzhen 518055 , PR China
- School of Life Sciences and Shenzhen Research Institute , The Chinese University of Hong Kong , Shenzhen 518063 , PR China
| | - Boyagane D I K Wijethunge
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , PR China
| | - Shao-Ming Zhou
- Division of Gastroenterology , Shenzhen Children's Hospital , Shenzhen 518038 , PR China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , PR China
| | - Lei Dai
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology , Chinese Academy of Sciences , Shenzhen 518055 , PR China
| | - Shan-Shan Wang
- School of Life Sciences and Shenzhen Research Institute , The Chinese University of Hong Kong , Shenzhen 518063 , PR China
| | - Chen Chen
- Department of Infectious Disease, Nanjing Second Hospital , Nanjing University of Chinese Medicine , Nanjing 210003 , PR China
| | - Li-Jun Fu
- Fujian Provincial Key Laboratory of Ecology-Toxicological Effects & Control for Emerging Contaminants , Putian University , Putian , Fujian 351100 , PR China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University and State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin , Hong Kong , PR China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education; Research and Development Center for Fine Chemicals , Guizhou University , Guiyang 550025 , PR China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , PR China
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High-throughput RNAi screening reveals cancer-selective lethal targets in the RNA spliceosome. Oncogene 2019; 38:4142-4153. [PMID: 30705407 DOI: 10.1038/s41388-019-0711-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [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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Hansen SR, Nikolai BJ, Spreacker PJ, Carrocci TJ, Hoskins AA. Chemical Inhibition of Pre-mRNA Splicing in Living Saccharomyces cerevisiae. Cell Chem Biol 2019; 26:443-448.e3. [PMID: 30639260 DOI: 10.1016/j.chembiol.2018.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022]
Abstract
The spliceosome mediates precursor mRNA splicing in eukaryotes, including the model organism Saccharomyces cerevisiae (yeast). Despite decades of study, no chemical inhibitors of yeast splicing in vivo are available. We have developed a system to efficiently inhibit splicing and block proliferation in living yeast cells using compounds that target the human spliceosome protein SF3B1. Potent inhibition is observed in yeast expressing a chimeric protein containing portions of human SF3B1. However, only a single point mutation in the yeast homolog of SF3B1 is needed for selective inhibition of splicing by pladienolide B, herboxidiene, or meayamycin in liquid culture. Mutations that enable inhibition also improve splicing of branch sites containing mismatches between the intron and small nuclear RNA-suggesting a link between inhibitor sensitivity and usage of weak branch sites in humans. This approach provides powerful new tools for manipulating splicing in live yeast and studies of spliceosome inhibitors.
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Affiliation(s)
- Sarah R Hansen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brandon J Nikolai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peyton J Spreacker
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Anufrieva KS, Shender VO, Arapidi GP, Lagarkova MA, Govorun VM. The Diverse Roles of Spliceosomal Proteins in the Regulation of Cell Processes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Improving the Efficiency of the Drug Development by Expanding the Scope of the Role of Medicinal Chemists in Drug Discovery. ACS Med Chem Lett 2018; 9:1153-1155. [PMID: 30613316 DOI: 10.1021/acsmedchemlett.8b00548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Improvements in the efficiency of the drug discovery process are needed in order to deliver life-saving medications to patients in a more cost-effective manner. While there are many reasons that the efficiency of this process has not gotten better, this Viewpoint proposes that the lack of integration of the three major disciplines (discovery, development, and clinical trials) plays a significant role in the ongoing high rate of failure in clinical trials for innovative drugs. Several specific proposals are made that may help to provide more integration, so that the gears of the human-driven drug discovery machine may mesh better in the future.
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Ghosh AK, Veitschegger AM, Nie S, MacRae NRAJ, Jurica MS. Enantioselective Synthesis of Thailanstatin A Methyl Ester and Evaluation of in Vitro Splicing Inhibition. J Org Chem 2018; 83:5187-5198. [PMID: 29696980 PMCID: PMC5972027 DOI: 10.1021/acs.joc.8b00593] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thailanstatin A has been isolated recently from the fermentation broth of B. thailandensis MSMB43. We describe here an enantioselective convergent synthesis of thailanstatin A methyl ester and evaluation of its splicing activity. Synthesis of both highly functionalized tetrahydropyran rings were carried out from commercially available tri- O-acetyl-d-glucal as the key starting material. Our convergent synthesis involved the synthesis of both tetrahydropyran fragments in a highly stereoselective manner. The fragments were then coupled using cross-metathesis as the key step. The synthesis of the diene subunit included a highly stereoselective Claisen rearrangement, a Cu(I)-mediated conjugate addition of MeLi to set the C-14 methyl stereochemistry, a reductive amination reaction to install the C16-amine functionality, and a Wittig olefination reaction to incorporate the diene unit. The epoxy alcohol subunit was synthesized by a highly selective anomeric allylation, a Peterson olefination, and a vanadium catalyzed epoxidation that installed the epoxide stereoselectively. Cross-metathesis of the olefins provided the methyl ester derivative of thailanstatin A. We have carried out in vitro splicing studies of the methyl ester derivative, which proved to be a potent inhibitor of the spliceosome.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
| | - Anne M. Veitschegger
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
| | - Shenyou Nie
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
| | - Nicola Relitti Andrew J. MacRae
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
| | - Melissa S. Jurica
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
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31
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Cretu C, Agrawal AA, Cook A, Will CL, Fekkes P, Smith PG, Lührmann R, Larsen N, Buonamici S, Pena V. Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds. Mol Cell 2018; 70:265-273.e8. [DOI: 10.1016/j.molcel.2018.03.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/22/2022]
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32
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Jyotsana N, Heuser M. Exploiting differential RNA splicing patterns: a potential new group of therapeutic targets in cancer. Expert Opin Ther Targets 2017; 22:107-121. [PMID: 29235382 DOI: 10.1080/14728222.2018.1417390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Mutations in genes associated with splicing have been found in hematologic malignancies, but also in solid cancers. Aberrant cancer specific RNA splicing either results from mutations or misexpression of the spliceosome genes directly, or from mutations in splice sites of oncogenes or tumor suppressors. Areas covered: In this review, we present molecular targets of aberrant splicing in various malignancies, information on existing and emerging therapeutics against such targets, and strategies for future drug development. Expert opinion: Alternative splicing is an important mechanism that controls gene expression, and hence pharmacologic and genetic control of aberrant alternative RNA splicing has been proposed as a potential therapy in cancer. To identify and validate aberrant RNA splicing patterns as therapeutic targets we need to (1) characterize the most common genetic aberrations of the spliceosome and of splice sites, (2) understand the dysregulated downstream pathways and (3) exploit in-vivo disease models of aberrant splicing. Antisense oligonucleotides show promising activity, but will benefit from improved delivery tools. Inhibitors of mutated splicing factors require improved specificity, as alternative and aberrant splicing are often intertwined like two sides of the same coin. In summary, targeting aberrant splicing is an early but emerging field in cancer treatment.
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Affiliation(s)
- Nidhi Jyotsana
- a Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation , Hannover Medical School , Hannover , Germany
| | - Michael Heuser
- a Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation , Hannover Medical School , Hannover , Germany
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33
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Elenitoba-Johnson KSJ, Lim MS. New Insights into Lymphoma Pathogenesis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2017; 13:193-217. [PMID: 29140757 DOI: 10.1146/annurev-pathol-020117-043803] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lymphomas represent clonal proliferations of lymphocytes that are broadly classified based upon their maturity (peripheral or mature versus precursor) and lineage (B cell, T cell, and natural killer cell). Insights into the pathogenetic mechanisms involved in lymphoma impact the classification of lymphoma and have significant implications for the diagnosis and clinical management of patients. Serial scientific and technologic advances over the last 30 years in immunology, cytogenetics, molecular biology, gene expression profiling, mass spectrometry-based proteomics, and, more recently, next-generation sequencing have contributed to greatly enhance our understanding of the pathogenetic mechanisms in lymphoma. Novel and emerging concepts that challenge our previously accepted paradigms about lymphoma biology and how these impact diagnosis, molecular testing, disease monitoring, drug development, and personalized and precision medicine for lymphoma are discussed.
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Affiliation(s)
- Kojo S J Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , .,Center for Personalized Diagnostics and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Megan S Lim
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; , .,Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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34
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Agrawal AA, Yu L, Smith PG, Buonamici S. Targeting splicing abnormalities in cancer. Curr Opin Genet Dev 2017; 48:67-74. [PMID: 29136527 DOI: 10.1016/j.gde.2017.10.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/19/2017] [Accepted: 10/13/2017] [Indexed: 01/11/2023]
Abstract
Recently splicing has been recognized as a key pathway in cancer. Although aberrant splicing has been shown to be a consequence of mutations or the abnormal expression of splicing factors (trans-effect changes) or mutations in the splicing sequences (cis-effect mutations), the connections between aberrant splicing and cancer initiation or progression are still not well understood. Here we review the mutational landscape of splicing factors in cancer and associated splicing consequences, along with the most important examples of the therapeutic approaches targeting the spliceosome currently being investigated in oncology.
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Affiliation(s)
| | - Lihua Yu
- H3 Biomedicine, Inc., Cambridge, MA, USA
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35
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Armstrong RN, Steeples V, Singh S, Sanchi A, Boultwood J, Pellagatti A. Splicing factor mutations in the myelodysplastic syndromes: target genes and therapeutic approaches. Adv Biol Regul 2017; 67:13-29. [PMID: 28986033 DOI: 10.1016/j.jbior.2017.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 10/25/2022]
Abstract
Mutations in splicing factor genes (SF3B1, SRSF2, U2AF1 and ZRSR2) are frequently found in patients with myelodysplastic syndromes (MDS), suggesting that aberrant spliceosome function plays a key role in the pathogenesis of MDS. Splicing factor mutations have been shown to result in aberrant splicing of many downstream target genes. Recent functional studies have begun to characterize the splicing dysfunction in MDS, identifying some key aberrantly spliced genes that are implicated in disease pathophysiology. These findings have led to the development of therapeutic strategies using splicing-modulating agents and rapid progress is being made in this field. Splicing inhibitors are promising agents that exploit the preferential sensitivity of splicing factor-mutant cells to these compounds. Here, we review the known target genes associated with splicing factor mutations in MDS, and discuss the potential of splicing-modulating therapies for these disorders.
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Affiliation(s)
- Richard N Armstrong
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Violetta Steeples
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Shalini Singh
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Andrea Sanchi
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
| | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and Oxford BRC Haematology Theme, Oxford, UK.
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36
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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] [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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37
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Rohrs TM, Qin Q, Floreancig PE. Re 2
O 7
-Mediated Dehydrative Cyclization Reactions: Total Synthesis of Herboxidiene and Its 12-Desmethyl Analogue. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tyler M. Rohrs
- Department of Chemistry; University of Pittsburgh; Pittsburgh PA 15260 USA
| | - Qi Qin
- Department of Chemistry; University of Pittsburgh; Pittsburgh PA 15260 USA
| | - Paul E. Floreancig
- Department of Chemistry; University of Pittsburgh; Pittsburgh PA 15260 USA
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38
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Lee SCW, Abdel-Wahab O. Therapeutic targeting of splicing in cancer. Nat Med 2017; 22:976-86. [PMID: 27603132 DOI: 10.1038/nm.4165] [Citation(s) in RCA: 385] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023]
Abstract
Recent studies have highlighted that splicing patterns are frequently altered in cancer and that mutations in genes encoding spliceosomal proteins, as well as mutations affecting the splicing of key cancer-associated genes, are enriched in cancer. In parallel, there is also accumulating evidence that several molecular subtypes of cancer are highly dependent on splicing function for cell survival. These findings have resulted in a growing interest in targeting splicing catalysis, splicing regulatory proteins, and/or specific key altered splicing events in the treatment of cancer. Here we present strategies that exist and that are in development to target altered dependency on the spliceosome, as well as aberrant splicing, in cancer. These include drugs to target global splicing in cancer subtypes that are preferentially dependent on wild-type splicing for survival, methods to alter post-translational modifications of splicing-regulating proteins, and strategies to modulate pathologic splicing events and protein-RNA interactions in cancer.
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Affiliation(s)
- Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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39
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Rohrs TM, Qin Q, Floreancig PE. Re 2 O 7 -Mediated Dehydrative Cyclization Reactions: Total Synthesis of Herboxidiene and Its 12-Desmethyl Analogue. Angew Chem Int Ed Engl 2017; 56:10900-10904. [PMID: 28686815 DOI: 10.1002/anie.201705924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Indexed: 12/27/2022]
Abstract
Re2 O7 catalysis effects efficient and stereoselective dehydrative cyclization reactions from monoallylic diols, with stereocontrol arising from thermodynamic equilibration. This method was applied to a rapid synthesis of the spliceosome inhibitor herboxidiene. The route was also utilized for the synthesis of an analogue that highlights the importance of a single methyl group in biasing the conformation in the acyclic region of the molecule.
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Affiliation(s)
- Tyler M Rohrs
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Qi Qin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Paul E Floreancig
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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40
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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41
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AlShareef S, Ling Y, Butt H, Mariappan KG, Benhamed M, Mahfouz MM. Herboxidiene triggers splicing repression and abiotic stress responses in plants. BMC Genomics 2017; 18:260. [PMID: 28347276 PMCID: PMC5369228 DOI: 10.1186/s12864-017-3656-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/22/2017] [Indexed: 12/28/2022] Open
Abstract
Background Constitutive and alternative splicing of pre-mRNAs from multiexonic genes controls the diversity of the proteome; these precisely regulated processes also fine-tune responses to cues related to growth, development, and stresses. Small-molecule inhibitors that perturb splicing provide invaluable tools for use as chemical probes to uncover the molecular underpinnings of splicing regulation and as potential anticancer compounds. Results Here, we show that herboxidiene (GEX1A) inhibits both constitutive and alternative splicing. Moreover, GEX1A activates genome-wide transcriptional patterns involved in abiotic stress responses in plants. GEX1A treatment -activated ABA-inducible promoters, and led to stomatal closure. Interestingly, GEX1A and pladienolide B (PB) elicited similar cellular changes, including alterations in the patterns of transcription and splicing, suggesting that these compounds might target the same spliceosome complex in plant cells. Conclusions Our study establishes GEX1A as a potent splicing inhibitor in plants that can be used to probe the assembly, dynamics, and molecular functions of the spliceosome and to study the interplay between splicing stress and abiotic stresses, as well as having potential biotechnological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3656-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sahar AlShareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Kiruthiga G Mariappan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Moussa Benhamed
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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Chung FFL, Tan PFTM, Raja VJ, Tan BS, Lim KH, Kam TS, Hii LW, Tan SH, See SJ, Tan YF, Wong LZ, Yam WK, Mai CW, Bradshaw TD, Leong CO. Jerantinine A induces tumor-specific cell death through modulation of splicing factor 3b subunit 1 (SF3B1). Sci Rep 2017; 7:42504. [PMID: 28198434 PMCID: PMC5309811 DOI: 10.1038/srep42504] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/13/2017] [Indexed: 02/08/2023] Open
Abstract
Precursor mRNA (pre-mRNA) splicing is catalyzed by a large ribonucleoprotein complex known as the spliceosome. Numerous studies have indicated that aberrant splicing patterns or mutations in spliceosome components, including the splicing factor 3b subunit 1 (SF3B1), are associated with hallmark cancer phenotypes. This has led to the identification and development of small molecules with spliceosome-modulating activity as potential anticancer agents. Jerantinine A (JA) is a novel indole alkaloid which displays potent anti-proliferative activities against human cancer cell lines by inhibiting tubulin polymerization and inducing G2/M cell cycle arrest. Using a combined pooled-genome wide shRNA library screen and global proteomic profiling, we showed that JA targets the spliceosome by up-regulating SF3B1 and SF3B3 protein in breast cancer cells. Notably, JA induced significant tumor-specific cell death and a significant increase in unspliced pre-mRNAs. In contrast, depletion of endogenous SF3B1 abrogated the apoptotic effects, but not the G2/M cell cycle arrest induced by JA. Further analyses showed that JA stabilizes endogenous SF3B1 protein in breast cancer cells and induced dissociation of the protein from the nucleosome complex. Together, these results demonstrate that JA exerts its antitumor activity by targeting SF3B1 and SF3B3 in addition to its reported targeting of tubulin polymerization.
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Affiliation(s)
- Felicia Fei-Lei Chung
- Center for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | | | - Vijay Joseph Raja
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA
| | - Boon-Shing Tan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuan-Hon Lim
- School of Pharmacy, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Toh-Seok Kam
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ling-Wei Hii
- Center for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
- School of Postgraduate Studies, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | - Si Hoey Tan
- Center for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
- School of Postgraduate Studies, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | - Sze-Jia See
- Center for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | - Yuen-Fen Tan
- Center for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
- School of Postgraduate Studies, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | - Li-Zhe Wong
- Center for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
- School of Postgraduate Studies, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | - Wai Keat Yam
- School of Pharmacy, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | - Chun Wai Mai
- School of Pharmacy, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
| | - Tracey D. Bradshaw
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Chee-Onn Leong
- Center for Cancer and Stem Cell Research, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
- School of Pharmacy, International Medical University, Bukit Jalil, 57000 Kuala Lumpur, Malaysia
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43
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Paolella BR, Gibson WJ, Urbanski LM, Alberta JA, Zack TI, Bandopadhayay P, Nichols CA, Agarwalla PK, Brown MS, Lamothe R, Yu Y, Choi PS, Obeng EA, Heckl D, Wei G, Wang B, Tsherniak A, Vazquez F, Weir BA, Root DE, Cowley GS, Buhrlage SJ, Stiles CD, Ebert BL, Hahn WC, Reed R, Beroukhim R. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. eLife 2017; 6. [PMID: 28177281 PMCID: PMC5357138 DOI: 10.7554/elife.23268] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor SF3B1, is also frequently mutated in cancer. We validated SF3B1 as a CYCLOPS gene and found that human cancer cells harboring partial SF3B1 copy-loss lack a reservoir of SF3b complex that protects cells with normal SF3B1 copy number from cell death upon partial SF3B1 suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type SF3B1 as a novel, non-driver cancer gene dependency.
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Affiliation(s)
- Brenton R Paolella
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - William J Gibson
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Laura M Urbanski
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - John A Alberta
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Travis I Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pratiti Bandopadhayay
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Caitlin A Nichols
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Pankaj K Agarwalla
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Meredith S Brown
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Rebecca Lamothe
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Yong Yu
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Peter S Choi
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Esther A Obeng
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Dirk Heckl
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Guo Wei
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Belinda Wang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Barbara A Weir
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States
| | - Charles D Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Benjamin L Ebert
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - William C Hahn
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
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44
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Fraile JM, Manchado E, Lujambio A, Quesada V, Campos-Iglesias D, Webb TR, Lowe SW, López-Otín C, Freije JMP. USP39 Deubiquitinase Is Essential for KRAS Oncogene-driven Cancer. J Biol Chem 2017; 292:4164-4175. [PMID: 28154181 DOI: 10.1074/jbc.m116.762757] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/24/2017] [Indexed: 01/08/2023] Open
Abstract
KRAS is the most frequently mutated oncogene in human cancer, but its therapeutic targeting remains challenging. Here, we report a synthetic lethal screen with a library of deubiquitinases and identify USP39, which encodes an essential splicing factor, as a critical gene for the viability of KRAS-dependent cells. We show that splicing fidelity inhibitors decrease preferentially the proliferation rate of KRAS-active cells. Moreover, depletion of DHX38, encoding an USP39-interacting splicing factor, also reduces the viability of these cells. In agreement with these results, USP39 depletion caused a significant reduction in pre-mRNA splicing efficiency, as demonstrated through RNA-seq experiments. Furthermore, we show that USP39 is up-regulated in lung and colon carcinomas and its expression correlates with KRAS levels and poor clinical outcome. Accordingly, our work provides critical information for the development of splicing-directed antitumor treatments and supports the potential of USP39-targeting strategies as the basis of new anticancer therapies.
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Affiliation(s)
- Julia M Fraile
- From the Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain.,the Centro de Investigación Biomédica en Red de Cáncer, Spain
| | - Eusebio Manchado
- the Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, and
| | - Amaia Lujambio
- the Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, and
| | - Víctor Quesada
- From the Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain.,the Centro de Investigación Biomédica en Red de Cáncer, Spain
| | - Diana Campos-Iglesias
- From the Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Thomas R Webb
- the Division of Biosciences, SRI International, Menlo Park, California 94025
| | - Scott W Lowe
- the Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, and
| | - Carlos López-Otín
- From the Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain.,the Centro de Investigación Biomédica en Red de Cáncer, Spain
| | - José M P Freije
- From the Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain, .,the Centro de Investigación Biomédica en Red de Cáncer, Spain
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45
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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] [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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46
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Shi Y, Park J, Lagisetti C, Zhou W, Sambucetti LC, Webb TR. A triple exon-skipping luciferase reporter assay identifies a new CLK inhibitor pharmacophore. Bioorg Med Chem Lett 2016; 27:406-412. [PMID: 28049589 DOI: 10.1016/j.bmcl.2016.12.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/19/2022]
Abstract
The splicing of pre-mRNA is a critical process in normal cells and is deregulated in cancer. Compounds that modulate this process have recently been shown to target a specific vulnerability in tumors. We have developed a novel cell-based assay that specifically activates luciferase in cells exposed to SF3B1 targeted compounds, such as sudemycin D6. This assay was used to screen a combined collection of approved drugs and bioactive compounds. This screening approach identified several active hits, the most potent of which were CGP-74514A and aminopurvalanol A, both have been reported to be cyclin-dependent kinases (CDKs) inhibitors. We found that these compounds, and their analogs, show significant cdc2-like kinase (CLK) inhibition and clear structure-activity relationships (SAR) at CLKs. We prepared a set of analogs and were able to 'dial out' the CDK activity and simultaneously developed CLK inhibitors with low nanomolar activity. Thus, we have demonstrated the utility of our exon-skipping assay and identified new molecules that exhibit potency and selectivity for CLK, as well as some structurally related dual CLK/CDK inhibitors.
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Affiliation(s)
- Yihui Shi
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Jaehyeon Park
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Chandraiah Lagisetti
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Wei Zhou
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Lidia C Sambucetti
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Thomas R Webb
- Division of Biosciences, SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA.
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47
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Splicing factor gene mutations in hematologic malignancies. Blood 2016; 129:1260-1269. [PMID: 27940478 DOI: 10.1182/blood-2016-10-692400] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/25/2016] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing generates a diversity of messenger RNA (mRNA) transcripts from a single mRNA precursor and contributes to the complexity of our proteome. Splicing is perturbed by a variety of mechanisms in cancer. Recurrent mutations in splicing factors have emerged as a hallmark of several hematologic malignancies. Splicing factor mutations tend to occur in the founding clone of myeloid cancers, and these mutations have recently been identified in blood cells from normal, healthy elderly individuals with clonal hematopoiesis who are at increased risk of subsequently developing a hematopoietic malignancy, suggesting that these mutations contribute to disease initiation. Splicing factor mutations change the pattern of splicing in primary patient and mouse hematopoietic cells and alter hematopoietic differentiation and maturation in animal models. Recent developments in this field are reviewed here, with an emphasis on the clinical consequences of splicing factor mutations, mechanistic insights from animal models, and implications for development of novel therapies targeting the precursor mRNA splicing pathway.
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48
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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] [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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49
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de Necochea-Campion R, Shouse GP, Zhou Q, Mirshahidi S, Chen CS. Aberrant splicing and drug resistance in AML. J Hematol Oncol 2016; 9:85. [PMID: 27613060 PMCID: PMC5018179 DOI: 10.1186/s13045-016-0315-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/02/2016] [Indexed: 02/08/2023] Open
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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50
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Pellagatti A, Boultwood J. Splicing factor gene mutations in the myelodysplastic syndromes: impact on disease phenotype and therapeutic applications. Adv Biol Regul 2016; 63:59-70. [PMID: 27639445 DOI: 10.1016/j.jbior.2016.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 01/05/2023]
Abstract
Splicing factor gene mutations are the most frequent mutations found in patients with the myeloid malignancy myelodysplastic syndrome (MDS), suggesting that spliceosomal dysfunction plays a major role in disease pathogenesis. The aberrantly spliced target genes and deregulated cellular pathways associated with the commonly mutated splicing factor genes in MDS (SF3B1, SRSF2 and U2AF1) are being identified, illuminating the molecular mechanisms underlying MDS. Emerging data from mouse modeling studies indicate that the presence of splicing factor gene mutations can lead to bone marrow hematopoietic stem/myeloid progenitor cell expansion, impaired hematopoiesis and dysplastic differentiation that are hallmarks of MDS. Importantly, recent evidence suggests that spliceosome inhibitors and splicing modulators may have therapeutic value in the treatment of splicing factor mutant myeloid malignancies.
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Affiliation(s)
- Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford; NIHR Biomedical Research Centre, Oxford, UK.
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford; NIHR Biomedical Research Centre, Oxford, UK.
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