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Le Sénéchal R, Keruzoré M, Quillévéré A, Loaëc N, Dinh VT, Reznichenko O, Guixens-Gallardo P, Corcos L, Teulade-Fichou MP, Granzhan A, Blondel M. Alternative splicing of BCL-x is controlled by RBM25 binding to a G-quadruplex in BCL-x pre-mRNA. Nucleic Acids Res 2023; 51:11239-11257. [PMID: 37811881 PMCID: PMC10639069 DOI: 10.1093/nar/gkad772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/05/2023] [Accepted: 09/09/2023] [Indexed: 10/10/2023] Open
Abstract
BCL-x is a master regulator of apoptosis whose pre-mRNA is alternatively spliced into either a long (canonical) anti-apoptotic Bcl-xL isoform, or a short (alternative) pro-apoptotic Bcl-xS isoform. The balance between these two antagonistic isoforms is tightly regulated and overexpression of Bcl-xL has been linked to resistance to chemotherapy in several cancers, whereas overexpression of Bcl-xS is associated to some forms of diabetes and cardiac disorders. The splicing factor RBM25 controls alternative splicing of BCL-x: its overexpression favours the production of Bcl-xS, whereas its downregulation has the opposite effect. Here we show that RBM25 directly and specifically binds to GQ-2, an RNA G-quadruplex (rG4) of BCL-x pre-mRNA that forms at the vicinity of the alternative 5' splice site leading to the alternative Bcl-xS isoform. This RBM25/rG4 interaction is crucial for the production of Bcl-xS and depends on the RE (arginine-glutamate-rich) motif of RBM25, thus defining a new type of rG4-interacting domain. PhenDC3, a benchmark G4 ligand, enhances the binding of RBM25 to the GQ-2 rG4 of BCL-x pre-mRNA, thereby promoting the alternative pro-apoptotic Bcl-xS isoform and triggering apoptosis. Furthermore, the screening of a combinatorial library of 90 putative G4 ligands led to the identification of two original compounds, PhenDH8 and PhenDH9, superior to PhenDC3 in promoting the Bcl-xS isoform and apoptosis. Thus, favouring the interaction between RBM25 and the GQ-2 rG4 of BCL-x pre-mRNA represents a relevant intervention point to re-sensitize cancer cells to chemotherapy.
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Affiliation(s)
- Ronan Le Sénéchal
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Marc Keruzoré
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Alicia Quillévéré
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Nadège Loaëc
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Van-Trang Dinh
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Oksana Reznichenko
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Pedro Guixens-Gallardo
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Laurent Corcos
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Marie-Paule Teulade-Fichou
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Marc Blondel
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
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Alves-Ferreira M, Azevedo A, Coelho T, Santos D, Sequeiros J, Alonso I, Sousa A, Lemos C. Beyond Val30Met transthyretin (TTR): variants associated with age-at-onset in hereditary ATTRv amyloidosis. Amyloid 2021; 28:100-106. [PMID: 33461327 DOI: 10.1080/13506129.2020.1857236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES V30M in transthyretin (TTR) gene is causative for hereditary ATTRv amyloidosis (familial amyloid polyneuropathy). ATTRv amyloidosis shows a wide variation in age-at-onset (AO) between clusters, families, and among generations. We aim at identifying genetic modifiers of disease onset that may contribute to this variability in Portuguese patients by identifying other variants in TTR locus, beyond the ATTRv amyloidosis causing variant that could play a regulatory role in its expression level. METHODS We analysed DNA samples of 330 ATTRV30M carriers (299 patients, 31 aged-asymptomatic carriers aged >40 years) from 120 families currently under follow-up. A generalised estimating equation analysis (GEE) was used to take into account non-independency of AO between relatives. An intensive in silico analysis was performed in order to understand a possible regulation of gene expression. RESULTS We found 11 rare variants in the promoter, coding and intron/exon boundaries of the TTR gene associated with the onset of symptoms before and after age 40 years, namely 2 novel ones and a tandem CA-dinucleotide repeat. Furthermore, of the 4 common variants found, one was significantly associated with AO and may influence the constitutive splicing of TTR pre-mRNA. The seven ATTRV30M/V30M homozygous do not carry any of the variants identified in this study, including the common ones. In silico analysis disclosed significant alterations in the mechanism of splicing, transcription factors and miRNAs binding. CONCLUSIONS Variants within the promoter region may modify disease expressivity and variants in the 3'UTR can impact the efficacy of novel therapeutic interventions. Importantly, the putative mechanisms of regulation of gene expression within the TTR gene deserve to be better explored, in order to be used in the future as potential therapeutical targets.
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Affiliation(s)
- Miguel Alves-Ferreira
- UnIGENe, IBMC - Institute for Molecular and Cell Biology, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ana Azevedo
- ICBAS - Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Teresa Coelho
- Unidade Corino de Andrade (UCA), Centro Hospitalar do Porto (CHP), Porto, Portugal
| | - Diana Santos
- UnIGENe, IBMC - Institute for Molecular and Cell Biology, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Jorge Sequeiros
- UnIGENe, IBMC - Institute for Molecular and Cell Biology, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Isabel Alonso
- UnIGENe, IBMC - Institute for Molecular and Cell Biology, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Alda Sousa
- UnIGENe, IBMC - Institute for Molecular and Cell Biology, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Carolina Lemos
- UnIGENe, IBMC - Institute for Molecular and Cell Biology, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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Pendergraff H, Schmidt S, Vikeså J, Weile C, Øverup C, W. Lindholm M, Koch T. Nuclear and Cytoplasmatic Quantification of Unconjugated, Label-Free Locked Nucleic Acid Oligonucleotides. Nucleic Acid Ther 2020; 30:4-13. [PMID: 31618108 PMCID: PMC6987631 DOI: 10.1089/nat.2019.0810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022] Open
Abstract
Methods for the quantification of antisense oligonucleotides (AONs) provide insightful information on biodistribution and intracellular trafficking. However, the established methods have not provided information on the absolute number of molecules in subcellular compartments or about how many AONs are needed for target gene reduction for unconjugated AONs. We have developed a new method for nuclear AON quantification that enables us to determine the absolute number of AONs per nucleus without relying on AON conjugates such as fluorophores that may alter AON distribution. This study describes an alternative and label-free method using subcellular fractionation, nucleus counting, and locked nucleic acid (LNA) sandwich enzyme-linked immunosorbent assay to quantify absolute numbers of oligonucleotides in nuclei. Our findings show compound variability (diversity) by which 247,000-693,000 LNAs/nuclei results in similar target reduction for different compounds. This method can be applied to any antisense drug discovery platform providing information on specific and clinically relevant AONs. Finally, this method can directly compare nuclear entry of AON with target gene knockdown for any compound design and nucleobase sequence, gene target, and phosphorothioate stereochemistry.
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Affiliation(s)
- Hannah Pendergraff
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Steffen Schmidt
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Jonas Vikeså
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Christian Weile
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Charlotte Øverup
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Marie W. Lindholm
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Troels Koch
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
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Yang L, Ma F, Liu F, Chen J, Zhao X, Xu Q. Efficient Delivery of Antisense Oligonucleotides Using Bioreducible Lipid Nanoparticles In Vitro and In Vivo. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 19:1357-1367. [PMID: 32160706 PMCID: PMC7036716 DOI: 10.1016/j.omtn.2020.01.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/30/2019] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
The efficient delivery of antisense oligonucleotides (ASOs) to the targeted cells and organs remains a challenge, in particular, in vivo. Here, we investigated the ability of a library of biodegradable lipid nanoparticles (LNPs) in delivering ASO to both cultured human cells and animal models. We first identified three top-performing lipids through in vitro screening using GFP-expressing HEK293 cells. Next, we explored these three candidates for delivering ASO to target proprotein convertase subtilisin/kexin type 9 (PCSK9) mRNA in mice. We found that lipid 306-O12B-3 showed efficiency with the median effective dose (ED50) as low as 0.034 mg·kg-1, which is a notable improvement over the efficiency reported in the literature. No liver or kidney toxicity was observed with a dose up to 5 mg·kg-1 of this ASO/LNP formulation. The biodegradable LNPs are efficient and safe in the delivery of ASO and pave the way for clinical translation.
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Affiliation(s)
- Liu Yang
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Feihe Ma
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Fang Liu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Jinjin Chen
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Xuewei Zhao
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA.
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Montazersaheb S, Hejazi MS, Nozad Charoudeh H. Potential of Peptide Nucleic Acids in Future Therapeutic Applications. Adv Pharm Bull 2018; 8:551-563. [PMID: 30607328 PMCID: PMC6311635 DOI: 10.15171/apb.2018.064] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
Peptide nucleic acids (PNA) are synthetic analog of DNA with a repeating N-(2-aminoethyl)-glycine peptide backbone connected to purine and pyrimidine nucleobases via a linker. Considering the unique properties of PNA, including resistance to enzymatic digestion, higher biostability combined with great hybridization affinity toward DNA and RNA, it has attracted great attention toward PNA- based technology as a promising approach for gene alteration. However, an important challenge in utilizing PNA is poor intracellular uptake. Therefore, some strategies have been developed to enhance the delivery of PNA in order to reach cognate site. Although PNAs primarily demonstrated to act as an antisense and antigene agents for inhibition of transcription and translation of target genes, more therapeutic applications such as splicing modulation and gene editing are also used to produce specific genome modifications. Hence, several approaches based on PNAs technology have been designed for these purposes. This review briefly presents the properties and characteristics of PNA as well as different gene modulation mechanisms. Thereafter, current status of successful therapeutic applications of PNA as gene therapeutic intervention in different research areas with special interest in medical application in particular, anti-cancer therapy are discussed. Then it focuses on possible use of PNA as anti-mir agent and PNA-based strategies against clinically important bacteria.
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Affiliation(s)
- Soheila Montazersaheb
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Altered function of neuronal L-type calcium channels in ageing and neuroinflammation: Implications in age-related synaptic dysfunction and cognitive decline. Ageing Res Rev 2018; 42:86-99. [PMID: 29339150 DOI: 10.1016/j.arr.2018.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 12/29/2022]
Abstract
The rapid developments in science have led to an increase in human life expectancy and thus, ageing and age-related disorders/diseases have become one of the greatest concerns in the 21st century. Cognitive abilities tend to decline as we get older. This age-related cognitive decline is mainly attributed to aberrant changes in synaptic plasticity and neuronal connections. Recent studies show that alterations in Ca2+ homeostasis underlie the increased vulnerability of neurons to age-related processes like cognitive decline and synaptic dysfunctions. Dysregulation of Ca2+ can lead to dramatic changes in neuronal functions. We discuss in this review, the recent advances on the potential role of dysregulated Ca2+ homeostasis through altered function of L-type voltage gated Ca2+ channels (LTCC) in ageing, with an emphasis on cognitive decline. This review therefore focuses on age-related changes mainly in the hippocampus, and with mention of other brain areas, that are important for learning and memory. This review also highlights age-related memory deficits via synaptic alterations and neuroinflammation. An understanding of these mechanisms will help us formulate strategies to reverse or ameliorate age-related disorders like cognitive decline.
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Guo J, Che X, Wang X, Jia R. Inhibition of the expression of oncogene SRSF3 by blocking an exonic splicing suppressor with antisense oligonucleotides. RSC Adv 2018; 8:7159-7163. [PMID: 35540349 PMCID: PMC9078388 DOI: 10.1039/c7ra11267j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/05/2018] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have been widely used to regulate alternative splicing of pre-mRNA by targeting splice sites, branch points, or exonic splice enhancers to increase exon skipping or intron retention. So far, few studies have used ASOs to block exonic splicing suppressor (ESS) and increase exon inclusion. Previously, we demonstrated that serine and arginine rich splicing factor 3 (SRSF3) (also called SRp20) is an oncogene. The inclusion of its alternative exon 4 down-regulates its expression. An ESS motif is responsible for the skipping of alternative exon 4. Here, we used an economical method to screen effective anti-ESS ASO. We discovered that an ASO targeting the ESS motif can promote the inclusion of exon 4, reduce SRSF3 expression, and inhibit cell growth in oral cancer cells. Our results suggested that using anti-ESS ASOs can efficiently increase exon inclusion and be used as a potential anti-cancer drug. Inhibition of the expression of oncogene SRSF3 and cancer cell growth by blocking an exonic splicing suppressor in alternative exon 4 of SRSF3 with SR-3 antisense oligonucleotide.![]()
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Affiliation(s)
- Jihua Guo
- Hubei-MOST KLOS & KLOBME
- School & Hospital of Stomatology
- Wuhan University
- Wuhan
- PR China
| | - Xiaoxuan Che
- Hubei-MOST KLOS & KLOBME
- School & Hospital of Stomatology
- Wuhan University
- Wuhan
- PR China
| | - Xiaole Wang
- Hubei-MOST KLOS & KLOBME
- School & Hospital of Stomatology
- Wuhan University
- Wuhan
- PR China
| | - Rong Jia
- Hubei-MOST KLOS & KLOBME
- School & Hospital of Stomatology
- Wuhan University
- Wuhan
- PR China
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Abstract
Since its discovery in 1977, much has been known about RNA splicing and how it plays a central role in human development, function, and, notably, disease. Defects in RNA splicing account for at least 10% of all genetic disorders, with the number expected to increase as more information is uncovered on the contribution of noncoding genomic regions to disease. Splice modulation through the use of antisense oligonucleotides (AOs) has emerged as a promising avenue for the treatment of these disorders. In fact, two splice-switching AOs have recently obtained approval from the US Food and Drug Administration: eteplirsen (Exondys 51) for Duchenne muscular dystrophy, and nusinersen (Spinraza) for spinal muscular atrophy. These work by exon skipping and exon inclusion, respectively. In this chapter, we discuss the early development of AO-based splice modulation therapy-its invention, first applications, and its evolution into the approach we are now familiar with. We give a more extensive history of exon skipping in particular, as it is the splice modulation approach given the most focus in this book.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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9
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Niemietz C, Chandhok G, Schmidt H. Therapeutic Oligonucleotides Targeting Liver Disease: TTR Amyloidosis. Molecules 2015; 20:17944-75. [PMID: 26437390 PMCID: PMC6332041 DOI: 10.3390/molecules201017944] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 12/13/2022] Open
Abstract
The liver has become an increasingly interesting target for oligonucleotide therapy. Mutations of the gene encoding transthyretin (TTR), expressed in vast amounts by the liver, result in a complex degenerative disease, termed familial amyloid polyneuropathy (FAP). Misfolded variants of TTR are linked to the establishment of extracellular protein deposition in various tissues, including the heart and the peripheral nervous system. Recent progress in the chemistry and formulation of antisense (ASO) and small interfering RNA (siRNA) designed for a knockdown of TTR mRNA in the liver has allowed to address the issue of gene-specific molecular therapy in a clinical setting of FAP. The two therapeutic oligonucleotides bind to RNA in a sequence specific manner but exploit different mechanisms. Here we describe major developments that have led to the advent of therapeutic oligonucleotides for treatment of TTR-related disease.
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MESH Headings
- Amyloid Neuropathies, Familial/genetics
- Amyloid Neuropathies, Familial/therapy
- Animals
- Clinical Studies as Topic
- Drug Evaluation, Preclinical
- Gene Silencing
- Genetic Therapy
- Humans
- Liver Diseases/genetics
- Liver Diseases/therapy
- Mutation
- Oligonucleotides/administration & dosage
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Oligonucleotides/therapeutic use
- Oligonucleotides, Antisense/administration & dosage
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/therapeutic use
- Prealbumin/genetics
- RNA Interference
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/therapeutic use
- Treatment Outcome
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Affiliation(s)
- Christoph Niemietz
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, Gebäude A14, D-48149 Münster, Germany.
| | - Gursimran Chandhok
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, Gebäude A14, D-48149 Münster, Germany.
| | - Hartmut Schmidt
- Klinik für Transplantationsmedizin, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, Gebäude A14, D-48149 Münster, Germany.
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Bauman JA, Kole R. Modulation of RNA splicing as a potential treatment for cancer. Bioeng Bugs 2011; 2:125-8. [PMID: 21637003 PMCID: PMC3225653 DOI: 10.4161/bbug.2.3.15165] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 02/12/2011] [Accepted: 02/15/2011] [Indexed: 11/19/2022] Open
Abstract
Close to 90% of human genes are transcribed into pre-mRNA that undergoes alternative splicing, producing multiple mRNAs and proteins from single genes. This process is largely responsible for human proteome diversity, and about half of genetic disease-causing mutations affect splicing. Splice-switching oligonucleotides (SSOs) comprise an emerging class of antisense therapeutics that modify gene expression by directing pre-mRNA splice site usage. Bauman et al. investigated an SSO that up-regulated the expression of an anti-cancer splice variant while simultaneously eliminating an over-expressed cancer-causing splice variant. This was accomplished by targeting pre-mRNA of the apoptotic regulator Bcl-x, which is alternatively spliced to express anti- and pro-apoptotic splice variants Bcl-xL and Bcl-xS, respectively. High expression of Bcl-xL is a hallmark of many cancers and is considered a general mechanism used by cancer cells to evade apoptosis. Redirection of Bcl-x pre-mRNA splicing from Bcl-xL to -xS by SSO induced apoptotic and chemosensitizing effects in various cancer cell lines. Importantly, the paper shows that delivery of Bcl-x SSO using a lipid nanoparticle redirected Bcl-x splicing and reduced tumor burden in melanoma lung metastases. This was the first demonstration of SSO efficacy in tumors in vivo. SSOs are not limited to be solely potential anti-cancer drugs. SSOs were first applied to repair aberrant splicing in thalassemia, a genetic disease, they have been used to create novel proteins (e.g., ∆7TNFR1), and they have recently progressed to clinical trials for patients with Duchenne muscular dystrophy.
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Affiliation(s)
- John A Bauman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.
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Satoh N, Watanabe N, Kanda A, Sugaya-Fukasawa M, Hisatomi H. Expression of Glutathione Reductase Splice Variants in Human Tissues. Biochem Genet 2010; 48:816-21. [DOI: 10.1007/s10528-010-9362-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 04/02/2010] [Indexed: 10/19/2022]
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Shiraishi T, Eysturskarth J, Nielsen PE. Modulation of mdm2 pre-mRNA splicing by 9-aminoacridine-PNA (peptide nucleic acid) conjugates targeting intron-exon junctions. BMC Cancer 2010; 10:342. [PMID: 20591158 PMCID: PMC2910690 DOI: 10.1186/1471-2407-10-342] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 06/30/2010] [Indexed: 12/17/2022] Open
Abstract
Background Modulation of pre-mRNA splicing by antisense molecules is a promising mechanism of action for gene therapeutic drugs. In this study, we have examined the potential of peptide nucleic acid (PNA) 9-aminoacridine conjugates to modulate the pre-mRNA splicing of the mdm2 human cancer gene in JAR cells. Methods We screened 10 different 15 mer PNAs targeting intron2 at both the 5' - and the 3'-splice site for their effects on the splicing of mdm2 using RT-PCR analysis. We also tested a PNA (2512) targeting the 3'-splice site of intron3 with a complementarity of 4 bases to intron3 and 11 bases to exon4 for its splicing modulation effect. This PNA2512 was further tested for the effects on the mdm2 protein level as well as for inhibition of cell growth in combination with the DNA damaging agent camptothecin (CPT). Results We show that several of these PNAs effectively inhibit the splicing thereby producing a larger mRNA still containing intron2, while skipping of exon3 was not observed by any of these PNAs. The most effective PNA (PNA2406) targeting the 3'-splice site of intron2 had a complementarity of 4 bases to intron2 and 11 bases to exon3. PNA (2512) targeting the 3'-splice site of intron3 induced both splicing inhibition (intron3 skipping) and skipping of exon4. Furthermore, treatment of JAR cells with this PNA resulted in a reduction in the level of MDM2 protein and a concomitant increase in the level of tumor suppressor p53. In addition, a combination of this PNA with CPT inhibited cell growth more than CPT alone. Conclusion We have identified several PNAs targeting the 5'- or 3'-splice sites in intron2 or the 3'-splice site of intron3 of mdm2 pre-mRNA which can inhibit splicing. Antisense targeting of splice junctions of mdm2 pre-mRNA may be a powerful method to evaluate the cellular function of MDM2 splice variants as well as a promising approach for discovery of mdm2 targeted anticancer drugs.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Health Science Faculty, 2200 Copenhagen N, Denmark.
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14
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Cooper C, Guo J, Yan Y, Chooniedass-Kothari S, Hube F, Hamedani MK, Murphy LC, Myal Y, Leygue E. Increasing the relative expression of endogenous non-coding Steroid Receptor RNA Activator (SRA) in human breast cancer cells using modified oligonucleotides. Nucleic Acids Res 2009; 37:4518-31. [PMID: 19483093 PMCID: PMC2715257 DOI: 10.1093/nar/gkp441] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Products of the Steroid Receptor RNA Activator gene (SRA1) have the unusual property to modulate the activity of steroid receptors and other transcription factors both at the RNA (SRA) and the protein (SRAP) level. Balance between these two genetically linked entities is controlled by alternative splicing of intron-1, whose retention alters SRAP reading frame. We have previously found that both fully-spliced SRAP-coding and intron-1-containing non-coding SRA RNAs co-exist in breast cancer cell lines. Herein, we report a significant (Student's t-test, P < 0.003) higher SRA–intron-1 relative expression in breast tumors with higher progesterone receptor contents. Using an antisense oligoribonucleotide, we have successfully reprogrammed endogenous SRA splicing and increased SRA RNA–intron-1 relative level in T5 breast cancer cells. This increase is paralleled by significant changes in the expression of genes such as plasminogen urokinase activator and estrogen receptor beta. Estrogen regulation of other genes, including the anti-metastatic NME1 gene, is also altered. Overall, our results suggest that the balance coding/non-coding SRA transcripts not only characterizes particular tumor phenotypes but might also, through regulating the expression of specific genes, be involved in breast tumorigenesis and tumor progression.
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Affiliation(s)
- Charlton Cooper
- Department of Biochemistry & Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba R3E0W3, Canada
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RNA repair restores hemoglobin expression in IVS2-654 thalassemic mice. Proc Natl Acad Sci U S A 2009; 106:1205-10. [PMID: 19164558 DOI: 10.1073/pnas.0812436106] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Repair of beta-globin pre-mRNA rendered defective by a thalassemia-causing splicing mutation, IVS2-654, in intron 2 of the human beta-globin gene was accomplished in vivo in a mouse model of IVS2-654 thalassemia. This was effected by a systemically delivered splice-switching oligonucleotide (SSO), a morpholino oligomer conjugated to an arginine-rich peptide. The SSO blocked the aberrant splice site in the targeted pre-mRNA and forced the splicing machinery to reselect existing correct splice sites. Repaired beta-globin mRNA restored significant amounts of hemoglobin in the peripheral blood of the IVS2-654 mouse, improving the number and quality of erythroid cells.
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Wilhelm E, Pellay FX, Benecke A, Bell B. Determining the impact of alternative splicing events on transcriptome dynamics. BMC Res Notes 2008; 1:94. [PMID: 18950505 PMCID: PMC2584107 DOI: 10.1186/1756-0500-1-94] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 10/24/2008] [Indexed: 11/10/2022] Open
Abstract
Background The complete sequencing of the human genome and its subsequent analysis revealed a predominant role for alternative splicing in the generation of proteome diversity. Splice switching oligonucleotides (SSOs) are a powerful and specific tool to experimentally control alternative splicing of endogenous messenger RNAs in living cells. SSOs also have therapeutic potential to treat diseases that are caused by aberrant splicing. The assignment of biological roles to alternative splicing events of currently unknown function promises to provide a largely untapped source of potential new therapeutic targets. Here we have developed a protocol that combines high sensitivity microarrays with the transfection of SSOs to monitor global changes in gene expression downstream of alternate, endogenous splice events. Results When applied to a well-characterized splicing event in the Bcl-x gene, the application of high sensitivity microarrays revealed a link between the induction of the Bcl-xS isoform and the repression of genes involved in protein synthesis. Conclusion The strategy introduced herein provides a useful approach to define the biological impact of any given alternative splicing event on global gene expression patterns. Furthermore, our data provide the first link between Bcl-xS expression and the repression of ribosomal protein gene expression.
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Affiliation(s)
- Emmanuelle Wilhelm
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, Québec J1H 5N4, Canada.
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17
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Fabani MM, Ivanova GD, Gait MJ. Peptide–Peptide Nucleic Acid Conjugates for Modulation of Gene Expression. THERAPEUTIC OLIGONUCLEOTIDES 2008. [DOI: 10.1039/9781847558275-00080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Martin M. Fabani
- Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK
| | - Gabriela D. Ivanova
- Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK
| | - Michael J. Gait
- Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK
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Bessa C, Teixeira CA, Dias A, Alves M, Rocha S, Lacerda L, Loureiro L, Guimarães A, Ribeiro MG. CLN2/TPP1 deficiency: the novel mutation IVS7-10A>G causes intron retention and is associated with a mild disease phenotype. Mol Genet Metab 2008; 93:66-73. [PMID: 17959406 DOI: 10.1016/j.ymgme.2007.08.124] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 08/28/2007] [Accepted: 08/28/2007] [Indexed: 11/19/2022]
Abstract
The classical form of late infantile neuronal ceroid lipofuscinosis (LINCL) is a childhood hereditary neurodegenerative disease usually fatal in the first decade of life. The underlying gene, CLN2, encodes the lysosomal soluble enzyme tripeptidyl-peptidase 1 (TPP1). In a Portuguese patient with juvenile form of the disease, the histochemical study revealed the presence of curvilinear inclusions typical of LINCL. In vitro TPP1 activity was deficient in patient's cells. CLN2 gene analysis revealed the transition IVS7-10A>G (g.4196A>G) in both alleles. In silico analysis suggested that A-to-G change in the A-rich region of intron 7 could cause aberrant splicing of exon 8 by creating a novel acceptor splice site. However, because the wild-type acceptor of intron 7 is weak and it was not apparently affected, the severity of this mutation could not be established through sequencing data of gDNA. Normal level of spliced CLN2/mRNA was observed in patient's fibroblasts. In the cDNA, the 9-nt retention of intronic sequence (c.886_887ins9) was observed. The mutation is predicted to result in a protein with three extra amino acids between proline 295 and glycine 296. In patient's fibroblasts the level of mutant CLN2p was reduced to about 60% but the migration pattern was similar to the wild-type protein, suggesting that it was correctly targeted to the lysosomes. Taken together, these findings suggest that the first "ag" is selected for splicing and the mutant protein must retain some residual catalytic activity, thus explaining the late onset and the delayed progression of the disease.
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Affiliation(s)
- C Bessa
- Unidade de Enzimologia, Instituto de Genética Médica Jacinto Magalhães, Pç. Pedro Nunes 88, 4050-466 Porto, Portugal
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19
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Kuraoka I, Ito S, Wada T, Hayashida M, Lee L, Saijo M, Nakatsu Y, Matsumoto M, Matsunaga T, Handa H, Qin J, Nakatani Y, Tanaka K. Isolation of XAB2 complex involved in pre-mRNA splicing, transcription, and transcription-coupled repair. J Biol Chem 2007; 283:940-50. [PMID: 17981804 DOI: 10.1074/jbc.m706647200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleotide excision repair is a versatile repair pathway that counteracts the deleterious effects of various DNA lesions. In nucleotide excision repair, there is a transcription-coupled repair (TCR) pathway that focuses on DNA damage that blocks RNA polymerase IIo in transcription elongation. XAB2 (XPA-binding protein 2), containing tetratricopeptide repeats, has been isolated by virtue of its ability to interact with xeroderma pigmentosum group A protein (XPA). Moreover, XAB2 has been shown to interact with Cockayne syndrome group A and B proteins (CSA and CSB) and RNA polymerase II, as well as XPA, and is involved in TCR and transcription. Here we purified XAB2 as a multimeric protein complex consisting of hAquarius, XAB2, hPRP19, CCDC16, hISY1, and PPIE, which are involved in pre-mRNA splicing. Knockdown of XAB2 with small interfering RNA in HeLa cells resulted in a hypersensitivity to killing by UV light and a decreased recovery of RNA synthesis after UV irradiation and regular RNA synthesis. Enhanced interaction of XAB2 with RNA polymerase IIo or XPA was observed in cells treated with DNA-damaging agents, indicating DNA damage-responsive activity of the XAB2 complex. These results indicated that the XAB2 complex is a multifunctional factor involved in pre-mRNA splicing, transcription, and TCR.
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Affiliation(s)
- Isao Kuraoka
- Laboratories for Organismal Biosystems, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
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Ulanova M, Schreiber AD, Befus AD. The future of antisense oligonucleotides in the treatment of respiratory diseases. BioDrugs 2006; 20:1-11. [PMID: 16573347 PMCID: PMC7100773 DOI: 10.2165/00063030-200620010-00001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antisense oligonucleotides (ASO) are short synthetic DNA molecules designed to inhibit translation of a targeted gene to protein via interaction with messenger RNA. More recently, small interfering (si)RNA have been developed as potent tools to specifically inhibit gene expression. ASO directed against signaling molecules, cytokine receptors, and transcription factors involved in allergic immune and inflammatory responses, have been applied in experimental models of asthma and demonstrate potential as therapeutics. Several ASO-based drugs directed against oncogenes have been developed for therapy of lung cancer, and some have recently reached clinical trials. ASO and siRNA to respiratory syncytial virus infection have demonstrated good potential to treat this condition, particularly in combination with an antiviral drug. Although ASO-based therapeutics are promising for lung diseases, issues of specificity, identification of correct molecular targets, delivery and carrier systems, as well as potential adverse effects must be carefully evaluated before clinical application.
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Affiliation(s)
- Marina Ulanova
- Department of Medicine, Pulmonary Research Group, University of Alberta, Room 550A HMRC, Edmonton, AB T6G 2S2 Canada
- Northern Ontario School of Medicine, Thunder Bay, Ontario Canada
| | - Alan D. Schreiber
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania USA
| | - A. Dean Befus
- Department of Medicine, Pulmonary Research Group, University of Alberta, Room 550A HMRC, Edmonton, AB T6G 2S2 Canada
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Soret J, Gabut M, Tazi J. SR Proteins as Potential Targets for Therapy. ALTERNATIVE SPLICING AND DISEASE 2006; 44:65-87. [PMID: 17076265 DOI: 10.1007/978-3-540-34449-0_4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Serine- and arginine-rich (SR) proteins constitute a highly conserved family of pre-mRNA splicing factors that play key roles in the regulation of splice site selection, and thereby in the control of alternative splicing processes. In addition to conserved sequences at the splice junctions, splice site selection also depends upon different sets of auxiliary cis regulatory elements known as exonic and intronic splicing enhancers (ESEs and ISEs) or exonic and intronic silencers (ESSs and ISSs). Specific binding of SR proteins to their cognate splicing enhancers as well as binding of splicing repressor to silencer sequences serve to enhance or inhibit recognition of weak splice sites by the splicing machinery. Given that the vast majority of human genes contain introns and that most pre-mRNAs containing multiple exons undergo alternative splicing, mutations disrupting or creating such auxiliary elements can result in aberrant splicing events at the origin of various human diseases. In the past few years, numerous studies have reported several approaches allowing correction of such aberrant splicing events by targeting either the mutated sequences or the splicing regulators whose binding is affected by the mutation. The aim of the present review is to highlight the different means by which it is possible to modulate the activity of SR splicing factors and to bring out those holding the greatest promises for the development of therapeutic treatments.
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Affiliation(s)
- Johann Soret
- Institut de Génétique Moléculaire de Montpellier, UMR 5535, IFR 122, Centre National de Recherche Scientifique, 1919, route de Mende, 34293 Montpellier, France
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Xu H, Somers ZB, Robinson ML, Hebert MD. Tim50a, a nuclear isoform of the mitochondrial Tim50, interacts with proteins involved in snRNP biogenesis. BMC Cell Biol 2005; 6:29. [PMID: 16008839 PMCID: PMC1177934 DOI: 10.1186/1471-2121-6-29] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Accepted: 07/11/2005] [Indexed: 11/16/2022] Open
Abstract
Background The Cajal body (CB) is a nuclear suborganelle involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs), which are vital for pre-mRNA splicing. Newly imported Sm-class snRNPs traffic through CBs, where the snRNA component of the snRNP is modified, and then target to other nuclear domains such as speckles and perichromatin fibrils. It is not known how nascent snRNPs localize to the CB and are released from this structure after modification. The marker protein for CBs, coilin, may play a role in snRNP biogenesis given that it can interact with snRNPs and SMN, the protein mutated in Spinal Muscular Atrophy. Loss of coilin function in mice leads to significant viability and fertility problems and altered CB formation. Results In this report, we identify a minor isoform of the mitochondrial Tim50, Tim50a, as a coilin interacting protein. The Tim50a transcript can be detected in some cancer cell lines and normal brain tissue. The Tim50a protein differs only from Tim50 in that it contains an additional 103 aa N-terminal to the translation start of Tim50. Importantly, a putative nuclear localization signal is found within these 103 residues. In contrast to Tim50, which localizes to the cytoplasm and mitochondria, Tim50a is strictly nuclear and is enriched in speckles with snRNPs. In addition to coilin, Tim50a interacts with snRNPs and SMN. Competition binding experiments demonstrate that coilin competes with Sm proteins of snRNPs and SMN for binding sites on Tim50a. Conclusion Tim50a may play a role in snRNP biogenesis given its cellular localization and protein interaction characteristics. We hypothesize that Tim50a takes part in the release of snRNPs and SMN from the CB.
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Affiliation(s)
- Hongzhi Xu
- Department of Biochemistry, The University of Mississippi Medical Center Jackson, MS 39216-4505, USA
| | - Z Brad Somers
- Department of Biochemistry, The University of Mississippi Medical Center Jackson, MS 39216-4505, USA
| | - Melvin L Robinson
- Department of Biochemistry, The University of Mississippi Medical Center Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Biochemistry, The University of Mississippi Medical Center Jackson, MS 39216-4505, USA
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Gabut M, Miné M, Marsac C, Brivet M, Tazi J, Soret J. The SR protein SC35 is responsible for aberrant splicing of the E1alpha pyruvate dehydrogenase mRNA in a case of mental retardation with lactic acidosis. Mol Cell Biol 2005; 25:3286-94. [PMID: 15798212 PMCID: PMC1069624 DOI: 10.1128/mcb.25.8.3286-3294.2005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyruvate dehydrogenase (PDH) complex deficiency is a major cause of lactic acidosis and Leigh's encephalomyelopathies in infancy and childhood, resulting in early death in the majority of patients. Most of the molecular defects have been localized in the coding regions of the E1alpha PDH gene. Recently, we identified a novel mutation of the E1alpha PDH gene in a patient with an encephalopathy and lactic acidosis. This mutation, located downstream of exon 7, activates a cryptic splice donor and leads to the retention of intronic sequences. Here, we demonstrate that the mutation results in an increased binding of the SR protein SC35. Consistently, ectopic overexpression of this splicing factor enhanced the use of the cryptic splice site, whereas small interfering RNA-mediated reduction of the SC35 protein levels in primary fibroblasts from the patient resulted in the almost complete disappearance of the aberrantly spliced E1alpha PDH mRNA. Our findings open the exciting prospect for a novel therapy of an inherited disease by altering the level of a specific splicing factor.
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Affiliation(s)
- Mathieu Gabut
- UMR 5535, IFR122, CNRS-UMII, Institut de Génétique Moléculaire de Montpellier, 1919 route de Mende, 34293 Montpellier, France
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24
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Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nat Methods 2004; 1:233-9. [PMID: 15782199 DOI: 10.1038/nmeth719] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Accepted: 09/27/2004] [Indexed: 01/27/2023]
Abstract
It is becoming increasingly clear that alternative splicing enables the complex development and homeostasis of higher organisms. To gain a better understanding of how splicing contributes to regulatory pathways, we have developed an alternative splicing library approach for the identification of alternatively spliced exons and their flanking regions by alternative splicing sequence enriched tags sequencing. Here, we have applied our approach to mouse melan-c melanocyte and B16-F10Y melanoma cell lines, in which 5,401 genes were found to be alternatively spliced. These genes include those encoding important regulatory factors such as cyclin D2, Ilk, MAPK12, MAPK14, RAB4, melastatin 1 and previously unidentified splicing events for 436 genes. Real-time PCR further identified cell line-specific exons for Tmc6, Abi1, Sorbs1, Ndel1 and Snx16. Thus, the ASL approach proved effective in identifying splicing events, which suggest that alternative splicing is important in melanoma development.
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Affiliation(s)
- Akira Watahiki
- Genome Science Laboratory, RIKEN, Wako main campus, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
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Ravichandran LV, Dean NM, Marcusson EG. Use of antisense oligonucleotides in functional genomics and target validation. Oligonucleotides 2004; 14:49-64. [PMID: 15104896 DOI: 10.1089/154545704322988058] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
With the completion of sequencing of the human genome, a great deal of interest has been shifted toward functional genomics-based research for identification of novel drug targets for treatment of various diseases. The major challenge facing the pharmaceutical industry is to identify disease-causing genes and elucidate additional roles for genes of known functions. Gene functionalization and target validation are probably the most important steps involved in identifying novel potential drug targets. This review focuses on recent advances in antisense technology and its use for rapid identification and validation of new drug targets. The significance and applicability of this technology as a beginning of the drug discovery process are underscored by relevant cell culture-based assays and positive correlation in specific animal disease models. Some of the antisense inhibitors used to validate gene targets are themselves being developed as drugs. The current clinical trials based on such leads that were identified in a very short time further substantiate the importance of antisense technology-based functional genomics as an integral part of target validation and drug target identification.
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Arzumanov A, Stetsenko DA, Malakhov AD, Reichelt S, Sørensen MD, Babu BR, Wengel J, Gait MJ. A structure-activity study of the inhibition of HIV-1 Tat-dependent trans-activation by mixmer 2'-O-methyl oligoribonucleotides containing locked nucleic acid (LNA), alpha-L-LNA, or 2'-thio-LNA residues. Oligonucleotides 2004; 13:435-53. [PMID: 15025911 DOI: 10.1089/154545703322860762] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The HIV-1 trans-activation responsive element (TAR) RNA stem-loop interacts with the HIV trans-activator protein Tat and other cellular factors to stimulate transcriptional elongation from the viral long terminal repeat (LTR). Inhibitors of these interactions block full-length transcription and, hence, would potentially inhibit HIV replication. We have studied structure-activity relationships in inhibition of trans-activation by steric block 2'-O-methyl (OMe) oligonucleotides chimeras (mixmers) containing locked nucleic acid (LNA) units. Inhibition was measured both in Tat-dependent in vitro transcription from an HIV-1 DNA template directed by HeLa cell nuclear extract and in a robust HeLa cell reporter assay that involves use of stably integrated plasmids to express firefly luciferase Tat dependently and Renilla luciferase Tat-independently. OMe oligonucleotides with optimally 40%-50% LNA units and a minimum of 12 residues in length were active in the cellular assay when delivered with cationic gemini surfactant GS11 at 50% inhibitory concentrations of 230 +/- 40 nM, whereas activity in the in vitro transcription assay was observed down to 9 residues. No cellular activity was observed for OMe oligonucleotides of 12 or 16 residues, which was shown to be due to poor cellular uptake. Both 12-mer mixmers containing alpha -L-LNA or 2'-thio-LNA (S-LNA) were also active in in vitro transcription and the former in cellular reporter inhibition assays, demonstrating that the property of promotion of cellular uptake by LNA is not due to specific sugar conformational effects. Covalent conjugates of OMe/LNA chimeras with Kaposi-fibroblast growth factor (K-FGF) or Transportan peptides failed to enter HeLa cells without a delivery agent but were fully active when delivered by cationic gemini surfactant, showing that in principle, peptide conjugation does not interfere with cellular activity. Thus, OMe/LNA mixmers are powerful reagents for use as steric block inhibitors of gene expression regulated by protein-RNA interactions within HeLa cell nuclei.
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Affiliation(s)
- Andrey Arzumanov
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
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Concin N, Becker K, Slade N, Erster S, Mueller-Holzner E, Ulmer H, Daxenbichler G, Zeimet A, Zeillinger R, Marth C, Moll UM. Transdominant DeltaTAp73 isoforms are frequently up-regulated in ovarian cancer. Evidence for their role as epigenetic p53 inhibitors in vivo. Cancer Res 2004; 64:2449-60. [PMID: 15059898 DOI: 10.1158/0008-5472.can-03-1060] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite strong homology, the roles of TP53 and TP73 in tumorigenesis seem to be fundamentally different. In contrast to TP53, tumor-associated overexpression of TP73 in many different cancers, combined with virtual absence of inactivating mutations and lack of a cancer phenotype in the TP73 null mouse are inconsistent with a suppressor function but instead support an oncogenic function. The discovery of NH(2)-terminally truncated p73 isoforms, collectively called DeltaTAp73, is now the focus of intense interest because they act as potent transdominant inihibitors of wild-type p53 and transactivation-competent TAp73. Therefore, establishing deregulated DeltaTAp73 expression in tumors could be the crucial link to decipher which of the two opposing roles of this bipolar gene is the biologically relevant one. This study is the largest to date and encompasses 100 ovarian carcinomas with complete expression profile of all NH(2)-terminal isoforms, discriminating between TAp73 and DeltaTAp73 (DeltaNp73, DeltaN'p73, Ex2p73, and Ex2/3p73) by isoform-specific real-time reverse transcription-PCR. We find that the set of NH(2)-terminal p73 isoforms distinguishes ovarian cancer patients from healthy controls and thus is a molecular marker for this diagnosis. Ovarian cancers strongly and almost universally overexpress DeltaN'p73 compared with normal tissues (95% of cancers). About one-third of tumors also exhibit concomitant up-regulation of the antagonistic TAp73, whereas only a small subgroup of tumors overexpress DeltaNp73. Thus, deregulation of the E2F1-responsive P1 promoter, rather than the alternate P2 promoter, is mainly responsible for the production of transdominant p53/TAp73 antagonists in ovarian cancer. Tumor stage, grade, presence of metastases, p53 status, and residual disease after resection are significant prognostic markers for overall and recurrence-free survival. A trend is found for better overall survival in patients with low expression of DeltaN'p73/DeltaNp73, compared with patients with high expression. A strong correlation between deregulated DeltaTAp73 and p53 status exists. p53 wild-type cancers exhibit significantly higher deregulation of DeltaN'p73, DeltaNp73, and Ex2/3p73 than p53 mutant cancers. This data strongly supports the hypothesis that overexpression of transdominant p73 isoforms can function as epigenetic inhibitors of p53 in vivo, thereby alleviating selection pressure for p53 mutations in tumors.
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Affiliation(s)
- Nicole Concin
- Department of Pathology, State University of New York at Stony Brook, Stony Brook, New York, USA
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Abstract
Alternative splicing is a critical post-transcriptional event leading to an increase in the transcriptome diversity. Recent bioinformatics studies revealed a high frequency of alternative splicing. Although the extent of AS conservation among mammals is still being discussed, it has been argued that major forms of alternatively spliced transcripts are much better conserved than minor forms. It suggests that alternative splicing plays a major role in genome evolution allowing new exons to evolve with less constraint.
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Villemaire J, Dion I, Elela SA, Chabot B. Reprogramming alternative pre-messenger RNA splicing through the use of protein-binding antisense oligonucleotides. J Biol Chem 2003; 278:50031-9. [PMID: 14522969 DOI: 10.1074/jbc.m308897200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative pre-messenger RNA splicing is a major contributor to proteomic diversity in higher eukaryotes and represents a key step in the control of protein function in a large variety of biological systems. As a means of artificially altering splice site choice, we have investigated the impact of positioning proteins in the vicinity of 5' splice sites. We find that a recombinant GST-MS2 protein interferes with 5' splice site use, most efficiently when it binds upstream of that site. To broaden the use of proteins as steric inhibitors of splicing, we have tested the activity of antisense oligonucleotides carrying binding sites for the heterogeneous nuclear ribonucleoprotein A1/A2 proteins. In a HeLa cell extract, tailed oligonucleotides complementary to exonic sequences elicit strong shifts in 5' splice site selection. In four different human cell lines, an interfering oligonucleotide carrying A1/A2 binding sites also shifted the alternative splicing of the Bcl-x pre-mRNA more efficiently than oligonucleotides acting through duplex formation only. The use of protein-binding oligonucleotides that interfere with U1 small nuclear ribonucleoprotein binding therefore represents a novel and powerful approach to control splice site selection in cells.
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Affiliation(s)
- Jonathan Villemaire
- Département de microbiologie et d'infectiologie, RNA/RNP Group, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Abstract
The importance of alternative RNA splicing in the generation of genetic diversity is now widely accepted. This article highlights how alternative RNA splicing can have an impact on drug efficacy and safety, and demonstrates its potential pharmacogenomic value. The analysis of the repertoire of alternative RNA splicing events could potentially identify markers of pharmacogenomic relevance with high sensitivity and specificity and also provides a route through which genes can be selected for single nucleotide polymorphism (SNP) genotyping. Recent methodological advances, including microarray and splice-dedicated expression profiling, have made it possible to perform high-throughput alternative splicing analyses.
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Affiliation(s)
- Laurent Bracco
- ExonHit Therapeutics, 65 Boulevard Masséna, 75013 Paris, France.
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Holmes SC, Arzumanov AA, Gait MJ. Steric inhibition of human immunodeficiency virus type-1 Tat-dependent trans-activation in vitro and in cells by oligonucleotides containing 2'-O-methyl G-clamp ribonucleoside analogues. Nucleic Acids Res 2003; 31:2759-68. [PMID: 12771202 PMCID: PMC156719 DOI: 10.1093/nar/gkg384] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the synthesis of a novel 2'-O-methyl (OMe) riboside phosphoramidite derivative of the G-clamp tricyclic base and incorporation into a series of small steric blocking OMe oligonucleotides targeting the apical stem-loop region of human immunodeficiency virus type 1 (HIV-1) trans- activation-responsive (TAR) RNA. Binding to TAR RNA is substantially enhanced for certain single site substitutions in the centre of the oligonucleotide, and doubly substituted anti-TAR OMe 9mers or 12mers exhibit remarkably low binding constants of <0.1 nM. G-clamp-containing oligomers achieved 50% inhibition of Tat-dependent in vitro transcription at approximately 25 nM, 4-fold lower than for a TAR 12mer OMe oligonucleotide and better than found for any other oligonucleotide tested to date. Addition of one or two OMe G-clamps did not impart cellular trans-activation inhibition activity to cellularly inactive OMe oligonucleotides. Addition of an OMe G-clamp to a 12mer OMe-locked nucleic acid chimera maintained, but did not enhance, inhibition of Tat-dependent in vitro transcription and cellular trans-activation in HeLa cells. The results demonstrate clearly that an OMe G-clamp has remarkable RNA-binding enhancement ability, but that oligonucleotide effectiveness in steric block inhibition of Tat-dependent trans-activation both in vitro and in cells is governed by factors more complex than RNA-binding strength alone.
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Affiliation(s)
- Stephen C Holmes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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Abstract
Antisense offers a precise and specific means of knocking down expression of a target gene, and is a major focus of research in neuroscience and other areas. It has application as a tool in gene function and target validation studies and is emerging as a therapeutic technology in its own right. It has become increasingly obvious, however, that there are a number of hurdles to overcome before antisense can be used effectively in the CNS, most notably finding suitable nucleic acid chemistries and an effective delivery vehicle to transport antisense oligonucleotides (AS-ODNs) across the blood-brain barrier (BBB) to their site of action. Despite these problems, a number of potential applications of AS-ODNs in CNS therapeutics have been validated in vitro and, in some cases, in vivo. Here the authors outline available nucleic acid chemistries and review progress in the development of non-invasive delivery vehicles that may be applicable to CNS therapeutics. Further to this, they discuss a number of experimental applications of AS-ODNs to CNS research and speculate on the development of antisense techniques to treat CNS disease.
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Affiliation(s)
- Jenny Godfray
- ExpressOn BioSystems Ltd, The Logan Building, Roslin BioCentre, Roslin, Midlothian EH25 9TT, Scotland.
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33
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Affiliation(s)
- Nuno André Faustino
- Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
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Mercatante DR, Mohler JL, Kole R. Cellular response to an antisense-mediated shift of Bcl-x pre-mRNA splicing and antineoplastic agents. J Biol Chem 2002; 277:49374-82. [PMID: 12381725 DOI: 10.1074/jbc.m209236200] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Overexpression of Bcl-xL, an anti-apoptotic member of the Bcl-2 family, negatively correlates with the sensitivity of various cancers to chemotherapeutic agents. We show here that high levels of expression of Bcl-xL promoted apoptosis of cells treated with an antisense oligonucleotide (5'Bcl-x AS) that shifts the splicing pattern of Bcl-x pre-mRNA from the anti-apoptotic variant, Bcl-xL, to the pro-apoptotic variant, Bcl-xS. This surprising finding illustrates the advantage of antisense-induced modulation of alternative splicing versus down-regulation of targeted genes. It also suggests a specificity of the oligonucleotide effects since non-cancerous cells with low levels of Bcl-xL should resist the treatment. 5'Bcl-x AS sensitized cells to several antineoplastic agents and radiation and was effective in promoting apoptosis of MCF-7/ADR cells, a breast cancer cell line resistant to doxorubicin via overexpression of the mdr1 gene. Efficacy of 5'Bcl-x AS combined with chemotherapeutic agents in the PC3 prostate cancer cell line may be translated to clinical prostate cancer since recurrent prostate cancer tissue samples expressed higher levels of Bcl-xL than benign prostate tissue. Treatment with 5'Bcl-x AS may enhance the efficacy of standard anti-cancer regimens and should be explored, especially in recurrent prostate cancer.
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Affiliation(s)
- Danielle R Mercatante
- UNC Lineberger Comprehensive Cancer Center and Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599-7295, USA
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Fletcher TM. Telomerase - strategies to exploit an important chemotherapeutic target. Expert Opin Ther Targets 2001; 5:363-378. [PMID: 12540271 DOI: 10.1517/14728222.5.3.363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Telomeres, unique protein-DNA complexes located at the chromosome ends, have important functions involving both DNA protection and cellular signalling. Telomere structure is very dynamic yet tightly controlled. One important factor is the presence of telomerase, a telomere-specific DNA polymerase activated in a majority of cancer cells. Cancer and normal cell telomeres may have dissimilar structures due to variances in telomere length, telomerase activity and levels of telomere binding proteins. In designing compounds to strictly target cancer cells, these distinctions should be investigated. Much of the recent focus has been on the development of highly effective telomerase inhibitors. Another novel group of small molecules target telomere DNA, thereby disrupting both telomerase activity and telomere structure. This class of compounds should have an immediate impact on cell growth and viability. Since many molecular characteristics of telomeres are unknown, small molecules should also be useful in probing differences in telomere dynamics unique to cancer cells.
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Affiliation(s)
- Terace M Fletcher
- National Institutes of Health, National Cancer Institute, Division of Basic Sciences, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD 20892-5055, USA.
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