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Maji D, Jenkins JL, Boutz PL, Kielkopf CL. Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions. Biochemistry 2024. [PMID: 39388459 DOI: 10.1021/acs.biochem.4c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
De novo mutations affecting the pre-mRNA splicing factor U2AF2 are associated with developmental delays and intellectual disabilities, yet the molecular basis is unknown. Here, we demonstrated by fluorescence anisotropy RNA binding assays that recurrent missense mutants (Arg149Trp, Arg150His, or Arg150Cys) decreased the binding affinity of U2AF2 for a consensus splice site RNA. Crystal structures at 1.4 Å resolutions showed that Arg149Trp or Arg150His disrupted hydrogen bonds between U2AF2 and the terminal nucleotides of the RNA site. Reanalysis of publicly available RNaseq data confirmed that U2AF2 depletion altered splicing of transcripts encoding RNA binding proteins (RBPs). These results confirmed that the impaired RNA interactions of Arg149Trp and Arg150His U2AF2 variants could contribute to dysregulating an RBP-governed neurodevelopmental program of alternative splicing.
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Affiliation(s)
- Debanjana Maji
- Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Paul L Boutz
- Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
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2
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Choi S, Cho N, Kim EM, Kim KK. The role of alternative pre-mRNA splicing in cancer progression. Cancer Cell Int 2023; 23:249. [PMID: 37875914 PMCID: PMC10594706 DOI: 10.1186/s12935-023-03094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Alternative pre-mRNA splicing is a critical mechanism that generates multiple mRNA from a single gene, thereby increasing the diversity of the proteome. Recent research has highlighted the significance of specific splicing isoforms in cellular processes, particularly in regulating cell numbers. In this review, we examine the current understanding of the role of alternative splicing in controlling cancer cell growth and discuss specific splicing factors and isoforms and their molecular mechanisms in cancer progression. These isoforms have been found to intricately control signaling pathways crucial for cell cycle progression, proliferation, and apoptosis. Furthermore, studies have elucidated the characteristics and functional importance of splicing factors that influence cell numbers. Abnormal expression of oncogenic splicing isoforms and splicing factors, as well as disruptions in splicing caused by genetic mutations, have been implicated in the development and progression of tumors. Collectively, these findings provide valuable insights into the complex interplay between alternative splicing and cell proliferation, thereby suggesting the potential of alternative splicing as a therapeutic target for cancer.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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3
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Harms FL, Dingemans AJM, Hempel M, Pfundt R, Bierhals T, Casar C, Müller C, Niermeijer JMF, Fischer J, Jahn A, Hübner C, Majore S, Agolini E, Novelli A, van der Smagt J, Ernst R, van Binsbergen E, Mancini GMS, van Slegtenhorst M, Barakat TS, Wakeling EL, Kamath A, Downie L, Pais L, White SM, de Vries BBA, Kutsche K. De novo PHF5A variants are associated with craniofacial abnormalities, developmental delay, and hypospadias. Genet Med 2023; 25:100927. [PMID: 37422718 DOI: 10.1016/j.gim.2023.100927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE The SF3B splicing complex is composed of SF3B1-6 and PHF5A. We report a developmental disorder caused by de novo variants in PHF5A. METHODS Clinical, genomic, and functional studies using subject-derived fibroblasts and a heterologous cellular system were performed. RESULTS We studied 9 subjects with congenital malformations, including preauricular tags and hypospadias, growth abnormalities, and developmental delay who had de novo heterozygous PHF5A variants, including 4 loss-of-function (LOF), 3 missense, 1 splice, and 1 start-loss variant. In subject-derived fibroblasts with PHF5A LOF variants, wild-type and variant PHF5A mRNAs had a 1:1 ratio, and PHF5A mRNA levels were normal. Transcriptome sequencing revealed alternative promoter use and downregulated genes involved in cell-cycle regulation. Subject and control fibroblasts had similar amounts of PHF5A with the predicted wild-type molecular weight and of SF3B1-3 and SF3B6. SF3B complex formation was unaffected in 2 subject cell lines. CONCLUSION Our data suggest the existence of feedback mechanisms in fibroblasts with PHF5A LOF variants to maintain normal levels of SF3B components. These compensatory mechanisms in subject fibroblasts with PHF5A or SF3B4 LOF variants suggest disturbed autoregulation of mutated splicing factor genes in specific cell types, that is, neural crest cells, during embryonic development rather than haploinsufficiency as pathomechanism.
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Affiliation(s)
- Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Casar
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Müller
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Jan Fischer
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Arne Jahn
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Christoph Hübner
- Department of Neuropaediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Silvia Majore
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Jasper van der Smagt
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Robert Ernst
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Discovery Unit, Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Emma L Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Arveen Kamath
- All Wales Medical Genomics Service/ Pennaeth Labordy Genomeg Cymru Gyfan, University Hospital of Wales, Heath Park, Cardiff, United Kingdom
| | - Lilian Downie
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, VIC; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lynn Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Susan M White
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, VIC; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Regulation of Arp5 expression by alternative splicing coupled to nonsense-mediated RNA decay. Biochem Biophys Res Commun 2023; 657:50-58. [PMID: 36977368 DOI: 10.1016/j.bbrc.2023.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
Actin-related protein 5 (ARP5) inhibits the differentiation of skeletal, smooth, and cardiac muscle tissues, and ARP5 expression increases or decreases according to physiological and pathological changes in the muscle differentiation status. However, the regulatory mechanisms of ARP5 expression are largely unknown. Here, we identified a novel Arp5 mRNA isoform that contains premature termination codons in alternative exon 7b and is thus targeted by nonsense-mediated mRNA decay (NMD). In mouse skeletal muscle cells, switching from the canonical Arp5 isoform, i.e., Arp5(7a), to the NMD-targeted isoform Arp5(7b) occurred during differentiation, suggesting that Arp5 expression is regulated by alternative splicing coupled to NMD (AS-NMD). We developed an original method to accurately quantify the proportion of both Arp5 isoforms and measured higher levels of Arp5(7b) in muscle and brain tissues, where ARP5 is less expressed. The 3' splice site in Arp5 exon 7 has an unusual acceptor sequence that often leads to the skip of the authentic splice site and the use of the cryptic splice site localized 16 bases downstream. When the unusual acceptor sequence was mutated to the usual one, the Arp5(7b) isoform was barely detectable. The expression of several splicing factors involved in 3' splice site recognition was reduced after muscle differentiation. Additionally, knockdown of splicing factors increased the levels of Arp5(7b) and decreased the expression of Arp5(7a). Furthermore, strong positive correlations were found between Arp5 expression and the levels of these splicing factors in human skeletal and cardiac muscle tissues. Thus, Arp5 expression in muscle tissues is most likely regulated by the AS-NMD pathway.
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Zhao Y, Cai W, Hua Y, Yang X, Zhou J. The Biological and Clinical Consequences of RNA Splicing Factor U2AF1 Mutation in Myeloid Malignancies. Cancers (Basel) 2022; 14:4406. [PMID: 36139566 PMCID: PMC9496927 DOI: 10.3390/cancers14184406] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Mutations of spliceosome genes have been frequently identified in myeloid malignancies with the large-scale application of advanced sequencing technology. U2 small nuclear RNA auxiliary factor 1 (U2AF1), an essential component of U2AF heterodimer, plays a pivotal role in the pre-mRNA splicing processes to generate functional mRNAs. Over the past few decades, the mutation landscape of U2AF1 (most frequently involved S34 and Q157 hotspots) has been drawn in multiple cancers, particularly in myeloid malignancies. As a recognized early driver of myelodysplastic syndromes (MDSs), U2AF1 mutates most frequently in MDS, followed by acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPNs). Here, for the first time, we summarize the research progress of U2AF1 mutations in myeloid malignancies, including the correlations between U2AF1 mutations with clinical and genetic characteristics, prognosis, and the leukemic transformation of patients. We also summarize the adverse effects of U2AF1 mutations on hematopoietic function, and the alterations in downstream alternative gene splicing and biological pathways, thus providing comprehensive insights into the roles of U2AF1 mutations in the myeloid malignancy pathogenesis. U2AF1 mutations are expected to be potential novel molecular markers for myeloid malignancies, especially for risk stratification, prognosis assessment, and a therapeutic target of MDS patients.
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Affiliation(s)
- Yangjing Zhao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Weili Cai
- Institute of Medical Genetics and Reproductive Immunity, School of Medical Science and Laboratory Medicine, Jiangsu College of Nursing, Huai’an 223005, China
| | - Ye Hua
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China
| | - Xiaochen Yang
- Department of Thyroid and Breast Surgery, Affiliated Kunshan Hospital of Jiangsu University, Kunshan 215300, China
| | - Jingdong Zhou
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China
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6
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Fuentes-Fayos AC, Pérez-Gómez JM, G-García ME, Jiménez-Vacas JM, Blanco-Acevedo C, Sánchez-Sánchez R, Solivera J, Breunig JJ, Gahete MD, Castaño JP, Luque RM. SF3B1 inhibition disrupts malignancy and prolongs survival in glioblastoma patients through BCL2L1 splicing and mTOR/ß-catenin pathways imbalances. J Exp Clin Cancer Res 2022; 41:39. [PMID: 35086552 PMCID: PMC8793262 DOI: 10.1186/s13046-022-02241-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glioblastoma is one of the most devastating cancer worldwide based on its locally aggressive behavior and because it cannot be cured by current therapies. Defects in alternative splicing process are frequent in cancer. Recently, we demonstrated that dysregulation of the spliceosome is directly associated with glioma development, progression, and aggressiveness. METHODS Different human cohorts and a dataset from different glioma mouse models were analyzed to determine the mutation frequency as well as the gene and protein expression levels between tumor and control samples of the splicing-factor-3B-subunit-1 (SF3B1), an essential and druggable spliceosome component. SF3B1 expression was also explored at the single-cell level across all cell subpopulations and transcriptomic programs. The association of SF3B1 expression with relevant clinical data (e.g., overall survival) in different human cohorts was also analyzed. Different functional (proliferation/migration/tumorspheres and colonies formation/VEGF secretion/apoptosis) and mechanistic (gene expression/signaling pathways) assays were performed in three different glioblastomas cell models (human primary cultures and cell lines) in response to SF3B1 blockade (using pladienolide B treatment). Moreover, tumor progression and formation were monitored in response to SF3B1 blockade in two preclinical xenograft glioblastoma mouse models. RESULTS Our data provide novel evidence demonstrating that the splicing-factor-3B-subunit-1 (SF3B1, an essential and druggable spliceosome component) is low-frequency mutated in human gliomas (~ 1 %) but widely overexpressed in glioblastoma compared with control samples from the different human cohorts and mouse models included in the present study, wherein SF3B1 levels are associated with key molecular and clinical features (e.g., overall survival, poor prognosis and/or drug resistance). Remarkably, in vitro and in vivo blockade of SF3B1 activity with pladienolide B drastically altered multiple glioblastoma pathophysiological processes (i.e., reduction in proliferation, migration, tumorspheres formation, VEGF secretion, tumor initiation and increased apoptosis) likely by suppressing AKT/mTOR/ß-catenin pathways, and an imbalance of BCL2L1 splicing. CONCLUSIONS Together, we highlight SF3B1 as a potential diagnostic and prognostic biomarker and an efficient pharmacological target in glioblastoma, offering a clinically relevant opportunity worth to be explored in humans.
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Affiliation(s)
- Antonio C Fuentes-Fayos
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Jesús M Pérez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Miguel E G-García
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Cristóbal Blanco-Acevedo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- Department of Neurosurgery, Reina Sofia University Hospital, 14004, Cordoba, Spain
| | - Rafael Sánchez-Sánchez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- Pathology Service, Reina Sofia University Hospital, 14004, Cordoba, Spain
| | - Juan Solivera
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- Department of Neurosurgery, Reina Sofia University Hospital, 14004, Cordoba, Spain
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004, Córdoba, Spain.
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004, Cordoba, Spain.
- Reina Sofia University Hospital (HURS), 14004, Cordoba, Spain.
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004, Cordoba, Spain.
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A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell Chem Biol 2021; 28:1145-1157.e6. [PMID: 33689684 PMCID: PMC8380659 DOI: 10.1016/j.chembiol.2021.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 12/20/2022]
Abstract
Dysregulated pre-mRNA splicing is an emerging Achilles heel of cancers and myelodysplasias. To expand the currently limited portfolio of small-molecule drug leads, we screened for chemical modulators of the U2AF complex, which nucleates spliceosome assembly and is mutated in myelodysplasias. A hit compound specifically enhances RNA binding by a U2AF2 subunit. Remarkably, the compound inhibits splicing of representative substrates and stalls spliceosome assembly at the stage of U2AF function. Computational docking, together with structure-guided mutagenesis, indicates that the compound bridges the tandem U2AF2 RNA recognition motifs via hydrophobic and electrostatic moieties. Cells expressing a cancer-associated U2AF1 mutant are preferentially killed by treatment with the compound. Altogether, our results highlight the potential of trapping early spliceosome assembly as an effective pharmacological means to manipulate pre-mRNA splicing. By extension, we suggest that stabilizing assembly intermediates may offer a useful approach for small-molecule inhibition of macromolecular machines.
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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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Abstract
In recent years CMML has received increased attention as the most commonly observed MDS/MPN overlap syndrome. Renewed interest has occurred in part due to widespread adoption of next-generation sequencing panels that help render the diagnosis in the absence of morphologic dysplasia. Although most CMML patients exhibit somatic mutations in epigenetic modifiers, spliceosome components, transcription factors and signal transduction genes, it is increasingly clear that a small subset harbors an inherited predisposition to CMML and other myeloid neoplasms. More intriguing is the fact that the mutational spectrum observed in CMML is found in other types of myeloid leukemias, begging the question of how similar genetic backgrounds can lead to such divergent clinical phenotypes. In this review we present a contemporary snapshot of the genetic complexity inherent to CMML, explore the relationship between genotype-phenotype and present a stepwise model of CMML pathogenesis and progression.
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Affiliation(s)
- Ami B Patel
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael W Deininger
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
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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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11
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Maji D, Glasser E, Henderson S, Galardi J, Pulvino MJ, Jenkins JL, Kielkopf CL. Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing. J Biol Chem 2020; 295:17148-17157. [PMID: 33020180 PMCID: PMC7863893 DOI: 10.1074/jbc.ra120.015339] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/21/2020] [Indexed: 12/17/2022] Open
Abstract
High-throughput sequencing of hematologic malignancies and other cancers has revealed recurrent mis-sense mutations of genes encoding pre-mRNA splicing factors. The essential splicing factor U2AF2 recognizes a polypyrimidine-tract splice-site signal and initiates spliceosome assembly. Here, we investigate representative, acquired U2AF2 mutations, namely N196K or G301D amino acid substitutions associated with leukemia or solid tumors, respectively. We determined crystal structures of the wild-type (WT) compared with N196K- or G301D-substituted U2AF2 proteins, each bound to a prototypical AdML polypyrimidine tract, at 1.5, 1.4, or 1.7 Å resolutions. The N196K residue appears to stabilize the open conformation of U2AF2 with an inter-RNA recognition motif hydrogen bond, in agreement with an increased apparent RNA-binding affinity of the N196K-substituted protein. The G301D residue remains in a similar position as the WT residue, where unfavorable proximity to the RNA phosphodiester could explain the decreased RNA-binding affinity of the G301D-substituted protein. We found that expression of the G301D-substituted U2AF2 protein reduces splicing of a minigene transcript carrying prototypical splice sites. We further show that expression of either N196K- or G301D-substituted U2AF2 can subtly alter splicing of representative endogenous transcripts, despite the presence of endogenous, WT U2AF2 such as would be present in cancer cells. Altogether, our results demonstrate that acquired U2AF2 mutations such as N196K and G301D are capable of dysregulating gene expression for neoplastic transformation.
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Affiliation(s)
- Debanjana Maji
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Eliezra Glasser
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Steven Henderson
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Justin Galardi
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mary J Pulvino
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jermaine L Jenkins
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Clara L Kielkopf
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
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12
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Pollyea DA, Kim HM, Stevens BM, Lee FFY, Harris C, Hedin BR, Knapp JR, O'Connor BP, Jordan CT, Pietras EM, Tan AC, Alper S. MDS-associated SF3B1 mutations enhance proinflammatory gene expression in patient blast cells. J Leukoc Biol 2020; 110:197-205. [PMID: 33155727 DOI: 10.1002/jlb.6ab0520-318rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/29/2022] Open
Abstract
Two factors known to contribute to the development of myelodysplastic syndrome (MDS) and other blood cancers are (i) somatically acquired mutations in components of the spliceosome and (ii) increased inflammation. Spliceosome genes, including SF3B1, are mutated at high frequency in MDS and other blood cancers; these mutations are thought to be neomorphic or gain-of-function mutations that drive disease pathogenesis. Likewise, increased inflammation is thought to contribute to MDS pathogenesis; inflammatory cytokines are strongly elevated in these patients, with higher levels correlating with worsened patient outcome. In the current study, we used RNAseq to analyze pre-mRNA splicing and gene expression changes present in blast cells isolated from MDS patients with or without SF3B1 mutations. We determined that SF3B1 mutations lead to enhanced proinflammatory gene expression in these cells. Thus, these studies suggest that SF3B1 mutations could contribute to MDS pathogenesis by enhancing the proinflammatory milieu in these patients.
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Affiliation(s)
- Daniel A Pollyea
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Hyun Min Kim
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brett M Stevens
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Frank Fang-Yao Lee
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Chelsea Harris
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Brenna R Hedin
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Jennifer R Knapp
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Brian P O'Connor
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Craig T Jordan
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eric M Pietras
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Aik Choon Tan
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, USA
| | - Scott Alper
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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13
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Yoshida H, Park SY, Sakashita G, Nariai Y, Kuwasako K, Muto Y, Urano T, Obayashi E. Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1. Nat Commun 2020; 11:4744. [PMID: 32958768 PMCID: PMC7505975 DOI: 10.1038/s41467-020-18559-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes. Here, we describe the first crystal structures of wild-type and pathogenic mutant U2AF1 complexed with target RNA, revealing the mechanism of 3´ splice site selection, and how aberrant splicing results from clinically important mutations. Unexpected features of this mechanism may assist the future development of new treatments against diseases caused by splicing errors. U2AF1 binds to the 3’ splice site of introns and its mutation lead to abnormal splicing. Here the authors solve the crystal structures of wild type and pathogenic mutant U2AF1 bound to target RNA, showing that different target sequence is preferred by pathogenic mutant.
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Affiliation(s)
- Hisashi Yoshida
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sam-Yong Park
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Gyosuke Sakashita
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan
| | - Yuko Nariai
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan
| | - Kanako Kuwasako
- Faculty of Pharmacy and Research institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shin-machi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Yutaka Muto
- Faculty of Pharmacy and Research institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shin-machi, Nishitokyo-shi, Tokyo, 202-8585, Japan.
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan
| | - Eiji Obayashi
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan.
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14
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Fan J, Slowikowski K, Zhang F. Single-cell transcriptomics in cancer: computational challenges and opportunities. Exp Mol Med 2020; 52:1452-1465. [PMID: 32929226 PMCID: PMC8080633 DOI: 10.1038/s12276-020-0422-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/26/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Intratumor heterogeneity is a common characteristic across diverse cancer types and presents challenges to current standards of treatment. Advancements in high-throughput sequencing and imaging technologies provide opportunities to identify and characterize these aspects of heterogeneity. Notably, transcriptomic profiling at a single-cell resolution enables quantitative measurements of the molecular activity that underlies the phenotypic diversity of cells within a tumor. Such high-dimensional data require computational analysis to extract relevant biological insights about the cell types and states that drive cancer development, pathogenesis, and clinical outcomes. In this review, we highlight emerging themes in the computational analysis of single-cell transcriptomics data and their applications to cancer research. We focus on downstream analytical challenges relevant to cancer research, including how to computationally perform unified analysis across many patients and disease states, distinguish neoplastic from nonneoplastic cells, infer communication with the tumor microenvironment, and delineate tumoral and microenvironmental evolution with trajectory and RNA velocity analysis. We include discussions of challenges and opportunities for future computational methodological advancements necessary to realize the translational potential of single-cell transcriptomic profiling in cancer.
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Affiliation(s)
- Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
| | - Kamil Slowikowski
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Fan Zhang
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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15
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Warnasooriya C, Feeney CF, Laird KM, Ermolenko DN, Kielkopf CL. A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation. Nucleic Acids Res 2020; 48:5695-5709. [PMID: 32343311 PMCID: PMC7261175 DOI: 10.1093/nar/gkaa293] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/09/2020] [Accepted: 04/17/2020] [Indexed: 02/02/2023] Open
Abstract
An essential heterodimer of the U2AF1 and U2AF2 pre-mRNA splicing factors nucleates spliceosome assembly at polypyrimidine (Py) signals preceding the major class of 3′ splice sites. U2AF1 frequently acquires an S34F-encoding mutation among patients with myelodysplastic syndromes (MDS). The influence of the U2AF1 subunit and its S34F mutation on the U2AF2 conformations remains unknown. Here, we employ single molecule Förster resonance energy transfer (FRET) to determine the influence of wild-type or S34F-substituted U2AF1 on the conformational dynamics of U2AF2 and its splice site RNA complexes. In the absence of RNA, the U2AF1 subunit stabilizes a high FRET value, which by structure-guided mutagenesis corresponds to a closed conformation of the tandem U2AF2 RNA recognition motifs (RRMs). When the U2AF heterodimer is bound to a strong, uridine-rich splice site, U2AF2 switches to a lower FRET value characteristic of an open, side-by-side arrangement of the RRMs. Remarkably, the U2AF heterodimer binds weak, uridine-poor Py tracts as a mixture of closed and open U2AF2 conformations, which are modulated by the S34F mutation. Shifts between open and closed U2AF2 may underlie U2AF1-dependent splicing of degenerate Py tracts and contribute to a subset of S34F-dysregulated splicing events in MDS patients.
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Affiliation(s)
- Chandani Warnasooriya
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Callen F Feeney
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Kholiswa M Laird
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Dmitri N Ermolenko
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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16
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Pei J, Kinch LN, Otwinowski Z, Grishin NV. Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PLoS Comput Biol 2020; 16:e1007775. [PMID: 32413045 PMCID: PMC7255613 DOI: 10.1371/journal.pcbi.1007775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/28/2020] [Accepted: 03/06/2020] [Indexed: 12/19/2022] Open
Abstract
The human genome harbors a variety of genetic variations. Single-nucleotide changes that alter amino acids in protein-coding regions are one of the major causes of human phenotypic variation and diseases. These single-amino acid variations (SAVs) are routinely found in whole genome and exome sequencing. Evaluating the functional impact of such genomic alterations is crucial for diagnosis of genetic disorders. We developed DeepSAV, a deep-learning convolutional neural network to differentiate disease-causing and benign SAVs based on a variety of protein sequence, structural and functional properties. Our method outperforms most stand-alone programs, and the version incorporating population and gene-level information (DeepSAV+PG) has similar predictive power as some of the best available. We transformed DeepSAV scores of rare SAVs in the human population into a quantity termed "mutation severity measure" for each human protein-coding gene. It reflects a gene's tolerance to deleterious missense mutations and serves as a useful tool to study gene-disease associations. Genes implicated in cancer, autism, and viral interaction are found by this measure as intolerant to mutations, while genes associated with a number of other diseases are scored as tolerant. Among known disease-associated genes, those that are mutation-intolerant are likely to function in development and signal transduction pathways, while those that are mutation-tolerant tend to encode metabolic and mitochondrial proteins.
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Affiliation(s)
- Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Zbyszek Otwinowski
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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17
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Kaur H, Groubert B, Paulson JC, McMillan S, Hoskins AA. Impact of cancer-associated mutations in Hsh155/SF3b1 HEAT repeats 9-12 on pre-mRNA splicing in Saccharomyces cerevisiae. PLoS One 2020; 15:e0229315. [PMID: 32320410 PMCID: PMC7176370 DOI: 10.1371/journal.pone.0229315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022] Open
Abstract
Mutations in the splicing machinery have been implicated in a number of human diseases. Most notably, the U2 small nuclear ribonucleoprotein (snRNP) component SF3b1 has been found to be frequently mutated in blood cancers such as myelodysplastic syndromes (MDS). SF3b1 is a highly conserved HEAT repeat (HR)-containing protein and most of these blood cancer mutations cluster in a hot spot located in HR4-8. Recently, a second mutational hotspot has been identified in SF3b1 located in HR9-12 and is associated with acute myeloid leukemias, bladder urothelial carcinomas, and uterine corpus endometrial carcinomas. The consequences of these mutations on SF3b1 functions during splicing have not yet been tested. We incorporated the corresponding mutations into the yeast homolog of SF3b1 and tested their impact on splicing. We find that all of these HR9-12 mutations can support splicing in yeast, and this suggests that none of them are loss of function alleles in humans. The Hsh155V502F mutation alters splicing of several pre-mRNA reporters containing weak branch sites as well as a genetic interaction with Prp2 and physical interactions with Prp5 and Prp3. The ability of a single allele of Hsh155 to perturb interactions with multiple factors functioning at different stages of the splicing reaction suggests that some SF3b1-mutant disease phenotypes may have a complex origin on the spliceosome.
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Affiliation(s)
- Harpreet Kaur
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brent Groubert
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua C. Paulson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sarah McMillan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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18
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Are all splicing mutations the same? Blood 2020; 135:978-979. [PMID: 32219349 DOI: 10.1182/blood.2020005032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Fujita KI, Ishizuka T, Mitsukawa M, Kurata M, Masuda S. Regulating Divergent Transcriptomes through mRNA Splicing and Its Modulation Using Various Small Compounds. Int J Mol Sci 2020; 21:ijms21062026. [PMID: 32188117 PMCID: PMC7139312 DOI: 10.3390/ijms21062026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/14/2022] Open
Abstract
Human transcriptomes are more divergent than genes and contribute to the sophistication of life. This divergence is derived from various isoforms arising from alternative splicing. In addition, alternative splicing regulated by spliceosomal factors and RNA structures, such as the RNA G-quadruplex, is important not only for isoform diversity but also for regulating gene expression. Therefore, abnormal splicing leads to serious diseases such as cancer and neurodegenerative disorders. In the first part of this review, we describe the regulation of divergent transcriptomes using alternative mRNA splicing. In the second part, we present the relationship between the disruption of splicing and diseases. Recently, various compounds with splicing inhibitor activity were established. These splicing inhibitors are recognized as a biological tool to investigate the molecular mechanism of splicing and as a potential therapeutic agent for cancer treatment. Food-derived compounds with similar functions were found and are expected to exhibit anticancer effects. In the final part, we describe the compounds that modulate the messenger RNA (mRNA) splicing process and their availability for basic research and future clinical potential.
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20
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Chang JW, Yeh HS, Park M, Erber L, Sun J, Cheng S, Bui AM, Fahmi NA, Nasti R, Kuang R, Chen Y, Zhang W, Yong J. mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control. Nucleic Acids Res 2019; 47:10373-10387. [PMID: 31504847 PMCID: PMC6821156 DOI: 10.1093/nar/gkz761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/23/2019] [Accepted: 08/23/2019] [Indexed: 01/13/2023] Open
Abstract
U2 auxiliary factor 1 (U2AF1) functions in 3′-splice site selection during pre-mRNA processing. Alternative usage of duplicated tandem exons in U2AF1 produces two isoforms, U2AF1a and U2AF1b, but their functional differences are unappreciated due to their homology. Through integrative approaches of genome editing, customized-transcriptome profiling and crosslinking-mediated interactome analyses, we discovered that the expression of U2AF1 isoforms is controlled by mTOR and they exhibit a distinctive molecular profile for the splice site and protein interactomes. Mechanistic dissection of mutually exclusive alternative splicing events revealed that U2AF1 isoforms’ inherent differential preferences of nucleotide sequences and their stoichiometry determine the 3′-splice site. Importantly, U2AF1a-driven transcriptomes feature alternative splicing events in the 5′-untranslated region (5′-UTR) that are favorable for translation. These findings unveil distinct roles of duplicated tandem exon-derived U2AF1 isoforms in the regulation of the transcriptome and suggest U2AF1a-driven 5′-UTR alternative splicing as a molecular mechanism of mTOR-regulated translational control.
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Affiliation(s)
- Jae-Woong Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Alexander M Bui
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Ryan Nasti
- Department of Genetics, Cell and Developmental Biology, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Rui Kuang
- Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
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21
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Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194440. [PMID: 31707043 DOI: 10.1016/j.bbagrm.2019.194440] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022]
Abstract
The pre-mRNA splicing factor SF3b1 exhibits recurrent mutations among hematologic malignancies and cancers, and consequently is a major therapeutic target of clinically-advanced spliceosome inhibitors. In this review, we highlight and rigorously analyze emerging views of SF3b1 conformational transitions, including the human SF3b particle either in isolation or bound to spliceosome inhibitors, and human or yeast spliceosome assemblies. Among spliceosome states characterized to date, an SF3b1 α-helical superhelix significantly closes to surround a U2 small nuclear RNA duplex with the pre-mRNA branch point sequence. The SF3b1 torus is locally unwound at an active site adenosine, whereas protein cofactors appear to stabilize overall closure in the spliceosome. Network analyses demonstrates that the natural SF3b1 dynamics mimic its conformational change in the spliceosome, raising the possibility of conformational selection underpinning spliceosome assembly. These dynamic SF3b1 conformations have consequences for gatekeeping of spliceosome assembly and therapeutic targeting of its cancer-associated dysfunction.
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22
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Kastner B, Will CL, Stark H, Lührmann R. Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes. Cold Spring Harb Perspect Biol 2019; 11:a032417. [PMID: 30765414 PMCID: PMC6824238 DOI: 10.1101/cshperspect.a032417] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spliceosome is a highly complex, dynamic ribonucleoprotein molecular machine that undergoes numerous structural and compositional rearrangements that lead to the formation of its active site. Recent advances in cyroelectron microscopy (cryo-EM) have provided a plethora of near-atomic structural information about the inner workings of the spliceosome. Aided by previous biochemical, structural, and functional studies, cryo-EM has confirmed or provided a structural basis for most of the prevailing models of spliceosome function, but at the same time allowed novel insights into splicing catalysis and the intriguing dynamics of the spliceosome. The mechanism of pre-mRNA splicing is highly conserved between humans and yeast, but the compositional dynamics and ribonucleoprotein (RNP) remodeling of the human spliceosome are more complex. Here, we summarize recent advances in our understanding of the molecular architecture of the human spliceosome, highlighting differences between the human and yeast splicing machineries.
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Affiliation(s)
- Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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23
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Yang Q, Zhao J, Zhang W, Chen D, Wang Y. Aberrant alternative splicing in breast cancer. J Mol Cell Biol 2019; 11:920-929. [PMID: 31065692 PMCID: PMC6884705 DOI: 10.1093/jmcb/mjz033] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/19/2019] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing is critical for human gene expression regulation, which plays a determined role in expanding the diversity of functional proteins. Importantly, alternative splicing is a hallmark of cancer and a potential target for cancer therapeutics. Based on the statistical data, breast cancer is one of the top leading causes of cancer-related deaths in women worldwide. Strikingly, alternative splicing is closely associated with breast cancer development. Here, we seek to provide a general review of the relationship between alternative splicing and breast cancer. We introduce the process of alternative splicing and its regulatory role in cancers. In addition, we highlight the functions of aberrant alternative splicing and mutations of splicing factors in breast cancer progression. Moreover, we discuss the role of alternative splicing in cancer drug resistance and the potential of being targets for cancer therapeutics.
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Affiliation(s)
- Quan Yang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Dan Chen
- Department of Pathology, First Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
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Borišek J, Saltalamacchia A, Gallì A, Palermo G, Molteni E, Malcovati L, Magistrato A. Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations. Biomolecules 2019; 9:E633. [PMID: 31640290 PMCID: PMC6843770 DOI: 10.3390/biom9100633] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
The spliceosome accurately promotes precursor messenger-RNA splicing by recognizing specific noncoding intronic tracts including the branch point sequence (BPS) and the 3'-splice-site (3'SS). Mutations of Hsh155 (yeast)/SF3B1 (human), which is a protein of the SF3b factor involved in BPS recognition and induces altered BPS binding and 3'SS selection, lead to mis-spliced mRNA transcripts. Although these mutations recur in hematologic malignancies, the mechanism by which they change gene expression remains unclear. In this study, multi-microsecond-long molecular-dynamics simulations of eighth distinct ∼700,000 atom models of the spliceosome Bact complex, and gene sequencing of SF3B1, disclose that these carcinogenic isoforms destabilize intron binding and/or affect the functional dynamics of Hsh155/SF3B1 only when binding non-consensus BPSs, as opposed to the non-pathogenic variants newly annotated here. This pinpoints a cross-talk between the distal Hsh155 mutation and BPS recognition sites. Our outcomes unprecedentedly contribute to elucidating the principles of pre-mRNA recognition, which provides critical insights on the mechanism underlying constitutive/alternative/aberrant splicing.
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Affiliation(s)
- Jure Borišek
- CNR-IOM-Democritos National Simulation Center c/o SISSA, 34136 Trieste, Italy.
- National Institute of Chemistry, 1000 Ljubljana, Slovenia.
| | | | - Anna Gallì
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy.
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside CA 92521, USA.
| | - Elisabetta Molteni
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | - Luca Malcovati
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy.
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
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25
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Borišek J, Saltalamacchia A, Spinello A, Magistrato A. Exploiting Cryo-EM Structural Information and All-Atom Simulations To Decrypt the Molecular Mechanism of Splicing Modulators. J Chem Inf Model 2019; 60:2510-2521. [DOI: 10.1021/acs.jcim.9b00635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jure Borišek
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrea Saltalamacchia
- International School for Advanced studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Spinello
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
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26
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Gupta AK, Murthy T, Paul KV, Ramirez O, Fisher JB, Rao S, Rosenberg AB, Seelig G, Minella AC, Pillai MM. Degenerate minigene library analysis enables identification of altered branch point utilization by mutant splicing factor 3B1 (SF3B1). Nucleic Acids Res 2019; 47:970-980. [PMID: 30462273 PMCID: PMC6344872 DOI: 10.1093/nar/gky1161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Cancer-associated mutations of the core splicing factor 3 B1 (SF3B1) result in selection of novel 3′ splice sites (3′SS), but precise molecular mechanisms of oncogenesis remain unclear. SF3B1 stabilizes the interaction between U2 snRNP and branch point (BP) on the pre-mRNA. It has hence been speculated that a change in BP selection is the basis for novel 3′SS selection. Direct quantitative determination of BP utilization is however technically challenging. To define BP utilization by SF3B1-mutant spliceosomes, we used an overexpression approach in human cells as well as a complementary strategy using isogenic murine embryonic stem cells with monoallelic K700E mutations constructed via CRISPR/Cas9-based genome editing and a dual vector homology-directed repair methodology. A synthetic minigene library with degenerate regions in 3′ intronic regions (3.4 million individual minigenes) was used to compare BP usage of SF3B1K700E and SF3B1WT. Using this model, we show that SF3B1K700E spliceosomes utilize non-canonical sequence variants (at position −1 relative to BP adenosine) more frequently than wild-type spliceosomes. These predictions were confirmed using minigene splicing assays. Our results suggest a model of BP utilization by mutant SF3B1 wherein it is able to utilize non-consensus alternative BP sequences by stabilizing weaker U2-BP interactions.
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Affiliation(s)
| | - Tushar Murthy
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kiran V Paul
- Section of Hematology, Yale Cancer Center, New Haven, CT, USA
| | - Oscar Ramirez
- Section of Hematology, Yale Cancer Center, New Haven, CT, USA
| | - Joseph B Fisher
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA
| | - Sridhar Rao
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA
| | | | - Georg Seelig
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Alex C Minella
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA
- Correspondence may also be addressed to Alex C. Minella. Tel: +1 414 937 6238;
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center, New Haven, CT, USA
- To whom correspondence should be addressed. Tel: +1 203 737 6403;
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27
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Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R. Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. Nucleic Acids Res 2019; 47:5293-5306. [PMID: 30916337 PMCID: PMC6547761 DOI: 10.1093/nar/gkz193] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/12/2019] [Indexed: 11/12/2022] Open
Abstract
Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a negative feedback loop, in which RBP binds its own pre-mRNA and causes alternative splicing to introduce a PTC. We present a bioinformatic analysis integrating three data sources, eCLIP assays for a large RBP panel, shRNA inactivation of NMD pathway, and shRNA-depletion of RBPs followed by RNA-seq, to identify novel such autoregulatory feedback loops. We show that RBPs frequently bind their own pre-mRNAs, their exons respond prominently to NMD pathway disruption, and that the responding exons are enriched with nearby eCLIP peaks. We confirm previously proposed models of autoregulation in SRSF7 and U2AF1 genes and present two novel models, in which (i) SFPQ binds its mRNA and promotes switching to an alternative distal 3'-UTR that is targeted by NMD, and (ii) RPS3 binding activates a poison 5'-splice site in its pre-mRNA that leads to a frame shift and degradation by NMD. We also suggest specific splicing events that could be implicated in autoregulatory feedback loops in RBM39, HNRNPM, and U2AF2 genes. The results are available through a UCSC Genome Browser track hub.
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Affiliation(s)
- Dmitri Pervouchine
- Skolkovo Institute of Science and Technology, Ulitsa Nobelya 3, Moscow 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, 119234 Moscow, Russia
| | - Yaroslav Popov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, 119234 Moscow, Russia
| | - Andy Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SA Hinxton, Cambridge, UK
| | - Beatrice Borsari
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SA Hinxton, Cambridge, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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28
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Palangat M, Anastasakis DG, Fei DL, Lindblad KE, Bradley R, Hourigan CS, Hafner M, Larson DR. The splicing factor U2AF1 contributes to cancer progression through a noncanonical role in translation regulation. Genes Dev 2019; 33:482-497. [PMID: 30842218 PMCID: PMC6499322 DOI: 10.1101/gad.319590.118] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 02/15/2019] [Indexed: 01/07/2023]
Abstract
Palangat et al. uncovered a noncanonical function of U2AF1, showing that it directly binds mature mRNA in the cytoplasm and negatively regulates mRNA translation. Somatic mutations in the genes encoding components of the spliceosome occur frequently in human neoplasms, including myeloid dysplasias and leukemias, and less often in solid tumors. One of the affected factors, U2AF1, is involved in splice site selection, and the most common change, S34F, alters a conserved nucleic acid-binding domain, recognition of the 3′ splice site, and alternative splicing of many mRNAs. However, the role that this mutation plays in oncogenesis is still unknown. Here, we uncovered a noncanonical function of U2AF1, showing that it directly binds mature mRNA in the cytoplasm and negatively regulates mRNA translation. This splicing-independent role of U2AF1 is altered by the S34F mutation, and polysome profiling indicates that the mutation affects translation of hundreds of mRNA. One functional consequence is increased synthesis of the secreted chemokine interleukin 8, which contributes to metastasis, inflammation, and cancer progression in mice and humans.
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Affiliation(s)
- Murali Palangat
- Laboratory of Receptor Biology and Gene Expression, National Cancer Insitute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dimitrios G Anastasakis
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Katherine E Lindblad
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Robert Bradley
- Computational Biology Program, Public Health Sciences and Biological Sciences, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Markus Hafner
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Insitute, National Institutes of Health, Bethesda, Maryland 20892, USA
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29
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Kennedy SD, Bauer WJ, Wang W, Kielkopf CL. Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites. Biochem Biophys Res Commun 2019; 511:416-421. [PMID: 30797552 DOI: 10.1016/j.bbrc.2019.02.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 11/19/2022]
Abstract
The pre-mRNA branch point sequence (BPS) anneals with a pseudouridine-modified region of the U2 small nuclear (sn)RNA, and offers a 2' hydroxyl group of a bulged adenosine as the nucleophile for the first catalytic step of pre-mRNA splicing. To increase our structural understanding of branch site selection, we characterized a duplex containing a BPS sequence that is common among multicellular eukaryotes (5'-UACUGAC-3') and the complementary U2 snRNA site using NMR. A major conformation of the expected branch site adenosine stacked within the duplex and paired with the conserved pseudouridine of the U2 snRNA strand. In contrast, the guanosine preceding the branch site appeared flexible and had weak contacts with the surrounding nucleotides. Pseudouridine-modified and unmodified U2 snRNA-BPS-containing duplexes remained structurally similar. These results highlight the importance of auxiliary factors to achieve the active bulged conformation of the branch site nucleophile for the first step of pre-mRNA splicing.
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Affiliation(s)
- Scott D Kennedy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA.
| | - William J Bauer
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Wenhua Wang
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA.
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30
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Yu Y, Zhen Z, Qi H, Yuan X, Gao X, Zhang M. U2AF65 enhances milk synthesis and growth of bovine mammary epithelial cells by positively regulating the mTOR-SREBP-1c signalling pathway. Cell Biochem Funct 2019; 37:93-101. [PMID: 30773658 DOI: 10.1002/cbf.3378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/14/2022]
Abstract
U2 snRNP auxiliary factor 65 kDa (U2AF65) is a splicing factor that promotes prespliceosome assembly. The function of U2AF65 in alternative splicing has been identified; however, the essential physiological role of U2AF65 remains poorly understood. In this study, we investigated the regulatory role of U2AF65 in milk synthesis and growth of bovine mammary epithelial cells (BMECs). Our results showed that U2AF65 localizes in the nucleus. Treatment with amino acids (Met and Leu) and hormones (prolactin and β-estradiol) upregulated the expression of U2AF65 in these cells. U2AF65 overexpression increased the synthesis of β-casein, triglycerides, and lactose; increased cell viability; and promoted proliferation of BMECs. Furthermore, our results showed that U2AF65 positively regulated mTOR phosphorylation and expression of mature mRNA of mTOR and SREBP-1c. Collectively, our findings demonstrate that U2AF65 regulates the mRNA expression of signalling molecules (mTOR and SREBP-1c) involved in milk synthesis and growth of BMECs, possibly via controlling the splicing and maturation of these mRNAs. U2 snRNP auxiliary factor 65 kDa (U2AF65) is a splicing factor that promotes prespliceosome assembly. The essential physiological role of U2AF65 remains poorly understood. In the present study, we confirmed that U2AF65 functions as a positive regulator of milk synthesis in and proliferation of bovine mammary epithelial cells via the mTOR-SREBP-1c signalling pathway. Therefore, our study uncovers the regulatory role of U2AF65 in milk synthesis and cell proliferation.
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Affiliation(s)
- Yanbo Yu
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| | - Zhen Zhen
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| | - Hao Qi
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| | - Xiaohan Yuan
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| | - Xuejun Gao
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
| | - Minghui Zhang
- Key Laboratory of Dairy Science of Education Ministry, Northeast Agricultural University, Harbin, China
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31
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Liu X, Klein PS. Glycogen synthase kinase-3 and alternative splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1501. [PMID: 30118183 DOI: 10.1002/wrna.1501] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022]
Abstract
Glycogen synthase kinase-3 (GSK-3) is a highly conserved negative regulator of receptor tyrosine kinase, cytokine, and Wnt signaling pathways. Stimulation of these pathways inhibits GSK-3 to modulate diverse downstream effectors that include transcription factors, nutrient sensors, glycogen synthesis, mitochondrial function, circadian rhythm, and cell fate. GSK-3 also regulates alternative splicing in response to T-cell receptor activation, and recent phosphoproteomic studies have revealed that multiple splicing factors and regulators of RNA biosynthesis are phosphorylated in a GSK-3-dependent manner. Furthermore, inhibition of GSK-3 alters the splicing of hundreds of mRNAs, indicating a broad role for GSK-3 in the regulation of RNA processing. GSK-3-regulated phosphoproteins include SF3B1, SRSF2, PSF, RBM8A, nucleophosmin 1 (NPM1), and PHF6, many of which are mutated in leukemia and myelodysplasia. As GSK-3 is inhibited by pathways that are pathologically activated in leukemia and loss of Gsk3 in hematopoietic cells causes a severe myelodysplastic neoplasm in mice, these findings strongly implicate GSK-3 as a critical regulator of mRNA processing in normal and malignant hematopoiesis. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Xiaolei Liu
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter S Klein
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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32
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Carrocci TJ, Paulson JC, Hoskins AA. Functional analysis of Hsh155/SF3b1 interactions with the U2 snRNA/branch site duplex. RNA (NEW YORK, N.Y.) 2018; 24:1028-1040. [PMID: 29752352 PMCID: PMC6049509 DOI: 10.1261/rna.065664.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/10/2018] [Indexed: 05/25/2023]
Abstract
SF3b1 is an essential component of the U2 snRNP implicated in branch site (BS) recognition and found to be frequently mutated in several human cancers. While recent structures of yeast and human SF3b1 have revealed its molecular architecture, the importance of specific RNA:protein contacts and conformational changes remains largely uncharacterized. Here, we performed mutational analysis of yeast SF3b1, guided by recent structures of the spliceosome. We find that conserved amino acids contacting the U2 snRNA backbone of the U2/BS duplex are nonessential, and that yeast can tolerate truncation of the HEAT repeats containing these amino acids. The pocket housing the branchpoint adenosine (BP-A) is also amenable to mutation despite strong conservation. However, mutations that support viability can still lead to defects in splicing pre-mRNAs with nonconsensus BS substitutions found at -3, -2, -1, and +1 positions relative to the BP-A or at the branchpoint position. Through the generation of yeast and human chimeric proteins, we further defined the functionally conserved regions of Hsh155 as well as identify changes in BS usage resulting from inclusion of human SF3b1 HEAT repeats. Moreover, these chimeric proteins confer a sensitivity to small molecule inhibition by pladienolide B to yeast splicing. Together, these data reveal the importance of individual contacts of Hsh155/SF3b1 to the U2/BS duplex and define their contribution to BS usage by the spliceosome.
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Affiliation(s)
- Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Joshua C Paulson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Hwang HM, Heo CK, Lee HJ, Kwak SS, Lim WH, Yoo JS, Yu DY, Lim KJ, Kim JY, Cho EW. Identification of anti-SF3B1 autoantibody as a diagnostic marker in patients with hepatocellular carcinoma. J Transl Med 2018; 16:177. [PMID: 29954402 PMCID: PMC6025833 DOI: 10.1186/s12967-018-1546-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/12/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Tumor-associated (TA) autoantibodies, which are generated by the immune system upon the recognition of abnormal TA antigens, are promising biomarkers for the early detection of tumors. In order to detect autoantibody biomarkers effectively, antibody-specific epitopes in the diagnostic test should maintain the specific conformations that are as close as possible to those presenting in the body. However, when using patients' serum as a source of TA autoantibodies the characterization of the autoantibody-specific epitope is not easy due to the limited amount of patient-derived serum. METHODS To overcome these limits, we constructed a B cell hybridoma pool derived from a hepatocellular carcinoma (HCC) model HBx-transgenic mouse and characterized autoantibodies derived from them as tumor biomarkers. Their target antigens were identified by mass spectrometry and the correlations with HCC were examined. With the assumption that TA autoantibodies generated in the tumor mouse model are induced in human cancer patients, the enzyme-linked immunosorbent assays (ELISA) based on the characteristics of mouse TA autoantibodies were developed for the detection of autoantibody biomarkers in human serum. To mimic natural antigenic structures, the specific epitopes against autoantibodies were screened from the phage display cyclic random heptapeptide library, and the streptavidin antigens fused with the specific epitopes were used as coating antigens. RESULTS In this study, one of HCC-associated autoantibodies derived from HBx-transgenic mouse, XC24, was characterized. Its target antigen was identified as splicing factor 3b subunit 1 (SF3B1) and the high expression of SF3B1 was confirmed in HCC tissues. The specific peptide epitopes against XC24 were selected and, among them, XC24p11 cyclic peptide (-CDATPPRLC-) was used as an epitope of anti-SF3B1 autoantibody ELISA. With this epitope, we could effectively distinguish between serum samples from HCC patients (n = 102) and healthy subjects (n = 85) with 73.53% sensitivity and 91.76% specificity (AUC = 0.8731). Moreover, the simultaneous detection of anti-XC24p11 epitope autoantibody and AFP enhanced the efficiency of HCC diagnosis with 87.25% sensitivity and 90.59% specificity (AUC = 0.9081). CONCLUSIONS ELISA using XC24p11 peptide epitope that reacts against anti-SF3B1 autoantibody can be used as a novel test to enhance the diagnostic efficiency of HCC.
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Affiliation(s)
- Hai-Min Hwang
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
| | - Chang-Kyu Heo
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
| | - Hye Jung Lee
- Proteometech Inc., 1101 Wooree Venture Town, 466 Gangseo-ro, Gangseo-gu, Seoul, 07573 South Korea
- Graduate Program for Nanomedical Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722 South Korea
| | - Sang-Seob Kwak
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
- Department of Functional Genomics, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Won-Hee Lim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
- Department of Functional Genomics, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Jong-Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, 162 YeonGuDanji-ro, Ochang-eup, Cheongju, Chungbuk 28119 South Korea
| | - Dae-Yuel Yu
- Disease Model Research Laboratory, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Kook Jin Lim
- Proteometech Inc., 1101 Wooree Venture Town, 466 Gangseo-ro, Gangseo-gu, Seoul, 07573 South Korea
- Graduate Program for Nanomedical Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722 South Korea
| | - Jeong-Yoon Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134 South Korea
| | - Eun-Wie Cho
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
- Department of Functional Genomics, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 South Korea
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34
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Corbett AH. Post-transcriptional regulation of gene expression and human disease. Curr Opin Cell Biol 2018; 52:96-104. [PMID: 29518673 PMCID: PMC5988930 DOI: 10.1016/j.ceb.2018.02.011] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 12/18/2022]
Abstract
A large number of mutations in genes that encode RNA binding proteins cause human disease. Many of these RNA binding proteins mediate key steps in post-transcriptional regulation of gene expression from mRNA processing to eventual decay in the cytoplasm. Surprisingly, these RNA binding proteins, which are ubiquitously expressed and play fundamental roles in gene expression, are often altered in tissue-specific disease. Mutations linked to disease impact nearly every post-transcriptional processing step and cause diverse disease phenotypes in a variety of specific tissues. This review summarizes steps in post-transcriptional regulation of gene expression that have been linked to disease providing specific examples of some of the many genes affected. Finally, recent advances that hold promise for treatment of some of these diseases are presented.
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Affiliation(s)
- Anita H Corbett
- Department of Biology, RRC 1021, Emory University, 1510 Clifton Road, NE, Atlanta 30322, GA, United States.
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Chen W, Moore J, Ozadam H, Shulha HP, Rhind N, Weng Z, Moore MJ. Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling. Cell 2018; 173:1031-1044.e13. [PMID: 29727662 PMCID: PMC6090549 DOI: 10.1016/j.cell.2018.03.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/09/2018] [Accepted: 03/23/2018] [Indexed: 12/31/2022]
Abstract
Full understanding of eukaryotic transcriptomes and how they respond to different conditions requires deep knowledge of all sites of intron excision. Although RNA sequencing (RNA-seq) provides much of this information, the low abundance of many spliced transcripts (often due to their rapid cytoplasmic decay) limits the ability of RNA-seq alone to reveal the full repertoire of spliced species. Here, we present "spliceosome profiling," a strategy based on deep sequencing of RNAs co-purifying with late-stage spliceosomes. Spliceosome profiling allows for unambiguous mapping of intron ends to single-nucleotide resolution and branchpoint identification at unprecedented depths. Our data reveal hundreds of new introns in S. pombe and numerous others that were previously misannotated. By providing a means to directly interrogate sites of spliceosome assembly and catalysis genome-wide, spliceosome profiling promises to transform our understanding of RNA processing in the nucleus, much as ribosome profiling has transformed our understanding mRNA translation in the cytoplasm.
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Affiliation(s)
- Weijun Chen
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jill Moore
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Hakan Ozadam
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Hennady P Shulha
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Zhiping Weng
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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Li B, Liu J, Jia Y, Wang J, Xu Z, Qin T, Shi Z, Song Z, Peng S, Huang H, Fang L, Zhang H, Pan L, Hu N, Qu S, Zhang Y, Wu J, Liu N, Ru K, Huang G, Xiao Z. Clinical features and biological implications of differentU2AF1mutation types in myelodysplastic syndromes. Genes Chromosomes Cancer 2017; 57:80-88. [PMID: 29057546 DOI: 10.1002/gcc.22510] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Bing Li
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
- State Key Laboratory of Experimental Hematology; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Jinqin Liu
- State Key Laboratory of Experimental Hematology; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Yujiao Jia
- Department of Pathology; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Jingya Wang
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Zefeng Xu
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
- State Key Laboratory of Experimental Hematology; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Tiejun Qin
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Zhongxun Shi
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Zhen Song
- Medical Service Division; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Shuailing Peng
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Huijun Huang
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Liwei Fang
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Hongli Zhang
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Lijuan Pan
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Naibo Hu
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Shiqiang Qu
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Yue Zhang
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
- State Key Laboratory of Experimental Hematology; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Jian Wu
- MyGenostic Inc; Beijing China
| | - Na Liu
- MyGenostic Inc; Beijing China
| | - Kun Ru
- Department of Pathology; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - Gang Huang
- Divisions of Pathology and Experimental Hematology and Cancer Biology; Cincinnati Children's Hospital Medical Center; Cincinnati OH
| | - Zhijian Xiao
- MDS and MPN Centre; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
- State Key Laboratory of Experimental Hematology; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
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38
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Kielkopf CL. Insights from structures of cancer-relevant pre-mRNA splicing factors. Curr Opin Genet Dev 2017; 48:57-66. [PMID: 29128695 DOI: 10.1016/j.gde.2017.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/10/2017] [Accepted: 10/13/2017] [Indexed: 12/21/2022]
Abstract
Pre-mRNA splicing factors recognize consensus signals within preliminary transcripts, and as cogs of the spliceosome machine, orchestrate the excision and rejoining of pre-mRNA regions for gene expression. Large-scale sequencing has demonstrated that mutations in key genes encoding pre-mRNA splicing factors are common among myeloid neoplasms and also occur in a variety of other cancers. This revelation offers new therapeutic opportunities to target pre-mRNA splicing vulnerabilities in hematologic and other malignancies. The mutated residues typically alter 3' splice site choice for a subset of transcripts. In this review, we highlight mechanistic insights from recent 3D structures that reveal the affected residues poised for pre-mRNA recognition.
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Affiliation(s)
- Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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39
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Galganski L, Urbanek MO, Krzyzosiak WJ. Nuclear speckles: molecular organization, biological function and role in disease. Nucleic Acids Res 2017; 45:10350-10368. [PMID: 28977640 PMCID: PMC5737799 DOI: 10.1093/nar/gkx759] [Citation(s) in RCA: 298] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022] Open
Abstract
The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Further studies on transcription and mRNA maturation and export revealed a more general role for splicing speckles in RNA metabolism. Here, we discuss the functional implications of the localization of numerous proteins crucial for epigenetic regulation, chromatin organization, DNA repair and RNA modification to nuclear speckles. We highlight recent advances suggesting that NSs facilitate integrated regulation of gene expression. In addition, we consider the influence of abundant regulatory and signaling proteins, i.e. protein kinases and proteins involved in protein ubiquitination, phosphoinositide signaling and nucleoskeletal organization, on pre-mRNA synthesis and maturation. While many of these regulatory proteins act within NSs, direct evidence for mRNA metabolism events occurring in NSs is still lacking. NSs contribute to numerous human diseases, including cancers and viral infections. In addition, recent data have demonstrated close relationships between these structures and the development of neurological disorders.
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Affiliation(s)
- Lukasz Galganski
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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40
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. A Challenging Pie to Splice: Drugging the Spliceosome. Angew Chem Int Ed Engl 2017; 56:12052-12063. [PMID: 28371109 PMCID: PMC6311392 DOI: 10.1002/anie.201701065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 02/05/2023]
Abstract
Since its discovery in 1977, the study of alternative RNA splicing has revealed a plethora of mechanisms that had never before been documented in nature. Understanding these transitions and their outcome at the level of the cell and organism has become one of the great frontiers of modern chemical biology. Until 2007, this field remained in the hands of RNA biologists. However, the recent identification of natural product and synthetic modulators of RNA splicing has opened new access to this field, allowing for the first time a chemical-based interrogation of RNA splicing processes. Simultaneously, we have begun to understand the vital importance of splicing in disease, which offers a new platform for molecular discovery and therapy. As with many natural systems, gaining clear mechanistic detail at the molecular level is key towards understanding the operation of any biological machine. This minireview presents recent lessons learned in this emerging field of RNA splicing chemistry and chemical biology.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - Warren C. Chan
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
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41
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. Das Spliceosom als Angriffspunkt für Pharmaka. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - Warren C. Chan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
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42
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Mutations of RNA splicing factors in hematological malignancies. Cancer Lett 2017; 409:1-8. [PMID: 28888996 DOI: 10.1016/j.canlet.2017.08.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/22/2017] [Accepted: 08/28/2017] [Indexed: 01/01/2023]
Abstract
Systematic large-scale cancer genomic studies have produced numerous significant findings. These studies have not only revealed new cancer-promoting genes, but they also have identified cancer-promoting functions of previously known "housekeeping" genes. These studies have identified numerous mutations in genes which play a fundamental role in nuclear precursor mRNA splicing. Somatic mutations and copy number variation in many of the splicing factors which participate in the formation of multiple spliceosomal complexes appear to play a role in many cancers and in particular in myelodysplastic syndromes (MDS). Mutated proteins seem to interfere with the recognition of the authentic splice sites (SS) leading to utilization of suboptimal alternative splicing sites generating aberrantly spliced mRNA isoforms. This short review is focusing on the function of the splice factors involved in the formation of splicing complexes and potential mechanisms which affect usage of the authentic splice site recognition.
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43
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Glasser E, Agrawal AA, Jenkins JL, Kielkopf CL. Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry 2017; 56:4757-4761. [PMID: 28850223 DOI: 10.1021/acs.biochem.7b00551] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acquired point mutations of pre-mRNA splicing factors recur among cancers, leukemias, and related neoplasms. Several studies have established that somatic mutations of a U2AF1 subunit, which normally recognizes 3' splice site junctions, recur among myelodysplastic syndromes. The U2AF2 splicing factor recognizes polypyrimidine signals that precede most 3' splice sites as a heterodimer with U2AF1. In contrast with those of the well-studied U2AF1 subunit, descriptions of cancer-relevant U2AF2 mutations and their structural relationships are lacking. Here, we survey databases of cancer-associated mutations and identify recurring missense mutations in the U2AF2 gene. We determine ultra-high-resolution structures of the U2AF2 RNA recognition motifs (RRM1 and RRM2) at 1.1 Å resolution and map the structural locations of the mutated U2AF2 residues. Comparison with prior, lower-resolution structures of the tandem U2AF2 RRMs in the RNA-bound and apo states reveals clusters of cancer-associated mutations at the U2AF2 RRM-RNA or apo-RRM1-RRM2 interfaces. Although the role of U2AF2 mutations in malignant transformation remains uncertain, our results show that cancer-associated mutations correlate with functionally important surfaces of the U2AF2 splicing factor.
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Affiliation(s)
- Eliezra Glasser
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Anant A Agrawal
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jermaine L Jenkins
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
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44
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Myeloid neoplasms with germline DDX41 mutation. Int J Hematol 2017; 106:163-174. [DOI: 10.1007/s12185-017-2260-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022]
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