Pathological mechanism and antisense oligonucleotide-mediated rescue of a non-coding variant suppressing factor 9 RNA biogenesis leading to hemophilia B
Autoři:
Simon Krooss aff001; Sonja Werwitzke aff003; Johannes Kopp aff001; Alice Rovai aff002; Dirk Varnholt aff003; Amelie S. Wachs aff001; Aurelie Goyenvalle aff004; Annemieke Aarstma-Rus aff005; Michael Ott aff002; Andreas Tiede aff003; Jörg Langemeier aff001; Jens Bohne aff001
Působiště autorů:
Institute of Virology, Hannover Medical School, Hannover, Germany
aff001; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School and Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
aff002; Clinic of Hematology, Oncology and Hemostaseology, Hannover Medical School, Hannover, Germany
aff003; Université de Versailles St-Quentin en Yvelines, INSERM U1179, France
aff004; Leiden University Medical Center, Leiden, Netherlands
aff005; Pediatric Intensive Care Unit, Children’s Hospital Bielefeld, Germany
aff006
Vyšlo v časopise:
Pathological mechanism and antisense oligonucleotide-mediated rescue of a non-coding variant suppressing factor 9 RNA biogenesis leading to hemophilia B. PLoS Genet 16(4): e32767. doi:10.1371/journal.pgen.1008690
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008690
Souhrn
Loss-of-function mutations in the human coagulation factor 9 (F9) gene lead to hemophilia B. Here, we dissected the consequences and the pathomechanism of a non-coding mutation (c.2545A>G) in the F9 3’ untranslated region. Using wild type and mutant factor IX (FIX) minigenes we revealed that the mutation leads to reduced F9 mRNA and FIX protein levels and to lower coagulation activity of cell culture supernatants. The phenotype could not be compensated by increased transcription. The pathomechanism comprises the de novo creation of a binding site for the spliceosomal component U1snRNP, which is able to suppress the nearby F9 poly(A) site. This second, splicing-independent function of U1snRNP was discovered previously and blockade of U1snRNP restored mutant F9 mRNA expression. In addition, we explored the vice versa approach and masked the mutation by antisense oligonucleotides resulting in significantly increased F9 mRNA expression and coagulation activity. This treatment may transform the moderate/severe hemophilia B into a mild or subclinical form in the patients. This antisense based strategy is applicable to other mutations in untranslated regions creating deleterious binding sites for cellular proteins.
Klíčová slova:
HeLa cells – CHO cells – Introns – Messenger RNA – Northern blot – Sequence motif analysis – Transfection – Antisense RNA
Zdroje
1. Manning KS, Cooper TA. The roles of RNA processing in translating genotype to phenotype. Nat Rev Mol Cell Biol. 2017;18(2):102–14. doi: 10.1038/nrm.2016.139 27847391; PubMed Central PMCID: PMC5544131.
2. Boyle EA, Li YI, Pritchard JK. An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell. 2017;169(7):1177–86. doi: 10.1016/j.cell.2017.05.038 28622505; PubMed Central PMCID: PMC5536862.
3. Anson DS, Choo KH, Rees DJ, Giannelli F, Gould K, Huddleston JA, et al. The gene structure of human anti-haemophilic factor IX. EMBO J. 1984;3(5):1053–60. 6329734; PubMed Central PMCID: PMC557470.
4. Mannucci PM, Tuddenham EG. The hemophilias—from royal genes to gene therapy. N Engl J Med. 2001;344(23):1773–9. doi: 10.1056/NEJM200106073442307 11396445.
5. Rallapalli PM, Kemball-Cook G, Tuddenham EG, Gomez K, Perkins SJ. An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of hemophilia B. J Thromb Haemost. 2013;11(7):1329–40. doi: 10.1111/jth.12276 23617593.
6. Vielhaber E, Jacobson DP, Ketterling RP, Liu JZ, Sommer SS. A mutation in the 3' untranslated region of the factor IX gene in four families with hemophilia B. Human molecular genetics. 1993;2(8):1309–10. doi: 10.1093/hmg/2.8.1309 8401514.
7. Chen SH, Schoof JM, Weinmann AF, Thompson AR. Heteroduplex screening for molecular defects in factor IX genes from haemophilia B families. British journal of haematology. 1995;89(2):409–12. doi: 10.1111/j.1365-2141.1995.tb03319.x 7873393.
8. Awidi A, Alhattab D, Bsoul N, Magablah A, Mefleh R, Dweiri M, et al. FIX mutation spectrum in haemophilia B patients from Jordan: identification of three novel mutations. Haemophilia: the official journal of the World Federation of Hemophilia. 2011;17(1):162–3. doi: 10.1111/j.1365-2516.2010.02365.x 20695909.
9. Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell. 2009;136(4):701–18. doi: 10.1016/j.cell.2009.02.009 19239890.
10. Roca X, Sachidanandam R, Krainer AR. Determinants of the inherent strength of human 5' splice sites. Rna. 2005;11(5):683–98. doi: 10.1261/rna.2040605 15840817.
11. Berg MG, Singh LN, Younis I, Liu Q, Pinto AM, Kaida D, et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell. 2012;150(1):53–64. Epub 2012/07/10. S0092-8674(12)00650-2 [pii] doi: 10.1016/j.cell.2012.05.029 22770214; PubMed Central PMCID: PMC3412174.
12. Langemeier J, Schrom EM, Rabner A, Radtke M, Zychlinski D, Saborowski A, et al. A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression. EMBO J. 2012;31(20):4035–44. Epub 2012/09/13. doi: 10.1038/emboj.2012.252 emboj2012252 [pii]. 22968171; PubMed Central PMCID: PMC3474926.
13. Kurosaki T, Maquat LE. Nonsense-mediated mRNA decay in humans at a glance. J Cell Sci. 2016;129(3):461–7. doi: 10.1242/jcs.181008 26787741; PubMed Central PMCID: PMC4760306.
14. Langemeier J, Radtke M, Bohne J. U1 snRNP-mediated poly(A) site suppression: Beneficial and deleterious for mRNA fate. RNA Biol. 2013;10(2). Epub 2013/01/18. 23314 [pii]. doi: 10.4161/rna.23314 23324605.
15. Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. Journal of computational biology: a journal of computational molecular cell biology. 2004;11(2–3):377–94. doi: 10.1089/1066527041410418 15285897.
16. Kaida D, Berg MG, Younis I, Kasim M, Singh LN, Wan L, et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature. 2010;468:664–8. doi: 10.1038/nature09479 20881964.
17. Shi J, Deng Y, Huang S, Huang C, Wang J, Xiang AP, et al. Suboptimal RNA-RNA interaction limits U1 snRNP inhibition of canonical mRNA 3' processing. RNA Biol. 2019;16(10):1448–60. doi: 10.1080/15476286.2019.1636596 31242075; PubMed Central PMCID: PMC6779394.
18. Chiu AC, Suzuki HI, Wu X, Mahat DB, Kriz AJ, Sharp PA. Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP. Mol Cell. 2018;69(4):648–63 e7. doi: 10.1016/j.molcel.2018.01.006 29398447.
19. Kurachi S, Hitomi Y, Furukawa M, Kurachi K. Role of intron I in expression of the human factor IX gene. J Biol Chem. 1995;270(10):5276–81. doi: 10.1074/jbc.270.10.5276 7890639.
20. Simioni P, Tormene D, Tognin G, Gavasso S, Bulato C, Iacobelli NP, et al. X-linked thrombophilia with a mutant factor IX (factor IX Padua). N Engl J Med. 2009;361(17):1671–5. doi: 10.1056/NEJMoa0904377 19846852.
21. Hansson K, Stenflo J. Post-translational modifications in proteins involved in blood coagulation. J Thromb Haemost. 2005;3(12):2633–48. doi: 10.1111/j.1538-7836.2005.01478.x 16129023.
22. Enjolras N, Perot E, Le Quellec S, Indalecio A, Girard J, Negrier C, et al. In vivo efficacy of human recombinant factor IX produced by the human hepatoma cell line HuH-7. Haemophilia: the official journal of the World Federation of Hemophilia. 2015;21(4):e317–21. doi: 10.1111/hae.12688 25981983.
23. Rodriguez MH, Enjolras N, Plantier JL, Rea M, Leboeuf M, Uzan G, et al. Expression of coagulation factor IX in a haematopoietic cell line. Thrombosis and haemostasis. 2002;87(3):366–73. 11916066.
24. Belvini D, Salviato R, Radossi P, Pierobon F, Mori P, Castaldo G, et al. Molecular genotyping of the Italian cohort of patients with hemophilia B. Haematologica. 2005;90(5):635–42. 15921378.
25. Dani C, Piechaczyk M, Audigier Y, El Sabouty S, Cathala G, Marty L, et al. Characterization of the transcription products of glyceraldehyde 3-phosphate-dehydrogenase gene in HeLa cells. Eur J Biochem. 1984;145(2):299–304. doi: 10.1111/j.1432-1033.1984.tb08552.x 6499844.
26. So BR, Di C, Cai Z, Venters CC, Guo J, Oh JM, et al. A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells. Mol Cell. 2019;76(4):590–9 e4. doi: 10.1016/j.molcel.2019.08.007 31522989; PubMed Central PMCID: PMC6874754.
27. Paz I, Kosti I, Ares M Jr., Cline M, Mandel-Gutfreund Y. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 2014;42(Web Server issue):W361–7. doi: 10.1093/nar/gku406 24829458; PubMed Central PMCID: PMC4086114.
28. Machado-Neto JA, Lazarini M, Favaro P, Franchi GC Jr., Nowill AE, Saad ST, et al. ANKHD1, a novel component of the Hippo signaling pathway, promotes YAP1 activation and cell cycle progression in prostate cancer cells. Exp Cell Res. 2014;324(2):137–45. doi: 10.1016/j.yexcr.2014.04.004 24726915
29. Zhou Z, Jiang H, Tu K, Yu W, Zhang J, Hu Z, et al. ANKHD1 is required for SMYD3 to promote tumor metastasis in hepatocellular carcinoma. Journal of experimental & clinical cancer research: CR. 2019;38(1):18. doi: 10.1186/s13046-018-1011-0 30646949; PubMed Central PMCID: PMC6332640.
30. Dowdy SF. Overcoming cellular barriers for RNA therapeutics. Nat Biotechnol. 2017;35(3):222–9. doi: 10.1038/nbt.3802 28244992.
31. van Ommen GJ, van Deutekom J, Aartsma-Rus A. The therapeutic potential of antisense-mediated exon skipping. Curr Opin Mol Ther. 2008;10(2):140–9. 18386226.
32. Voit T, Topaloglu H, Straub V, Muntoni F, Deconinck N, Campion G, et al. Safety and efficacy of drisapersen for the treatment of Duchenne muscular dystrophy (DEMAND II): an exploratory, randomised, placebo-controlled phase 2 study. The Lancet Neurology. 2014;13(10):987–96. doi: 10.1016/S1474-4422(14)70195-4 25209738.
33. Liu S, Asparuhova M, Brondani V, Ziekau I, Klimkait T, Schumperli D. Inhibition of HIV-1 multiplication by antisense U7 snRNAs and siRNAs targeting cyclophilin A. Nucleic Acids Res. 2004;32(12):3752–9. doi: 10.1093/nar/gkh715 15254276; PubMed Central PMCID: PMC484190.
34. Dominski Z, Marzluff WF. Formation of the 3' end of histone mRNA: getting closer to the end. Gene. 2007;396(2):373–90. doi: 10.1016/j.gene.2007.04.021 17531405.
35. Goyenvalle A, Babbs A, Wright J, Wilkins V, Powell D, Garcia L, et al. Rescue of severely affected dystrophin/utrophin-deficient mice through scAAV-U7snRNA-mediated exon skipping. Human molecular genetics. 2012;21(11):2559–71. doi: 10.1093/hmg/dds082 22388933; PubMed Central PMCID: PMC3349427.
36. Imbert M, Dias-Florencio G, Goyenvalle A. Viral Vector-Mediated Antisense Therapy for Genetic Diseases. Genes. 2017;8(2). doi: 10.3390/genes8020051 28134780; PubMed Central PMCID: PMC5333040.
37. Oh JM, Di C, Venters CC, Guo J, Arai C, So BR, et al. U1 snRNP telescripting regulates a size-function-stratified human genome. Nat Struct Mol Biol. 2017;24(11):993–9. doi: 10.1038/nsmb.3473 28967884; PubMed Central PMCID: PMC5685549.
38. Jirka SM, Tanganyika-de Winter CL, Boertje-van der Meulen JW, van Putten M, Hiller M, Vermue R, et al. Evaluation of 2'-Deoxy-2'-fluoro Antisense Oligonucleotides for Exon Skipping in Duchenne Muscular Dystrophy. Molecular therapy Nucleic acids. 2015;4:e265. doi: 10.1038/mtna.2015.39 26623937; PubMed Central PMCID: PMC5014533.
39. Chi X, Gatti P, Papoian T. Safety of antisense oligonucleotide and siRNA-based therapeutics. Drug discovery today. 2017;22(5):823–33. doi: 10.1016/j.drudis.2017.01.013 28159625.
40. Eckenfelder A, Tordo J, Babbs A, Davies KE, Goyenvalle A, Danos O. The Cellular Processing Capacity Limits the Amounts of Chimeric U7 snRNA Available for Antisense Delivery. Molecular therapy Nucleic acids. 2012;1:e31. doi: 10.1038/mtna.2012.24 23344083; PubMed Central PMCID: PMC3390224.
41. Nathwani AC, Reiss UM, Tuddenham EG, Rosales C, Chowdary P, McIntosh J, et al. Long-term safety and efficacy of factor IX gene therapy in hemophilia B. N Engl J Med. 2014;371(21):1994–2004. doi: 10.1056/NEJMoa1407309 25409372; PubMed Central PMCID: PMC4278802.
42. Goyenvalle A, Wright J, Babbs A, Wilkins V, Garcia L, Davies KE. Engineering multiple U7snRNA constructs to induce single and multiexon-skipping for Duchenne muscular dystrophy. Mol Ther. 2012;20(6):1212–21. Epub 2012/02/23. doi: 10.1038/mt.2012.26 mt201226 [pii]. 22354379; PubMed Central PMCID: PMC3369406.
43. Weidenfeld I, Gossen M, Low R, Kentner D, Berger S, Gorlich D, et al. Inducible expression of coding and inhibitory RNAs from retargetable genomic loci. Nucleic Acids Res. 2009;37(7):e50. doi: 10.1093/nar/gkp108 19264799; PubMed Central PMCID: PMC2673444.
44. Wong N, Wang X. miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 2015;43(Database issue):D146–52. doi: 10.1093/nar/gku1104 25378301; PubMed Central PMCID: PMC4383922.
45. Reese MG, Eeckman FH, Kulp D, Haussler D. Improved splice site detection in Genie. Journal of computational biology: a journal of computational molecular cell biology. 1997;4(3):311–23. doi: 10.1089/cmb.1997.4.311 9278062.
Článek vyšel v časopise
PLOS Genetics
2020 Číslo 4
- Může hubnutí souviset s vyšším rizikem nádorových onemocnění?
- Raději si zajděte na oční! Jak souvisí citlivost zraku s rozvojem demence?
- Co způsobuje pooperační infekce? Na vině může být i naše vlastní mikrobiota
- Čeká nás průlom v diagnostice karcinomu pankreatu?
- Polibek, který mi „vzal nohy“ aneb vzácný výskyt EBV u 70leté ženy – kazuistika
Nejčtenější v tomto čísle
- Analysis of genes within the schizophrenia-linked 22q11.2 deletion identifies interaction of night owl/LZTR1 and NF1 in GABAergic sleep control
- High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements
- Molecular genetics of maternally-controlled cell divisions
- Spastin mutations impair coordination between lipid droplet dispersion and reticulum