Short antisense oligonucleotides alleviate the pleiotropic toxicity of RNA harboring expanded CGG repeats.

Szczegóły
Abstrakt

Tytuł:: Short antisense oligonucleotides alleviate the pleiotropic toxicity of RNA harboring expanded CGG repeats.
Autorzy:: Derbis M; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland.
Kul E; Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto von Guericke University, Magdeburg, Germany.
Niewiadomska D; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland.
Sekrecki M; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland.
Piasecka A; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland.
Taylor K; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland.
Hukema RK; Department of Clinical Genetics, Erasmus MC, CA, Rotterdam, The Netherlands.; Department of Health Care Studies, Rotterdam University of Applied Sciences, HR, Rotterdam, The Netherlands.
Stork O; Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto von Guericke University, Magdeburg, Germany.
Sobczak K; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan, Poland. .
Źródło:: Nature communications [Nat Commun] 2021 Feb 24; Vol. 12 (1), pp. 1265. Date of Electronic Publication: 2021 Feb 24.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: [London] : Nature Pub. Group
MeSH Terms:: Ataxia/*metabolism
Fragile X Mental Retardation Protein/*metabolism
Fragile X Syndrome/*metabolism
Oligonucleotides, Antisense/*metabolism
Tremor/*metabolism
Trinucleotide Repeat Expansion/*genetics
Trinucleotide Repeat Expansion/*physiology
Alternative Splicing/genetics ; Alternative Splicing/physiology ; Animals ; Ataxia/genetics ; Exons/genetics ; Female ; Fragile X Mental Retardation Protein/genetics ; Fragile X Syndrome/genetics ; Male ; Mice ; Mice, Transgenic ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Oligonucleotides, Antisense/genetics ; Tremor/genetics
References:: Hagerman, R. J. et al. Fragile X syndrome. Nat. Rev. Dis. Prim. 3, 17065 (2017). (PMID: 2896018410.1038/nrdp.2017.65)
Hagerman, R. J. et al. Intention tremor, parkinsonism, and generalized brain atrophy in male carriers of fragile X. Neurology 57, 127–130 (2001). (PMID: 1144564110.1212/WNL.57.1.127)
Hagerman, R. J. & Hagerman, P. Fragile X-associated tremor/ataxia syndrome-features, mechanisms and management. Nat. Rev. Neurol. 12, 403–412 (2016). (PMID: 2734002110.1038/nrneurol.2016.82)
Glineburg, M. R., Todd, P. K., Charlet-Berguerand, N. & Sellier, C. Repeat-associated non-AUG (RAN) translation and other molecular mechanisms in Fragile X Tremor Ataxia syndrome. Brain Res. 1693, 43–54 (2018). (PMID: 29453961601062710.1016/j.brainres.2018.02.006)
Tassone, F. et al. Elevated levels of FMR1 mRNA carrier males: a new mechanism of involvement in the fragile-X syndrome. Am. J. Hum. Genet. 66, 6–15 (2000). (PMID: 10.1086/302720)
Loomis, E. W., Sanz, L. A., Chédin, F. & Hagerman, P. J. Transcription-associated R-loop formation across the human FMR1 CGG-repeat region. PLoS Genet. 10, e1004294 (2014).
Groh, M., Lufino, M. M. P., Wade-Martins, R. & Gromak, N. R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome. PLoS Genet. 10, e1004318 (2014).
Diab, M. A. et al. The g-rich repeats in FMR1 and C9orf72 loci are hotspots for local unpairing of DNA. Genetics 210, 1239–1252 (2018). (PMID: 30396881628316210.1534/genetics.118.301672)
Tassone, F., Iwahashi, C. & Hagerman, P. J. FMR1 RNA within the intranuclear inclusions of fragile X-associated tremor/ataxia syndrome (FXTAS). RNA Biol. 1, 103–105 (2004). (PMID: 10.4161/rna.1.2.103517179750)
Iwahashi, C. K. et al. Protein composition of the intranuclear inclusions of FXTAS. Brain 129, 256–271 (2006). (PMID: 1624686410.1093/brain/awh650)
Sofola, O. A. et al. RNA-binding proteins hnRNP A2/B1 and CUGBP1 suppress fragile X CGG premutation repeat-induced neurodegeneration in a Drosophila model of FXTAS. Neuron 55, 565–571 (2007). (PMID: 17698010221538810.1016/j.neuron.2007.07.021)
Jin, P. et al. Pur α binds to rCGG repeats and modulates repeat-mediated neurodegeneration in a Drosophila model of fragile X tremor/ataxia syndrome. Neuron 55, 556–564 (2007). (PMID: 17698009199481710.1016/j.neuron.2007.07.020)
Sellier, C. et al. Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients. EMBO J. 29, 1248–1261 (2010). (PMID: 20186122285746410.1038/emboj.2010.21)
Qurashi, A., Li, W., Zhou, J. Y., Peng, J. & Jin, P. Nuclear accumulation of stress response mRNAs contributes to the neurodegeneration caused by fragile X premutation rCGG repeats. PLoS Genet. 7, e1002102 (2011).
Sellier, C. et al. Sequestration of DROSHA and DGCR8 by expanded CGG RNA repeats Alters microRNA processing in fragile X-associated tremor/ataxia syndrome. Cell Rep. 3, 869–880 (2013). (PMID: 23478018363942910.1016/j.celrep.2013.02.004)
Cid-Samper, F. et al. An integrative study of protein-RNA condensates identifies scaffolding RNAs and reveals players in fragile X-associated tremor/ataxia syndrome. Cell Rep. 25, 3422–3434.e7 (2018). (PMID: 30566867631528510.1016/j.celrep.2018.11.076)
Banez-Coronel, M. & Ranum, L. P. W. Repeat-associated non-AUG (RAN) translation: insights from pathology. Lab. Investig. 99, 929–942 (2019). (PMID: 3091832610.1038/s41374-019-0241-x)
Todd, P. K. et al. CGG repeat-associated translation mediates neurodegeneration in fragile X tremor ataxia syndrome. Neuron 78, 440–455 (2013). (PMID: 10.1016/j.neuron.2013.03.02623602499)
Sellier, C. et al. Translation of expanded CGG repeats into FMRpolyG is pathogenic and may contribute to fragile X tremor ataxia syndrome. Neuron 93, 331–347 (2017). (PMID: 28065649526325810.1016/j.neuron.2016.12.016)
Disney, M. D. et al. A small molecule that targets r(CGG) and improves defects in fragile X-associated tremor ataxia syndrome. ACS Chem. Biol. 7, 1711–1718 (2012). (PMID: 22948243347725410.1021/cb300135h)
Tran, T. et al. Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides. ACS Chem. Biol. 9, 904–912 (2014). (PMID: 24506227428784310.1021/cb400875u)
Yang, W. Y. et al. Small molecule recognition and tools to study modulation of r(CGG)exp in fragile X-associated tremor ataxia syndrome. ACS Chem. Biol. 11, 2456–2465 (2016). (PMID: 27276216554979110.1021/acschembio.6b00147)
Derbis, M., Konieczny, P., Walczak, A., Sekrecki, M. & Sobczak, K. Quantitative evaluation of toxic polyglycine biosynthesis and aggregation in cell models expressing expanded CGG repeats. Front. Genet. 9, 216 (2018). (PMID: 29971092601853510.3389/fgene.2018.00216)
Rodriguez, C. M. et al. A native function for RAN translation and CGG repeats in regulating fragile X protein synthesis. Nat. Neurosci. 23, 386–397 (2020). (PMID: 32066985766839010.1038/s41593-020-0590-1)
Sobczak, K. et al. Structural diversity of triplet repeat RNAs. J. Biol. Chem. 285, 12755–12764 (2010). (PMID: 20159983285707710.1074/jbc.M109.078790)
Napierala, M., Michalowski, D., de Mezer, M. & Krzyzosiak, W. J. W. J. Facile FMR1 mRNA structure regulation by interruptions in CGG repeats. Nucleic Acids Res. 33, 451–463 (2005). (PMID: 1565957754834010.1093/nar/gki186)
Studzińska, S., Cywoniuk, P. & Sobczak, K. Application of ion pair chromatography coupled with mass spectrometry to assess antisense oligonucleotides concentrations in living cells. Analyst 144, 622–633 (2019). (PMID: 3046210510.1039/C8AN01603H)
Kozlowski, P., de Mezer, M. & Krzyzosiak, W. J. Trinucleotide repeats in human genome and exome. Nucleic Acids Res. 38, 4027–4039 (2010). (PMID: 20215431289652110.1093/nar/gkq127)
Crossley, M. P., Bocek, M. & Cimprich, K. A. R-loops as cellular regulators and genomic threats. Mol. Cell 73, 398–411 (2019). (PMID: 30735654640281910.1016/j.molcel.2019.01.024)
Mauger, D. M. et al. mRNA structure regulates protein expression through changes in functional half-life. Proc. Natl Acad. Sci. USA 116, 24075–24083 (2019). (PMID: 3171243310.1073/pnas.19080521166883848)
Wu, Q. et al. Translation affects mRNA stability in a codon-dependent manner in human cells. eLife 8, e45396 (2019).
Hukema, R. K. et al. Reversibility of neuropathology and motor deficits in an inducible mouse model for FXTAS. Hum. Mol. Genet. 24, 4948–4957 (2015). (PMID: 26060190452749210.1093/hmg/ddv216)
Castro, H. et al. Selective rescue of heightened anxiety but not gait ataxia in a premutation 90CGG mouse model of fragile X-associated tremor/ataxia syndrome. Hum. Mol. Genet. 26, 2133–2145 (2017). (PMID: 28369393607507610.1093/hmg/ddx108)
Yang, Z. & Wang, K. K. W. Glial fibrillary acidic protein: from intermediate filament assembly and gliosis to neurobiomarker. Trends Neurosci. 38, 364–374 (2015). (PMID: 25975510455928310.1016/j.tins.2015.04.003)
Schoch, K. M. & Miller, T. M. Antisense oligonucleotides: translation from mouse models to human neurodegenerative diseases. Neuron 94, 1056–1070 (2017). (PMID: 28641106582151510.1016/j.neuron.2017.04.010)
Mendell, J. R. et al. Eteplirsen for the treatment of Duchenne muscular dystrophy. Ann. Neurol. 74, 637–647 (2013). (PMID: 2390799510.1002/ana.23982)
Corey, D. R. Nusinersen an antisense oligonucleotide drug for spinal muscular atrophy. Nat. Neurosci. 20, 497–499 (2017). (PMID: 2819239310.1038/nn.4508)
Gebert, L. F. R. et al. Miravirsen (SPC3649) can inhibit the biogenesis of miR-122. Nucleic Acids Res. 42, 609–621 (2014). (PMID: 2406855310.1093/nar/gkt852)
Obad, S. et al. Silencing of microRNA families by seed-targeting tiny LNAs. Nat. Genet. 43, 371–380 (2011). (PMID: 21423181354168510.1038/ng.786)
Wheeler, T. M. et al. Reversal of RNA dominance by displacement of protein sequestered on triplet repeat RNA. Science 325, 336–339 (2009). (PMID: 19608921410997310.1126/science.1173110)
Wojtkowiak-Szlachcic, A. et al. Short antisense-locked nucleic acids (all-LNAs) correct alternative splicing abnormalities in myotonic dystrophy. Nucleic Acids Res. 43, 3318–3331 (2015). (PMID: 25753670438107210.1093/nar/gkv163)
Jain, A. & Vale, R. D. RNA phase transitions in repeat expansion disorders. Nature 546, 243–247 (2017). (PMID: 28562589555564210.1038/nature22386)
Fay, M. M., Anderson, P. J. & Ivanov, P. ALS/FTD-associated C9ORF72 repeat RNA promotes phase transitions in vitro and in cells. Cell Rep. 21, 3573–3584 (2017). (PMID: 29262335574110110.1016/j.celrep.2017.11.093)
Oh, S. Y. et al. RAN translation at CGG repeats induces ubiquitin proteasome system impairment in models of fragile X-associated tremor ataxia syndrome. Hum. Mol. Genet. 24, 4317–4326 (2015). (PMID: 25954027449239510.1093/hmg/ddv165)
Green, K. M. et al. RAN translation at C9orf72-associated repeat expansions is selectively enhanced by the integrated stress response. Nat. Commun. 8, 1-13 (2017).
Hu, J. et al. Allele-specific silencing of mutant huntingtin and ataxin-3 genes by targeting expanded CAG repeats in mRNAs. Nat. Biotechnol. 27, 478–484 (2009). (PMID: 19412185276521810.1038/nbt.1539)
Guo, W. et al. Ablation of Fmrp in adult neural stem cells disrupts hippocampus-dependent learning. Nat. Med. 17, 559–565 (2011). (PMID: 21516088314095210.1038/nm.2336)
Gohel, D. et al. FMRpolyG alters mitochondrial transcripts level and respiratory chain complex assembly in fragile X associated tremor/ataxia syndrome [FXTAS]. Biochim. Biophys. Acta Mol. basis Dis. 1865, 1379–1388 (2019). (PMID: 3077148710.1016/j.bbadis.2019.02.010)
Ishiura, H. et al. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. Nat. Genet. 51, 1222–1232 (2019). (PMID: 3133238010.1038/s41588-019-0458-z)
Sznajder, L. J. et al. Mechanistic determinants of MBNL activity. Nucleic Acids Res. 44, 10326–10342 (2016). (PMID: 277335045137450)
Lorson, C. L., Hahnen, E., Androphy, E. J. & Wirth, B. A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. Proc. Natl Acad. Sci. USA 96, 6307–6311 (1999). (PMID: 1033958310.1073/pnas.96.11.630726877)
Cywoniuk, P., Taylor, K., Sznajder, J. & Sobczak, K. Hybrid splicing minigene and antisense oligonucleotides as efficient tools to determine functional protein/RNA interactions. Sci. Rep. 7, 17587 (2017). (PMID: 29242583573056810.1038/s41598-017-17816-x)
Rovozzo, R. et al. CGG repeats in the 5′UTR of FMR1 RNA regulate translation of other RNAs localized in the same RNA granules. PLoS ONE 11, e0168204 (2016).
Garcia-Arocena, D. et al. Fibroblast phenotype in male carriers of FMR1 premutation alleles. Hum. Mol. Genet. 19, 299–312 (2010).
Bolte, S. & Cordelières, F. P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006). (PMID: 10.1111/j.1365-2818.2006.01706.x17210054)
Hukema, R. K. et al. Induced expression of expanded CGG RNA causes mitochondrial dysfunction in vivo. Cell Cycle 13, 2600–2608 (2014). (PMID: 25486200461466910.4161/15384101.2014.943112)
Buijsen, R. A. M. et al. FMRpolyG-positive inclusions in CNS and non-CNS organs of a fragile X premutation carrier with fragile X-associated tremor/ataxia syndrome. Acta Neuropathol. Commun. 2, 1–5 (2014). (PMID: 10.1186/s40478-014-0162-2)
Jiang, H., Lei, R., Ding, S.-W. & Zhu, S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinforma. 15, 182 (2014). (PMID: 10.1186/1471-2105-15-182)
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014). (PMID: 24695404410359010.1093/bioinformatics/btu170)
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015). (PMID: 25751142465581710.1038/nmeth.3317)
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013). (PMID: 10.1093/bioinformatics/bts63523104886)
Okonechnikov, K., Conesa, A. & García-Alcalde, F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 32, 292–294 (2016). (PMID: 26428292)
Li, B. & Dewey, C. N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011). (PMID: 21816040316356510.1186/1471-2105-12-323)
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Ritchie, M. E. et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015). (PMID: 25605792440251010.1093/nar/gkv007)
Law, C. W. et al. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research 5, 1408 (2016). (PMID: 10.12688/f1000research.9005.1)
Substance Nomenclature:: 0 (Fmr1 protein, mouse)
0 (MicroRNAs)
0 (Nuclear Proteins)
0 (Oligonucleotides, Antisense)
139135-51-6 (Fragile X Mental Retardation Protein)
SCR Disease Name:: Fragile X Tremor Ataxia Syndrome
Entry Date(s):: Date Created: 20210225 Date Completed: 20210303 Latest Revision: 20230129
Update Code:: 20240105
PubMed Central ID:: PMC7904788
DOI:: 10.1038/s41467-021-21021-w
PMID:: 33627639
: Czasopismo naukowe

Full Text Finder

Fragile X-associated tremor/ataxia syndrome (FXTAS) is an incurable neurodegenerative disorder caused by expansion of CGG repeats in the FMR1 5'UTR. The RNA containing expanded CGG repeats (rCGG exp ) causes cell damage by interaction with complementary DNA, forming R-loop structures, sequestration of nuclear proteins involved in RNA metabolism and initiation of translation of polyglycine-containing protein (FMRpolyG), which forms nuclear insoluble inclusions. Here we show the therapeutic potential of short antisense oligonucleotide steric blockers (ASOs) targeting directly the rCGG exp . In nuclei of FXTAS cells ASOs affect R-loop formation and correct miRNA biogenesis and alternative splicing, indicating that nuclear proteins are released from toxic sequestration. In cytoplasm, ASOs significantly decrease the biosynthesis and accumulation of FMRpolyG. Delivery of ASO into a brain of FXTAS mouse model reduces formation of inclusions, improves motor behavior and corrects gene expression profile with marginal signs of toxicity after a few weeks from a treatment.

Informacja