1
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Sergeeva OV, Shcherbinina EY, Shomron N, Zatsepin TS. Modulation of RNA Splicing by Oligonucleotides: Mechanisms of Action and Therapeutic Implications. Nucleic Acid Ther 2022; 32:123-138. [PMID: 35166605 DOI: 10.1089/nat.2021.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation via AS-NMD and NGD pathways. We briefly discuss the current progress and future perspectives of SSO therapy for rare and ultrarare diseases.
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Affiliation(s)
- Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry, Moscow State University, Moscow, Russia
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2
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Hotspot exons are common targets of splicing perturbations. Nat Commun 2021; 12:2756. [PMID: 33980843 PMCID: PMC8115636 DOI: 10.1038/s41467-021-22780-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/24/2021] [Indexed: 11/08/2022] Open
Abstract
High-throughput splicing assays have demonstrated that many exonic variants can disrupt splicing; however, splice-disrupting variants distribute non-uniformly across genes. We propose the existence of exons that are particularly susceptible to splice-disrupting variants, which we refer to as hotspot exons. Hotspot exons are also more susceptible to splicing perturbation through drug treatment and knock-down of RNA-binding proteins. We develop a classifier for exonic splice-disrupting variants and use it to infer hotspot exons. We estimate that 1400 exons in the human genome are hotspots. Using panels of splicing reporters, we demonstrate how the ability of an exon to tolerate a mutation is inversely proportional to the strength of its neighboring splice sites. Splicing-disrupting mutations are linked to diseases. By employing a machine learning approach, the authors show that certain exons, termed hotspot exons, are enriched for splicing-disruption variants and susceptible to splicing perturbations.
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3
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Buratti E, Peruzzo P, Braga L, Zanin I, Stuani C, Goina E, Romano M, Giacca M, Dardis A. Deferoxamine mesylate improves splicing and GAA activity of the common c.-32-13T>G allele in late-onset PD patient fibroblasts. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:227-236. [PMID: 33426149 PMCID: PMC7782201 DOI: 10.1016/j.omtm.2020.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022]
Abstract
Pompe disease (PD) is an autosomal recessive lysosomal storage disorder due to deficient activity of the acid alpha glucosidase enzyme (GAA). As a consequence of the enzymatic defect, undigested glycogen accumulates within lysosomes. Most patients affected by the late-onset (LO) phenotype carry in at least one allele the c.-32-13T>G variant, which leads to exon 2 exclusion from the pre-mRNA. These patients display a variable and suboptimal response to enzyme replacement therapy. To identify novel therapeutic approaches, we developed a fluorescent GAA exon 2 splicing assay and screened a library of US Food and Drug Administration (FDA)-approved compounds. This led to the identification of several drugs able to restore normal splicing. Among these, we further validated the effects of the iron chelator deferoxamine (Defe) in c.-32-13T>G fibroblasts. Defe treatment resulted in a 2-fold increase of GAA exon 2 inclusion and a 40% increase in enzymatic activity. Preliminary results suggest that this effect is mediated by the regulation of iron availability, at least partially. RNA-seq experiments also showed that Defe might shift the balance of splicing factor levels toward a profile promoting GAA exon 2 inclusion. This work provides the basis for drug repurposing and development of new chemically modified molecules aimed at improving the clinical outcome in LO-PD patients.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano, Trieste, Italy
| | - Paolo Peruzzo
- Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Luca Braga
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano, Trieste, Italy.,Department of Life Sciences, Via Valerio 28, University of Trieste, 34127 Trieste, Italy
| | - Irene Zanin
- Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano, Trieste, Italy
| | - Elisa Goina
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano, Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, Via Valerio 28, University of Trieste, 34127 Trieste, Italy
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano, Trieste, Italy.,School of Cardiovascular Medicine & Sciences, King's College London British Heart Foundation Centre, London SE5 9NU, United Kingdom
| | - Andrea Dardis
- Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
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4
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Decio P, Ustaoglu P, Derecka K, Hardy ICW, Roat TC, Malaspina O, Mongan N, Stöger R, Soller M. Thiamethoxam exposure deregulates short ORF gene expression in the honey bee and compromises immune response to bacteria. Sci Rep 2021; 11:1489. [PMID: 33452318 PMCID: PMC7811001 DOI: 10.1038/s41598-020-80620-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 12/23/2020] [Indexed: 01/29/2023] Open
Abstract
Maximizing crop yields relies on the use of agrochemicals to control insect pests. One of the most widely used classes of insecticides are neonicotinoids that interfere with signalling of the neurotransmitter acetylcholine, but these can also disrupt crop-pollination services provided by bees. Here, we analysed whether chronic low dose long-term exposure to the neonicotinoid thiamethoxam alters gene expression and alternative splicing in brains of Africanized honey bees, Apis mellifera, as adaptation to altered neuronal signalling. We find differentially regulated genes that show concentration-dependent responses to thiamethoxam, but no changes in alternative splicing. Most differentially expressed genes have no annotated function but encode short Open Reading Frames, a characteristic feature of anti-microbial peptides. As this suggested that immune responses may be compromised by thiamethoxam exposure, we tested the impact of thiamethoxam on bee immunity by injecting bacteria. We show that intrinsically sub-lethal thiamethoxam exposure makes bees more vulnerable to normally non-pathogenic bacteria. Our findings imply a synergistic mechanism for the observed bee population declines that concern agriculturists, conservation ecologists and the public.
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Affiliation(s)
- Pâmela Decio
- grid.410543.70000 0001 2188 478XInstitute of Biosciences, São Paulo State University (Unesp), Rio Claro, Brazil
| | - Pinar Ustaoglu
- grid.6572.60000 0004 1936 7486School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Kamila Derecka
- grid.4563.40000 0004 1936 8868School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Ian C. W. Hardy
- grid.4563.40000 0004 1936 8868School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Thaisa C. Roat
- grid.410543.70000 0001 2188 478XInstitute of Biosciences, São Paulo State University (Unesp), Rio Claro, Brazil
| | - Osmar Malaspina
- grid.410543.70000 0001 2188 478XInstitute of Biosciences, São Paulo State University (Unesp), Rio Claro, Brazil
| | - Nigel Mongan
- grid.4563.40000 0004 1936 8868School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Reinhard Stöger
- grid.4563.40000 0004 1936 8868School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Matthias Soller
- grid.6572.60000 0004 1936 7486School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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5
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Decio P, Ustaoglu P, Roat TC, Malaspina O, Devaud JM, Stöger R, Soller M. Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing. Sci Rep 2019; 9:19196. [PMID: 31844097 PMCID: PMC6915785 DOI: 10.1038/s41598-019-55534-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/20/2019] [Indexed: 12/19/2022] Open
Abstract
Securing food supply for a growing population is a major challenge and heavily relies on the use of agrochemicals to maximize crop yield. It is increasingly recognized, that some neonicotinoid insecticides have a negative impact on non-target organisms, including important pollinators such as the European honeybee Apis mellifera. Toxicity of neonicotinoids may be enhanced through simultaneous exposure with additional pesticides, which could help explain, in part, the global decline of honeybee colonies. Here we examined whether exposure effects of the neonicotinoid thiamethoxam on bee viability are enhanced by the commonly used fungicide carbendazim and the herbicide glyphosate. We also analysed alternative splicing changes upon pesticide exposure in the honeybee. In particular, we examined transcripts of three genes: (i) the stress sensor gene X box binding protein-1 (Xbp1), (ii) the Down Syndrome Cell Adhesion Molecule (Dscam) gene and iii) the embryonic lethal/abnormal visual system (elav) gene, which are important for neuronal function. Our results showed that acute thiamethoxam exposure is not enhanced by carbendazim, nor glyphosate. Toxicity of the compounds did not trigger stress-induced, alternative splicing in the analysed mRNAs, thereby leaving dormant a cellular response pathway to these man-made environmental perturbations.
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Affiliation(s)
- Pâmela Decio
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, and Department of Life Sciences, Imperial College London, Ground Floor, Flowers Building, South Kensington Campus, London, SW7 2AZ, UK
| | - Thaisa C Roat
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Osmar Malaspina
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Jean-Marc Devaud
- Research Center on Animal Cognition, Center for Integrative Biology, Toulouse University, CNRS, UPS, Toulouse, France
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, LE12 5RD, Nottingham/Sutton Bonington Campus, United Kingdom.
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom.
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6
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Balestra D, Branchini A. Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. Int J Mol Sci 2019; 20:ijms20123036. [PMID: 31234407 PMCID: PMC6627357 DOI: 10.3390/ijms20123036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular strategies tailored to promote/correct the expression and/or processing of defective coagulation factors would represent innovative therapeutic approaches beyond standard substitutive therapy. Here, we focus on the molecular mechanisms and determinants underlying innovative approaches acting at DNA, mRNA and protein levels in inherited coagulation factor deficiencies, and in particular on: (i) gene editing approaches, which have permitted intervention at the DNA level through the specific recognition, cleavage, repair/correction or activation of target sequences, even in mutated gene contexts; (ii) the rescue of altered pre-mRNA processing through the engineering of key spliceosome components able to promote correct exon recognition and, in turn, the synthesis and secretion of functional factors, as well as the effects on the splicing of missense changes affecting exonic splicing elements; this section includes antisense oligonucleotide- or siRNA-mediated approaches to down-regulate target genes; (iii) the rescue of protein synthesis/function through the induction of ribosome readthrough targeting nonsense variants or the correction of folding defects caused by amino acid substitutions. Overall, these approaches have shown the ability to rescue the expression and/or function of potentially therapeutic levels of coagulation factors in different disease models, thus supporting further studies in the future aimed at evaluating the clinical translatability of these new strategies.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
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7
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Impact, Characterization, and Rescue of Pre-mRNA Splicing Mutations in Lysosomal Storage Disorders. Genes (Basel) 2018; 9:genes9020073. [PMID: 29415500 PMCID: PMC5852569 DOI: 10.3390/genes9020073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/19/2018] [Accepted: 01/31/2018] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage disorders (LSDs) represent a group of more than 50 severe metabolic diseases caused by the deficiency of specific lysosomal hydrolases, activators, carriers, or lysosomal integral membrane proteins, leading to the abnormal accumulation of substrates within the lysosomes. Numerous mutations have been described in each disease-causing gene; among them, about 5-19% affect the pre-mRNA splicing process. In the last decade, several strategies to rescue/increase normal splicing of mutated transcripts have been developed and LSDs represent excellent candidates for this type of approach: (i) most of them are inherited in an autosomic recessive manner and patients affected by late-onset (LO) phenotypes often retain a fair amount of residual enzymatic activity; thus, even a small recovery of normal splicing may be beneficial in clinical settings; (ii) most LSDs still lack effective treatments or are currently treated with extremely expensive approaches; (iii) in few LSDs, a single splicing mutation accounts for up to 40-70% of pathogenic alleles. At present, numerous preclinical studies support the feasibility of reverting the pathological phenotype by partially rescuing splicing defects in LSDs. This review provides an overview of the impact of splicing mutations in LSDs and the related therapeutic approaches currently under investigation in these disorders.
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8
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Mthembu NN, Mbita Z, Hull R, Dlamini Z. Abnormalities in alternative splicing of angiogenesis-related genes and their role in HIV-related cancers. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2017; 9:77-93. [PMID: 28694706 PMCID: PMC5490432 DOI: 10.2147/hiv.s124911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi’s sarcoma, non-Hodgkin’s lymphoma, and cervical cancer. This aberrant splicing leads to abnormal production of protein and is caused by mutations in cis-acting elements or trans-acting factors in angiogenesis-related genes. Restoring the normal regulation of alternative splicing of angiogenic genes would alter the expression of protein isoforms and may confer normal cell physiology in patients with these cancers. This review highlights the abnormalities in alternative splicing of angiogenesis-related genes and their implication in HIV/AIDS-related cancers. This allows us to gain an insight into the pathogenesis of HIV/AIDS-related cancer and in turn elucidate the therapeutic potential of alternatively spliced genes in HIV/AIDS-related malignancies.
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Affiliation(s)
| | - Zukile Mbita
- Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Sovenga, South Africa
| | - Rodney Hull
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
| | - Zodwa Dlamini
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
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9
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Sigala I, Ganidis G, Thysiadis S, Zografos AL, Giannakouros T, Sarli V, Nikolakaki E. Lynamicin D an antimicrobial natural product affects splicing by inducing the expression of SR protein kinase 1. Bioorg Med Chem 2017; 25:1622-1629. [PMID: 28139279 DOI: 10.1016/j.bmc.2017.01.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/15/2016] [Accepted: 01/16/2017] [Indexed: 10/20/2022]
Abstract
The first total synthesis of the antimicrobial natural product lynamicin D has been developed using a Suzuki coupling to construct the bisindole pyrrole skeleton. An evaluation of the biological activity of lynamicin D reveals that it has a minor effect on cell viability but it can modulate splicing of pre-mRNAs. We provide evidence that this effect is mainly due to the ability of lynamicin D to alter the levels of SRPK1, the key kinase involved in both constitutive and alternative splicing.
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Affiliation(s)
- Ioanna Sigala
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - George Ganidis
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Savvas Thysiadis
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Alexandros L Zografos
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thomas Giannakouros
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Vasiliki Sarli
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece.
| | - Eleni Nikolakaki
- Department of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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10
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Grañé-Boladeras N, Spring CM, Hanna WJB, Pastor-Anglada M, Coe IR. Novel nuclear hENT2 isoforms regulate cell cycle progression via controlling nucleoside transport and nuclear reservoir. Cell Mol Life Sci 2016; 73:4559-4575. [PMID: 27271752 PMCID: PMC11108336 DOI: 10.1007/s00018-016-2288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 10/25/2022]
Abstract
Nucleosides participate in many cellular processes and are the fundamental building blocks of nucleic acids. Nucleoside transporters translocate nucleosides across plasma membranes although the mechanism by which nucleos(t)ides are translocated into the nucleus during DNA replication is unknown. Here, we identify two novel functional splice variants of equilibrative nucleoside transporter 2 (ENT2), which are present at the nuclear envelope. Under proliferative conditions, these splice variants are up-regulated and recruit wild-type ENT2 to the nuclear envelope to translocate nucleosides into the nucleus for incorporation into DNA during replication. Reduced presence of hENT2 splice variants resulted in a dramatic decrease in cell proliferation and dysregulation of cell cycle due to a lower incorporation of nucleotides into DNA. Our findings support a novel model of nucleoside compartmentalisation at the nuclear envelope and translocation into the nucleus through hENT2 and its variants, which are essential for effective DNA synthesis and cell proliferation.
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Affiliation(s)
- Natalia Grañé-Boladeras
- Department of Biochemistry and Molecular Biology, Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain.
- Oncology Program, CIBER EHD, Instituto de Salud Carlos III, 28029, Madrid, Spain.
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, M5B 2K3, Canada.
| | - Christopher M Spring
- Research Core Facilities, Keenan Research Centre, Li Ka Shing Knowledge Institute, Saint Michael's Hospital, Toronto, ON, M5B 1T8, Canada
| | - W J Brad Hanna
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Marçal Pastor-Anglada
- Department of Biochemistry and Molecular Biology, Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain
- Oncology Program, CIBER EHD, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Imogen R Coe
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, M5B 2K3, Canada
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11
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Miletta MC, Petkovic V, Eblé A, Flück CE, Mullis PE. Rescue of Isolated GH Deficiency Type II (IGHD II) via Pharmacologic Modulation of GH-1 Splicing. Endocrinology 2016; 157:3972-3982. [PMID: 27253996 DOI: 10.1210/en.2015-2038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Isolated GH deficiency (IGHD) type II, the autosomal dominant form of GHD, is mainly caused by mutations that affect splicing of GH-1. When misspliced RNA is translated, it produces a toxic 17.5-kDa GH isoform that reduces the accumulation and secretion of wild-type-human GH (wt-hGH). Usually, isolated GHD type II patients are treated with daily injections of recombinant human GH in order to maintain normal growth. However, this type of replacement therapy does not prevent toxic effects of the 17.5-kDa GH isoform on the pituitary gland, which can eventually lead to other hormonal deficiencies. Here, we tested the possibility to restore the constitutive splicing pattern of GH-1 by using butyrate, a drug that mainly acts as histone deacetylase inhibitor. To this aim, wt-hGH and/or different hGH-splice site mutants (GH-IVS3+2, GH-IVS3+6, and GH-ISE+28) were transfected in rat pituitary cells expressing human GHRH receptor (GHRHR) (GC-GHRHR). Upon butyrate treatment, GC-GHRHR cells coexpressing wt-hGH and each of the mutants displayed increased GH transcript level, intracellular GH content, and GH secretion when compared with the corresponding untreated condition. The effect of butyrate was most likely mediated by the alternative splicing factor/splicing factor 2. Overexpression of alternative ASF/SF2 in the same experimental setting, indeed, promoted the amount of full-length transcripts thus increasing synthesis and secretion of the 22-kDa GH isoform. In conclusion, our results support the hypothesis that modulation of GH-1 splicing pattern to increase the 22-kDa GH isoform levels can be clinically beneficial and hence a crucial challenge in GHD research.
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Affiliation(s)
- Maria Consolata Miletta
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, CH-3010 Switzerland
| | - Vibor Petkovic
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, CH-3010 Switzerland
| | - Andrée Eblé
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, CH-3010 Switzerland
| | - Christa E Flück
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, CH-3010 Switzerland
| | - Primus-E Mullis
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, CH-3010 Switzerland
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12
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Igreja S, Clarke LA, Botelho HM, Marques L, Amaral MD. Correction of a Cystic Fibrosis Splicing Mutation by Antisense Oligonucleotides. Hum Mutat 2015; 37:209-15. [PMID: 26553470 DOI: 10.1002/humu.22931] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/29/2015] [Indexed: 11/06/2022]
Abstract
Cystic fibrosis (CF), the most common life-threatening genetic disease in Caucasians, is caused by ∼2,000 different mutations in the CF transmembrane conductance regulator (CFTR) gene. A significant fraction of these (∼13%) affect pre-mRNA splicing for which novel therapies have been somewhat neglected. We have previously described the effect of the CFTR splicing mutation c.2657+5G>A in IVS16, showing that it originates transcripts lacking exon 16 as well as wild-type transcripts. Here, we tested an RNA-based antisense oligonucleotide (AON) strategy to correct the aberrant splicing caused by this mutation. Two AONs (AON1/2) complementary to the pre-mRNA IVS16 mutant region were designed and their effect on splicing was assessed at the RNA and protein levels, on intracellular protein localization and function. To this end, we used the 2657+5G>A mutant CFTR minigene stably expressed in HEK293 Flp-In cells that express a single copy of the transgene. RNA data from AON1-treated mutant cells show that exon 16 inclusion was almost completely restored (to 95%), also resulting in increased levels of correctly localized CFTR protein at the plasma membrane (PM) and with increased function. A novel two-color CFTR splicing reporter minigene developed here allowed the quantitative monitoring of splicing by automated microscopy localization of CFTR at the PM. The AON strategy is thus a promising therapeutic approach for the specific correction of alternative splicing.
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Affiliation(s)
- Susana Igreja
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Luka A Clarke
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Hugo M Botelho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Luís Marques
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
| | - Margarida D Amaral
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Portugal
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13
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Intravitreal Injection of Splice-switching Oligonucleotides to Manipulate Splicing in Retinal Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e250. [PMID: 26325627 PMCID: PMC4877449 DOI: 10.1038/mtna.2015.24] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 07/22/2015] [Indexed: 12/25/2022]
Abstract
Leber congenital amaurosis is a severe hereditary retinal dystrophy responsible for neonatal blindness. The most common disease-causing mutation (c.2991+1655A>G; 10-15%) creates a strong splice donor site that leads to insertion of a cryptic exon encoding a premature stop codon. Recently, we reported that splice-switching oligonucleotides (SSO) allow skipping of the mutant cryptic exon and the restoration of ciliation in fibroblasts of affected patients, supporting the feasibility of a SSO-mediated exon skipping strategy to correct the aberrant splicing. Here, we present data in the wild-type mouse, which demonstrate that intravitreal administration of 2'-OMePS-SSO allows selective alteration of Cep290 splicing in retinal cells, including photoreceptors as shown by successful alteration of Abca4 splicing using the same approach. We show that both SSOs and Cep290 skipped mRNA were detectable for at least 1 month and that intravitreal administration of oligonucleotides did not provoke any serious adverse event. These data suggest that intravitreal injections of SSO should be considered to bypass protein truncation resulting from the c.2991+1655A>G mutation as well as other truncating mutations in genes which like CEP290 or ABCA4 have a mRNA size that exceed cargo capacities of US Food and Drug Administration (FDA)-approved adeno-associated virus (AAV)-vectors, thus hampering gene augmentation therapy.
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14
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Himeda CL, Jones TI, Jones PL. Facioscapulohumeral muscular dystrophy as a model for epigenetic regulation and disease. Antioxid Redox Signal 2015; 22:1463-82. [PMID: 25336259 PMCID: PMC4432493 DOI: 10.1089/ars.2014.6090] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Aberrant epigenetic regulation is an integral aspect of many diseases and complex disorders. Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, is caused by disrupted genetic and epigenetic regulation of a macrosatellite repeat. FSHD provides a powerful model to investigate disease-relevant epigenetic modifiers and general mechanisms of epigenetic regulation that govern gene expression. RECENT ADVANCES In the context of a genetically permissive allele, the one aspect of FSHD that is consistent across all known cases is the aberrant epigenetic state of the disease locus. In addition, certain mutations in the chromatin regulator SMCHD1 (structural maintenance of chromosomes hinge-domain protein 1) are sufficient to cause FSHD2 and enhance disease severity in FSHD1. Thus, there are multiple pathways to generate the epigenetic dysregulation required for FSHD. CRITICAL ISSUES Why do some individuals with the genetic requirements for FSHD develop disease pathology, while others remain asymptomatic? Similarly, disease progression is highly variable among individuals. What are the relative contributions of genetic background and environmental factors in determining disease manifestation, progression, and severity in FSHD? What is the interplay between epigenetic factors regulating the disease locus and which, if any, are viable therapeutic targets? FUTURE DIRECTIONS Epigenetic regulation represents a potentially powerful therapeutic target for FSHD. Determining the epigenetic signatures that are predictive of disease severity and identifying the spectrum of disease modifiers in FSHD are vital to the development of effective therapies.
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Affiliation(s)
- Charis L Himeda
- The Wellstone Program and the Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School , Worcester, Massachusetts
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15
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Functional characterization of the spf/ash splicing variation in OTC deficiency of mice and man. PLoS One 2015; 10:e0122966. [PMID: 25853564 PMCID: PMC4390381 DOI: 10.1371/journal.pone.0122966] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/16/2015] [Indexed: 12/27/2022] Open
Abstract
The spf/ash mouse model of ornithine transcarbamylase (OTC) deficiency, a severe urea cycle disorder, is caused by a mutation (c.386G>A; p.R129H) in the last nucleotide of exon 4 of the Otc gene, affecting the 5' splice site and resulting in partial use of a cryptic splice site 48 bp into the adjacent intron. The equivalent nucleotide change and predicted amino acid change is found in OTC deficient patients. Here we have used liver tissue and minigene assays to dissect the transcriptional profile resulting from the "spf/ash" mutation in mice and man. For the mutant mouse, we confirmed liver transcripts corresponding to partial intron 4 retention by the use of the c.386+48 cryptic site and to normally spliced transcripts, with exon 4 always containing the c.386G>A (p.R129H) variant. In contrast, the OTC patient exhibited exon 4 skipping or c.386G>A (p.R129H)-variant exon 4 retention by using the natural or a cryptic splice site at nucleotide position c.386+4. The corresponding OTC tissue enzyme activities were between 3-6% of normal control in mouse and human liver. The use of the cryptic splice sites was reproduced in minigenes carrying murine or human mutant sequences. Some normally spliced transcripts could be detected in minigenes in both cases. Antisense oligonucleotides designed to block the murine cryptic +48 site were used in minigenes in an attempt to redirect splicing to the natural site. The results highlight the relevance of in depth investigations of the molecular mechanisms of splicing mutations and potential therapeutic approaches. Notably, they emphasize the fact that findings in animal models may not be applicable for human patients due to the different genomic context of the mutations.
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Identification of a novel function of CX-4945 as a splicing regulator. PLoS One 2014; 9:e94978. [PMID: 24743259 PMCID: PMC3990583 DOI: 10.1371/journal.pone.0094978] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/21/2014] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that CX-4945, a previously well-characterized inhibitor of casein kinase 2 (CK2) and a molecule currently in clinical trials (Phase II) for cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that CX-4945 potently inhibits the Cdc2-like kinases (Clks) in vitro and in turn, leads to suppression of the phosphorylation of serine/arginine-rich (SR) proteins in mammalian cells. Surprisingly, the overall efficacy of CX-4945 on Clks (IC50 = 3-90 nM) was stronger than that of TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by CX-4945 in an ATP-competitive manner. Our research revealed an unexpected activity of the drug candidate CX-4945 as a potent splicing modulator and also suggested a potential application for therapy of diseases caused by abnormal splicing.
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17
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Martínez-Montiel N, Rosas-Murrieta N, Martínez-Contreras R. [Alternative splicing regulation: implications in cancer diagnosis and treatment]. Med Clin (Barc) 2014; 144:317-23. [PMID: 24725854 DOI: 10.1016/j.medcli.2014.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 02/07/2014] [Accepted: 02/13/2014] [Indexed: 12/31/2022]
Abstract
The accurate expression of the genetic information is regulated by processes like mRNA splicing, proposed after the discoveries of Phil Sharp and Richard Roberts, who demonstrated the existence of intronic sequences, present in almost every structural eukaryotic gene, which should be precisely removed. This intron removal is called "splicing", which generates different proteins from a single mRNA, with different or even antagonistic functions. We currently know that alternative splicing is the most important source of protein diversity, given that 70% of the human genes undergo splicing and that mutations causing defects in this process could originate up to 50% of genetic diseases, including cancer. When these defects occur in genes involved in cell adhesion, proliferation and cell cycle regulation, there is an impact on cancer progression, rising the opportunity to diagnose and treat some types of cancer according to a particular splicing profile.
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Affiliation(s)
- Nancy Martínez-Montiel
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Nora Rosas-Murrieta
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Rebeca Martínez-Contreras
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México.
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Pérez-Carro R, Sánchez-Alcudia R, Pérez B, Navarrete R, Pérez-Cerdá C, Ugarte M, Desviat LR. Functional analysis and in vitro correction of splicing FAH mutations causing tyrosinemia type I. Clin Genet 2013; 86:167-71. [PMID: 23895425 DOI: 10.1111/cge.12243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/08/2013] [Accepted: 07/23/2013] [Indexed: 01/16/2023]
Abstract
Hereditary tyrosinemia type I (HT1) is a rare disease caused by a deficiency of fumarylacetoacetate hydrolase (FAH) in the tyrosine catabolic pathway, resulting mainly in hepatic alterations due to accumulation of the toxic metabolites fumarylacetoacetate, maleylacetoacetate and succinylacetone. We have characterized using minigenes four splicing mutations affecting exonic or intronic nucleotides of the FAH gene identified in two HT1 patients. Two of the mutations are novel, c.82-1G>A and c.913G>C and the other two have been previously associated with a splicing defect (c.836A>G and c.1062+5G>A). All mutations were confirmed to affect splicing in minigenes, resulting in exon skipping or activation of a cryptic splice site. We have analyzed the effect of different compounds known to modulate splicing (valproic acid, phenyl butyrate, M344, EIPA, and resveratrol) and the overexpression of splice factors of the SR protein family on the transcriptional profile of the mutant minigenes. For the c.836A>G mutation, a partial recovery of the correctly spliced transcript was observed. These results confirm the relevance of performing functional studies for mutations potentially affecting the splicing process and open the possibility of supplementary therapeutic approaches to diseases caused by splicing defects.
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Affiliation(s)
- R Pérez-Carro
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, Universidad Autónoma, CIBERER, IdiPaz, Madrid, Spain
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19
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Braicu C, Ladomery MR, Chedea VS, Irimie A, Berindan-Neagoe I. The relationship between the structure and biological actions of green tea catechins. Food Chem 2013; 141:3282-9. [PMID: 23871088 DOI: 10.1016/j.foodchem.2013.05.122] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 10/07/2012] [Accepted: 05/24/2013] [Indexed: 12/12/2022]
Abstract
Catechins and their gallate esters are a class of polyphenolic compounds. The catechin subclass known as flavan-3-ols have recently attracted much attention with regards to their beneficial effect on human health. Their biological actions are dependent on the structure of the compounds and vary according to cell type. They are best known as powerful antioxidants; however depending on the doses they also exhibit prooxidant effects. The anti- or prooxidant effects of green tea catechins have been implicated in the modulation of several cellular functions often associated with strong chemoprotective properties. This review summarises the benefit catechins to human health, the main molecular pathways modulated by catechins. The relationship between the structure and activity of the catechins needs to be studied further. In the future, the structure of catechins could be modified so as to synthesise novel compounds with more specific beneficial properties and higher bioavailability.
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Affiliation(s)
- Cornelia Braicu
- Department of Functional Genomics and Experimental Pathology, The Oncological Institute Prof. Dr. Ion Chiricuta, Cluj-Napoca, Romania.
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20
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Chen GL, Miller GM. Extensive alternative splicing of the repressor element silencing transcription factor linked to cancer. PLoS One 2013; 8:e62217. [PMID: 23614038 PMCID: PMC3628349 DOI: 10.1371/journal.pone.0062217] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/18/2013] [Indexed: 12/15/2022] Open
Abstract
The repressor element silencing transcription factor (REST) is a coordinate transcriptional and epigenetic regulator which functions as a tumor suppressor or an oncogene depending on cellular context, and a truncated splice variant REST4 has been linked to various types of cancer. We performed a comprehensive analysis of alternative splicing (AS) of REST by rapid amplification of cDNA ends and PCR amplification of cDNAs from various tissues and cell lines with specific primers. We identified 8 novel alternative exons including an alternate last exon which doubles the REST gene boundary, along with numerous 5'/3' splice sites and ends in the constitutive exons. With the combination of various splicing patterns (e.g. exon skipping and alternative usage of the first and last exons) that are predictive of altered REST activity, at least 45 alternatively spliced variants of coding and non-coding mRNA were expressed in a species- and cell-type/tissue-specific manner with individual differences. By examining the repertoire of REST pre-mRNA splicing in 27 patients with kidney, liver and lung cancer, we found that all patients without exception showed differential expression of various REST splice variants between paired tumor and adjacent normal tissues, with striking cell-type/tissue and individual differences. Moreover, we revealed that exon 3 skipping, which causes no frame shift but loss of a domain essential for nuclear translocation, was affected by pioglitazone, a highly selective activator of the peroxisome proliferator-activated receptor gamma (PPARγ) which contributes to cell differentiation and tumorigenesis besides its metabolic actions. Accordingly, this study demonstrates an extensive AS of REST pre-mRNA which redefines REST gene boundary and structure, along with a general but differential link between REST pre-mRNA splicing and various types of cancer. These findings advance our understanding of the complex, context-dependent regulation of REST gene expression and function, and provide potential biomarkers and therapeutic targets for cancer.
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Affiliation(s)
- Guo-Lin Chen
- Division of Neuroscience, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America.
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Shen M, Bellaousov S, Hiller M, de La Grange P, Creamer TP, Malina O, Sperling R, Mathews DH, Stoilov P, Stamm S. Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure. Nucleic Acids Res 2013; 41:3819-32. [PMID: 23393189 PMCID: PMC3616728 DOI: 10.1093/nar/gkt063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/08/2013] [Accepted: 01/15/2013] [Indexed: 01/17/2023] Open
Abstract
The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2'-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5'-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A-U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch.
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MESH Headings
- Alternative Splicing/drug effects
- Base Sequence
- Exons
- HEK293 Cells
- High-Throughput Screening Assays
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Pyrvinium Compounds/metabolism
- Pyrvinium Compounds/pharmacology
- RNA Editing
- RNA Precursors/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/drug effects
- RNA, Messenger/chemistry
- RNA, Messenger/drug effects
- RNA, Messenger/metabolism
- Receptor, Serotonin, 5-HT2C/genetics
- Receptor, Serotonin, 5-HT2C/metabolism
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Stanislav Bellaousov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Michael Hiller
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Pierre de La Grange
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Trevor P. Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Orit Malina
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Ruth Sperling
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - David H. Mathews
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Peter Stoilov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, Lexington, KY 40536, USA, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany and Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany GenoSplice technology, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris, France, Department of Biochemistry and Biophysics,University of Rochester Medical Center, University of Rochester, Rochester, NY 14642, USA, Department of Biochemistry, West Virginia University, Morgantown, P.O. Box 9142, WV 26506, USA, Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
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22
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Walsh CM, Suchanek AL, Cyphert TJ, Kohan AB, Szeszel-Fedorowicz W, Salati LM. Serine arginine splicing factor 3 is involved in enhanced splicing of glucose-6-phosphate dehydrogenase RNA in response to nutrients and hormones in liver. J Biol Chem 2012; 288:2816-28. [PMID: 23233666 DOI: 10.1074/jbc.m112.410803] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of G6PD is controlled by changes in the degree of splicing of the G6PD mRNA in response to nutrients in the diet. This regulation involves an exonic splicing enhancer (ESE) in exon 12 of the mRNA. Using the G6PD model, we demonstrate that nutrients and hormones control the activity of serine-arginine-rich (SR) proteins, a family of splicing co-activators, and thereby regulate the splicing of G6PD mRNA. In primary rat hepatocyte cultures, insulin increased the amount of phosphorylated SR proteins, and this effect was counteracted by arachidonic acid. The results of RNA affinity analysis with nuclear extracts from intact liver demonstrated that the SR splicing factor proteins SRSF3 and SRSF4 bound to the G6PD ESE. Consequently, siRNA-mediated depletion of SRSF3, but not SRSF4, in liver cells inhibited accumulation of both mRNA expressed from a minigene containing exon 12 and the endogenous G6PD mRNA. Consistent with the functional role of SRSF3 in regulating splicing, SRSF3 was observed to bind to the ESE in both intact cells and in animals using RNA immunoprecipitation analysis. Furthermore, refeeding significantly increased the binding of SRSF3 coincident with increased splicing and expression of G6PD. Together, these data establish that nutritional regulation of SRSF3 activity is involved in the differential splicing of the G6PD transcript in response to nutrients. Nutritional regulation of other SR proteins presents a regulatory mechanism that could cause widespread changes in mRNA splicing. Nutrients are therefore novel regulators of mRNA splicing.
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Affiliation(s)
- Callee M Walsh
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, USA
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Abstract
Persistent infection with cancer risk-related viruses leads to molecular, cellular and immune response changes in host organisms that in some cases direct cellular transformation. Alternative splicing is a conserved cellular process that increases the coding complexity of genomes at the pre-mRNA processing stage. Human and other animal tumour viruses use alternative splicing as a process to maximize their transcriptomes and proteomes. Medical therapeutics to clear persistent viral infections are still limited. However, specific lessons learned in some viruses [e.g. HIV and HCV (hepatitis C virus)] suggest that drug-directed inhibition of alternative splicing could be useful for this purpose. The present review describes the basic mechanisms of constitutive and alternative splicing in a cellular context and known splicing patterns and the mechanisms by which these might be achieved for the major human infective tumour viruses. The roles of splicing-related proteins expressed by these viruses in cellular and viral gene regulation are explored. Moreover, we discuss some currently available drugs targeting SR (serine/arginine-rich) proteins that are the main regulators of constitutive and alternative splicing, and their potential use in treatment for so-called persistent viral infections.
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Gupta VA, Kawahara G, Myers JA, Chen AT, Hall TE, Manzini MC, Currie PD, Zhou Y, Zon LI, Kunkel LM, Beggs AH. A splice site mutation in laminin-α2 results in a severe muscular dystrophy and growth abnormalities in zebrafish. PLoS One 2012; 7:e43794. [PMID: 22952766 PMCID: PMC3428294 DOI: 10.1371/journal.pone.0043794] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 07/24/2012] [Indexed: 11/18/2022] Open
Abstract
Congenital muscular dystrophy (CMD) is a clinically and genetically heterogeneous group of inherited muscle disorders. In patients, muscle weakness is usually present at or shortly after birth and is progressive in nature. Merosin deficient congenital muscular dystrophy (MDC1A) is a form of CMD caused by a defect in the laminin-α2 gene (LAMA2). Laminin-α2 is an extracellular matrix protein that interacts with the dystrophin-dystroglycan (DGC) complex in membranes providing stability to muscle fibers. In an N-ethyl-N-nitrosourea mutagenesis screen to develop zebrafish models of neuromuscular diseases, we identified a mutant fish that exhibits severe muscular dystrophy early in development. Genetic mapping identified a splice site mutation in the lama2 gene. This splice site is highly conserved in humans and this mutation results in mis-splicing of RNA and a loss of protein function. Homozygous lama2 mutant zebrafish, designated lama2cl501/cl501, exhibited reduced motor function and progressive degeneration of skeletal muscles and died at 8–15 days post fertilization. The skeletal muscles exhibited damaged myosepta and detachment of myofibers in the affected fish. Laminin-α2 deficiency also resulted in growth defects in the brain and eye of the mutant fish. This laminin-α2 deficient mutant fish represents a novel disease model to develop therapies for modulating splicing defects in congenital muscular dystrophies and to restore the muscle function in human patients with CMD.
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Affiliation(s)
- Vandana A. Gupta
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Genri Kawahara
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Jennifer A. Myers
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Aye T. Chen
- Stem Cell Program and Pediatric Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas E. Hall
- Australian Regenerative Medicine Institute, Monash University, Clayton Campus, Victoria, Australia
| | - M. Chiara Manzini
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Peter D. Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton Campus, Victoria, Australia
| | - Yi Zhou
- Stem Cell Program and Pediatric Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leonard I. Zon
- Stem Cell Program and Pediatric Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, San Francisco, California, United States of America
| | - Louis M. Kunkel
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
| | - Alan H. Beggs
- Genomics Program and Division of Genetics, Boston Children’s Hospital, Harvard Medical School, The Manton Center for Orphan Disease Research, Boston, Massachusetts, United States of America
- * E-mail:
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Splicing of mouse p53 pre-mRNA does not always follow the "first come, first served" principle and may be influenced by cisplatin treatment and serum starvation. Mol Biol Rep 2012; 39:9247-56. [PMID: 22740133 DOI: 10.1007/s11033-012-1798-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 06/09/2012] [Indexed: 10/28/2022]
Abstract
Transcription of a pre-mRNA in eukaryotic cells elongates from the 5' to the 3' end, but intron removal during a pre-mRNA splicing does not always proceed in this orientation. In this study, we identified eight mouse p53 transcripts that retained one or more of introns 6, 7 and 8. The 5' part of intron 9 was also retained while the 3' part was not studied. These intron-containing transcripts, abbreviated as p53-ICTs, were detected at low abundance in many mouse embryonic fibroblasts (MEF) as well as cancer cell lines and tissues, and the highest ratio of these p53-ICTs to the mature p53 mRNA was seen in the normal pancreas. Serum starvation decreased those p53-ICTs that retained introns 6 and 7 but increased the levels of those lacking these introns while the level of the mature p53 mRNA was unaffected. Treatment of several cancer cell lines with cisplatin increased the mature p53 mRNA level but decreased these p53-ICTs. Transfection of p53(-/-) MEF with the p53 cDNA or several p53-ICT mini-genes slightly increased the cell viability and rendered the cells resistant to cisplatin. These data also suggest that p53 pre-mRNA splicing may have multiple orders of intron removal, some of which may not follow the "first come, first served" principle. It remains possible that these p53-ICTs are splicing intermediates existing as a mechanism for the cell to respond more promptly to a demand for more p53 and that p53 protein may be required for a normal life of MEF.
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AON-mediated Exon Skipping Restores Ciliation in Fibroblasts Harboring the Common Leber Congenital Amaurosis CEP290 Mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e29. [PMID: 23344081 PMCID: PMC3390222 DOI: 10.1038/mtna.2012.21] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Leber congenital amaurosis (LCA) is a severe hereditary retinal dystrophy responsible for congenital or early-onset blindness. The most common disease-causing mutation (>10%) is located deep in intron 26 of the CEP290 gene (c.2991+1655A>G). It creates a strong splice donor site that leads to insertion of a cryptic exon encoding a premature stop codon. In the present study, we show that the use of antisense oligonucleotides (AONs) allow an efficient skipping of the mutant cryptic exon and the restoration of ciliation in fibroblasts of affected patients. These data support the feasibility of an AON-mediated exon skipping strategy to correct the aberrant splicing.
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Alternative splicing interference by xenobiotics. Toxicology 2012; 296:1-12. [DOI: 10.1016/j.tox.2012.01.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/21/2012] [Accepted: 01/23/2012] [Indexed: 12/21/2022]
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Sun Y, Cao S, Yang M, Wu S, Wang Z, Lin X, Song X, Liao DJ. Basic anatomy and tumor biology of the RPS6KA6 gene that encodes the p90 ribosomal S6 kinase-4. Oncogene 2012; 32:1794-810. [PMID: 22614021 PMCID: PMC3427418 DOI: 10.1038/onc.2012.200] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RPS6KA6 gene encodes the p90 ribosomal S6 kinase-4 (RSK4) that is still largely uncharacterized. In this study we identified a new RSK4 transcription initiation site and several alternative splice sites with a 5’RACE approach. The resulting mRNA variants encompass four possible first start codons. The first 15 nucleotides (nt) of exon 22 in mouse and the penultimate exon in both human (exon 21) and mouse (exon 24) RSK4 underwent alternative splicing, although the penultimate exon deleted variant appeared mainly in cell clines, but not in most normal tissues. Demethylation agent 5-azacytidine inhibited the deletion of the penultimate exon whereas two indolocarbazole-derived inhibitors of cyclin dependent kinase 4 or 6 induced deletion of the first 39 nt from exon 21 of human RSK4. In all human cancer cell lines studied, the 90-kD wild type RSK4 was sparse but, surprisingly, several isoforms at or smaller than 72-kD were expressed as detected by seven different antibodies. On immunoblots, each of these smaller isoforms often appeared as a duplet or triplet and the levels of these isoforms varied greatly among different cell lines and culture conditions. Cyclin D1 inhibited RSK4 expression and serum starvation enhanced the inhibition, whereas c-Myc and RSK4 inhibited cyclin D1. The effects of RSK4 on cell growth, cell death and chemoresponse depended on the mRNA variant or the protein isoform expressed, on the specificity of the cell lines, as well as on the anchorage-dependent or -independent growth conditions and the in vivo situation. Moreover, we also observed that even a given cDNA might be expressed to multiple proteins; therefore, when using a cDNA, one needs to exclude this possibility before attribution of the biological results from the cDNA to the anticipated protein. Collectively, our results suggest that whether RSK4 is oncogenic or tumor suppressive depends on many factors.
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Affiliation(s)
- Y Sun
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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Markus MA, Marques FZ, Morris BJ. Resveratrol, by modulating RNA processing factor levels, can influence the alternative splicing of pre-mRNAs. PLoS One 2011; 6:e28926. [PMID: 22174926 PMCID: PMC3236773 DOI: 10.1371/journal.pone.0028926] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 11/17/2011] [Indexed: 11/18/2022] Open
Abstract
Alternative pre-mRNA splicing defects can contribute to, or result from, various diseases, including cancer. Aberrant mRNAs, splicing factors and other RNA processing factors have therefore become targets for new therapeutic interventions. Here we report that the natural polyphenol resveratrol can modulate alternative splicing in a target-specific manner. We transfected minigenes of several alternatively spliceable primary mRNAs into HEK293 cells in the presence or absence of 1, 5, 20 and 50 µM resveratrol and measured exon levels by semi-quantitative PCR after separation by agarose gel electrophoresis. We found that 20 µg/ml and 50 µg/ml of resveratrol affected exon inclusion of SRp20 and SMN2 pre-mRNAs, but not CD44v5 or tau pre-mRNAs. By Western blotting and immunofluorescence we showed that this effect may be due to the ability of resveratrol to change the protein level but not the localization of several RNA processing factors. The processing factors that increased significantly were ASF/SF2, hnRNPA1 and HuR, but resveratrol did not change the levels of RBM4, PTBP1 and U2AF35. By means of siRNA-mediated knockdown we depleted cells of SIRT1, regarded as a major target of resveratrol, and showed that the effect on splicing was not dependent on SIRT1. Our results suggest that resveratrol might be an attractive small molecule to treat diseases in which aberrant splicing has been implicated, and justify more extensive research on the effects of resveratrol on the splicing machinery.
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Affiliation(s)
- M. Andrea Markus
- Basic and Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, Australia
| | - Francine Z. Marques
- Basic and Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, Australia
| | - Brian J. Morris
- Basic and Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, Australia
- * E-mail:
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Regulation of alternative splicing within the supraspliceosome. J Struct Biol 2011; 177:152-9. [PMID: 22100336 DOI: 10.1016/j.jsb.2011.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/02/2011] [Accepted: 11/05/2011] [Indexed: 12/12/2022]
Abstract
Alternative splicing is a fundamental feature in regulating the eukaryotic transcriptome, as ~95% of multi-exon human Pol II transcripts are subject to this process. Regulated splicing operates through the combinatorial interplay of positive and negative regulatory signals present in the pre-mRNA, which are recognized by trans-acting factors. All these RNA and protein components are assembled in a gigantic, 21 MDa, ribonucleoprotein splicing machine - the supraspliceosome. Because most alternatively spliced mRNA isoforms vary between different cell and tissue types, the ability to perform alternative splicing is expected to be an integral part of the supraspliceosome, which constitutes the splicing machine in vivo. Here we show that both the constitutively and alternatively spliced mRNAs of the endogenous human pol II transcripts: hnRNP A/B, survival of motor neuron (SMN) and ADAR2 are predominantly found in supraspliceosomes. This finding is consistent with our observations that the splicing regulators hnRNP G as well as all phosphorylated SR proteins are predominantly associated with supraspliceosomes. We further show that changes in alternative splicing of hnRNP A/B, affected by up regulation of SRSF5 (SRp40) or by treatment with C6-ceramide, occur within supraspliceosomes. These observations support the proposed role of the supraspliceosome in splicing regulation and alternative splicing.
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Poling JS, Phillips JA, Cogan JD, Hamid R. Pharmacologic correction of dominant-negative GH1 deficiency causing mutations. Clin Transl Sci 2011; 4:175-9. [PMID: 21707947 DOI: 10.1111/j.1752-8062.2011.00290.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
PURPOSE Dominant-negative growth hormone gene (GH1) mutations cause familial isolated growth hormone deficiency type II (IGHD II), which is characterized by GH deficiency, occasional multiple anterior pituitary hormone deficiencies, and anterior pituitary hypoplasia. We have previously shown that 17.5-/22-kDa GH1 transcript ratios correlate with the severity of the IGHD II phenotype. We hypothesized that different pharmaceutical agents could affect the GH1 transcript ratio by modulating alternative splicing. METHODS We exposed peripheral blood mononuclear cells from IGHD II patients and unaffected family members to different pharmacologic agents and then determined the 17.5-/22-kDa transcript ratios by real-time PCR. RESULTS Dexamethasone and digoxin significantly increased the 17.5-/22-kDa transcript ratio, while sodium butyrate and 5-iodotubericidin significantly decreased the ratio. CONCLUSION Since we have previously shown that the ratio of the 17.5-/22-kDa GH1 transcripts correlates with severity of the IGHD II phenotype, our findings here suggest that selected previously unconsidered agents could possibly reduce the severity of IGHD II, while other agents could possibly exacerbate the disease phenotype.
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Affiliation(s)
- Justin S Poling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Piva F, Giulietti M, Burini AB, Principato G. SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. Hum Mutat 2011; 33:81-5. [PMID: 21922594 DOI: 10.1002/humu.21609] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 08/24/2011] [Indexed: 12/19/2022]
Abstract
Splicing is the most frequently altered biological process by mutations within gene regions. Information for splicing is recognized by several factors that bind pre-mRNA sequence and, through coordinated interaction, yield mature transcripts. Some in silico methods have been developed to predict if a mutation leads to aberrant splicing patterns. We previously created SpliceAid tool that is able to minimize false positive predictions because it adopts strictly experimental RNA target motifs bound by splicing proteins in humans. In order to improve prediction accuracy and better understand the splicing outcome, the tissue specificity of each splicing regulatory factor has to be taken into account. Here, we have developed SpliceAid 2 by adding the expression data related to the splicing factors extracted from the main proteomic and transcriptomic databases, true 5' and 3' splice sites, polypyrimidine tracts, and branch point sequences. The new version collects 2,220 target sites of 62 human splicing proteins and their expression data in 320 tissues per cell. SpliceAid 2 can be useful to foresee the splicing pattern alteration, to guide the identification of the molecular effect due to the mutations and to understand the tissue-specific alternative splicing. SpliceAid 2 is freely accessible at www.introni.it/spliceaid.html.
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Affiliation(s)
- Francesco Piva
- Department of Specialized Clinical Sciences and Odontostomatology, Polytechnic University of Marche, Ancona, Italy.
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33
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Fan L, Lagisetti C, Edwards CC, Webb TR, Potter PM. Sudemycins, novel small molecule analogues of FR901464, induce alternative gene splicing. ACS Chem Biol 2011; 6:582-9. [PMID: 21344922 DOI: 10.1021/cb100356k] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two unrelated bacterial natural products, FR901464 and pladienolide B, have previously been shown to have significant antitumor activity in vivo. These compounds target the SF3b subunit of the spliceosome, with a derivative of pladienolide (E7107) entering clinical trials for cancer. However, due to the structural complexity of these molecules, their research and development has been significantly constrained. We have generated a set of novel analogues (Sudemycins) that possess the pharmacophore that is common to FR901464 and pladienolide, via a flexible enantioselective route, which allows for the production of gram quantities of drug. These compounds demonstrate cytotoxicity toward human tumor cell lines in culture and exhibit antitumor activity in a xenograft model. Here, we present evidence that Sudemycins are potent modulators of alternative splicing in human cells, both of endogenous genes and from minigene constructs. Furthermore, levels of alternative splicing are increased in tumor cells relative to normal cells, and these modifications can be observed in human tumor xenografts in vivo following exposure of animals to the drug. In addition, the change in the splicing pattern observed with the Sudemycins are similar to that observed with Spliceostatin A, a molecule known to interact with the SF3b subunit of the spliceosome. Hence, we conclude that Sudemycins can regulate the production of alternatively spliced RNA transcripts and these alterations are more prevalent in tumors, as compared to normal cells, following drug exposure. These studies suggest that modulation of alternative splicing may play a role in the antitumor activity of this class of agents.
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Affiliation(s)
- Liying Fan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Chandraiah Lagisetti
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Carol C. Edwards
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Thomas R. Webb
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Philip M. Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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Folco EG, Coil KE, Reed R. The anti-tumor drug E7107 reveals an essential role for SF3b in remodeling U2 snRNP to expose the branch point-binding region. Genes Dev 2011; 25:440-4. [PMID: 21363962 DOI: 10.1101/gad.2009411] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Duplex formation between the branch point-binding region (BBR) of U2 snRNA and the branch point sequence (BPS) in the intron is essential for splicing. Both the BBR and BPS interact with the U2 small nuclear ribonucleoprotein (snRNP)-associated SF3b complex, which is the target of the anti-tumor drug E7107. We show that E7107 blocks spliceosome assembly by preventing tight binding of U2 snRNP to pre-mRNA. E7107 has no apparent effect on U2 snRNP integrity. Instead, E7107 abolishes an ATP-dependent conformational change in U2 snRNP that exposes the BBR. We conclude that SF3b is required for this remodeling, which exposes the BBR for tight U2 snRNP binding to pre-mRNA.
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Affiliation(s)
- Eric G Folco
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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36
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Gene therapeutic approach using mutation-adapted U1 snRNA to correct a RPGR splice defect in patient-derived cells. Mol Ther 2011; 19:936-41. [PMID: 21326217 DOI: 10.1038/mt.2011.7] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Retinitis pigmentosa (RP) is a disease that primarily affects the peripheral retina and ultimately causes visual impairment. X-chromosomal forms of RP are frequently caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. We show that the novel splice donor site (SDS) mutation c.1245+3A>T in intron 10 of RPGR cosegregates with RP in a five-generation Caucasian family. The mutation causes in-frame skipping of exon 10 from RPGR transcripts in patient-derived primary fibroblasts. To correct the splice defect, we developed a gene therapeutic approach using mutation-adapted U1 small nuclear RNA (U1). U1 is required for SDS recognition of pre-mRNAs and initiates the splice process. The mutation described herein interferes with the recognition of the SDS by U1. To overcome the deleterious effects of the mutation, we generated four U1 isoforms with increasing complementarity to the SDS. Lentiviral particles were used to transduce patient-derived fibroblasts with these U1 variants. Full complementarity of U1 corrects the splice defect partially and increases recognition of the mutant SDS. The therapeutic effect is U1-concentration dependent as we show for endogenously expressed RPGR transcripts in patient-derived cells. U1-based gene therapeutic approaches constitute promising technologies to treat SDS mutations in inherited diseases including X-linked RP.
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Zhang Z, Kelemen O, van Santen MA, Yelton SM, Wendlandt AE, Sviripa VM, Bollen M, Beullens M, Urlaub H, Lührmann R, Watt DS, Stamm S. Synthesis and characterization of pseudocantharidins, novel phosphatase modulators that promote the inclusion of exon 7 into the SMN (survival of motoneuron) pre-mRNA. J Biol Chem 2011; 286:10126-36. [PMID: 21220421 DOI: 10.1074/jbc.m110.183970] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alternative pre-mRNA splicing is a central element of eukaryotic gene expression. Its deregulation can lead to disease, and methods to change splice site selection are developed as potential therapies. Spinal muscular atrophy is caused by the loss of the SMN1 (survival of motoneuron 1) gene. A therapeutic avenue for spinal muscular atrophy treatment is to promote exon 7 inclusion of the almost identical SMN2 (survival of motoneuron 2) gene. The splicing factor tra2-beta1 promotes inclusion of this exon and is antagonized by protein phosphatase (PP) 1. To identify new compounds that promote exon 7 inclusion, we synthesized analogs of cantharidin, an inhibitor of PP1, and PP2A. Three classes of compounds emerged from these studies. The first class blocks PP1 and PP2A activity, blocks constitutive splicing in vitro, and promotes exon 7 inclusion in vivo. The second class has no measurable effect on PP1 activity but activates PP2A. This class represents the first compounds described with these properties. These compounds cause a dephosphorylation of Thr-33 of tra2-beta1, which promotes exon 7 inclusion. The third class had no detectable effect on phosphatase activity and could promote exon 7 via allosteric effects. Our data show that subtle changes in similar compounds can turn a phosphatase inhibitor into an activator. These chemically related compounds influence alternative splicing by distinct mechanisms.
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Affiliation(s)
- Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
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Hastings ML, Berniac J, Liu YH, Abato P, Jodelka FM, Barthel L, Kumar S, Dudley C, Nelson M, Larson K, Edmonds J, Bowser T, Draper M, Higgins P, Krainer AR. Tetracyclines that promote SMN2 exon 7 splicing as therapeutics for spinal muscular atrophy. Sci Transl Med 2010; 1:5ra12. [PMID: 20161659 DOI: 10.1126/scitranslmed.3000208] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There is at present no cure or effective therapy for spinal muscular atrophy (SMA), a neurodegenerative disease that is the leading genetic cause of infant mortality. SMA usually results from loss of the SMN1 (survival of motor neuron 1) gene, which leads to selective motor neuron degeneration. SMN2 is nearly identical to SMN1 but has a nucleotide replacement that causes exon 7 skipping, resulting in a truncated, unstable version of the SMA protein. SMN2 is present in all SMA patients, and correcting SMN2 splicing is a promising approach for SMA therapy. We identified a tetracycline-like compound, PTK-SMA1, which stimulates exon 7 splicing and increases SMN protein levels in vitro and in vivo in mice. Unlike previously identified molecules that stimulate SMN production via SMN2 promoter activation or undefined mechanisms, PTK-SMA1 is a unique therapeutic candidate in that it acts by directly stimulating splicing of exon 7. Synthetic small-molecule compounds such as PTK-SMA1 offer an alternative to antisense oligonucleotide therapies that are being developed as therapeutics for a number of disease-associated splicing defects.
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Affiliation(s)
- Michelle L Hastings
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60044, USA.
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Berasain C, Goñi S, Castillo J, Latasa MU, Prieto J, Ávila MA. Impairment of pre-mRNA splicing in liver disease: Mechanisms and consequences. World J Gastroenterol 2010; 16:3091-102. [PMID: 20593494 PMCID: PMC2896746 DOI: 10.3748/wjg.v16.i25.3091] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pre-mRNA splicing is an essential step in the process of gene expression in eukaryotes and consists of the removal of introns and the linking of exons to generate mature mRNAs. This is a highly regulated mechanism that allows the alternative usage of exons, the retention of intronic sequences and the generation of exonic sequences of variable length. Most human genes undergo splicing events, and disruptions of this process have been associated with a variety of diseases, including cancer. Hepatocellular carcinoma (HCC) is a molecularly heterogeneous type of tumor that usually develops in a cirrhotic liver. Alterations in pre-mRNA splicing of some genes have been observed in liver cancer, and although still scarce, the available data suggest that splicing defects may have a role in hepatocarcinogenesis. Here we briefly review the general mechanisms that regulate pre-mRNA splicing, and discuss some examples that illustrate how this process is impaired in liver tumorigenesis, and may contribute to HCC development. We believe that a more thorough examination of pre-mRNA splicing is still needed to accurately draw the molecular portrait of liver cancer. This will surely contribute to a better understanding of the disease and to the development of new effective therapies.
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RNA splicing meets genetic testing: detection and interpretation of splicing defects in genetic diseases. Eur J Hum Genet 2010; 18:737-8. [PMID: 20179747 DOI: 10.1038/ejhg.2010.18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Abstract
Ninety-four percent of human genes are discontinuous, such that segments expressed as mRNA are contained within exons and separated by intervening segments, called introns. Following transcription, genes are expressed as precursor mRNAs (pre-mRNAs), which are spliced co-transcriptionally, and the flanking exons are joined together to form a continuous mRNA. One advantage of this architecture is that it allows alternative splicing by differential use of exons to generate multiple mRNAs from individual genes. Regulatory elements located within introns and exons guide the splicing complex, the spliceosome, and auxiliary RNA binding proteins to the correct sites for intron removal and exon joining. Misregulation of splicing and alternative splicing can result from mutations in cis-regulatory elements within the affected gene or from mutations that affect the activities of trans-acting factors that are components of the splicing machinery. Mutations that affect splicing can cause disease directly or contribute to the susceptibility or severity of disease. An understanding of the role of splicing in disease expands potential opportunities for therapeutic intervention by either directly addressing the cause or by providing novel approaches to circumvent disease processes.
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Affiliation(s)
- Amanda J Ward
- Departments of Molecular and Cellular Biology and Pathology, Baylor College of Medicine, Houston, TX 77030, USA
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Leiro JM, Varela M, Piazzon MC, Arranz JA, Noya M, Lamas J. The anti-inflammatory activity of the polyphenol resveratrol may be partially related to inhibition of tumour necrosis factor-α (TNF-α) pre-mRNA splicing. Mol Immunol 2010; 47:1114-20. [DOI: 10.1016/j.molimm.2009.10.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 10/15/2009] [Accepted: 10/25/2009] [Indexed: 12/20/2022]
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Rapid-response splicing reporter screens identify differential regulators of constitutive and alternative splicing. Mol Cell Biol 2010; 30:1718-28. [PMID: 20123975 DOI: 10.1128/mcb.01301-09] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bioactive compounds have been invaluable for dissecting the mechanisms, regulation, and functions of cellular processes. However, very few such reagents have been described for pre-mRNA splicing. To facilitate their systematic discovery, we developed a high-throughput cell-based assay that measures pre-mRNA splicing by utilizing a quantitative reporter system with advantageous features. The reporter, consisting of a destabilized, intron-containing luciferase expressed from a short-lived mRNA, allows rapid screens (<4 h), thereby obviating the potential toxicity of splicing inhibitors. We describe three inhibitors (out of >23,000 screened), all pharmacologically active: clotrimazole, flunarizine, and chlorhexidine. Interestingly, none was a general splicing inhibitor. Rather, each caused distinct splicing changes of numerous genes. We further discovered the target of action of chlorhexidine and show that it is a selective inhibitor of specific Cdc2-like kinases (Clks) that phosphorylate serine-arginine-rich (SR) protein splicing factors. Our findings reveal unexpected activities of clinically used drugs in splicing and uncover differential regulation of constitutively spliced introns.
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Baralle D, Lucassen A, Buratti E. Missed threads. The impact of pre-mRNA splicing defects on clinical practice. EMBO Rep 2009; 10:810-6. [PMID: 19648957 DOI: 10.1038/embor.2009.170] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Diana Baralle
- Human Genetics Division, University of Southampton School of Medicine, Southampton, UK.
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Tazi J, Bakkour N, Stamm S. Alternative splicing and disease. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1792:14-26. [PMID: 18992329 PMCID: PMC5632948 DOI: 10.1016/j.bbadis.2008.09.017] [Citation(s) in RCA: 382] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 09/19/2008] [Accepted: 09/30/2008] [Indexed: 12/11/2022]
Abstract
Almost all protein-coding genes are spliced and their majority is alternatively spliced. Alternative splicing is a key element in eukaryotic gene expression that increases the coding capacity of the human genome and an increasing number of examples illustrates that the selection of wrong splice sites causes human disease. A fine-tuned balance of factors regulates splice site selection. Here, we discuss well-studied examples that show how a disturbance of this balance can cause human disease. The rapidly emerging knowledge of splicing regulation now allows the development of treatment options.
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Affiliation(s)
- Jamal Tazi
- University of Montpellier II, Institute of Molecular Genetics, Centre Nationale de Recherche Scientifique, 1919 Route de Mende, France
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O'Brien K, Matlin AJ, Lowell AM, Moore MJ. The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing. J Biol Chem 2008; 283:33147-54. [PMID: 18826947 PMCID: PMC2586251 DOI: 10.1074/jbc.m805556200] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Membrane-permeable compounds that reversibly inhibit a particular step in
gene expression are highly useful tools for cell biological and
biochemical/structural studies. In comparison with other gene expression steps
where multiple small molecule effectors are available, very few compounds have
been described that act as general inhibitors of pre-mRNA splicing. Here we
report construction and validation of a set of mammalian cell lines suitable
for the identification of small molecule inhibitors of pre-mRNA splicing.
Using these cell lines, we identified the natural product isoginkgetin as a
general inhibitor of both the major and minor spliceosomes. Isoginkgetin
inhibits splicing both in vivo and in vitro at similar
micromolar concentrations. It appears to do so by preventing stable
recruitment of the U4/U5/U6 tri-small nuclear ribonucleoprotein, resulting in
accumulation of the prespliceosomal A complex. Like two other recently
reported general pre-mRNA splicing inhibitors, isoginkgetin has been
previously described as an anti-tumor agent. Our results suggest that splicing
inhibition is the mechanistic basis of the anti-tumor activity of
isoginkgetin. Thus, pre-mRNA splicing inhibitors may represent a novel avenue
for development of new anti-cancer agents.
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Affiliation(s)
- Kristine O'Brien
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
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