Design and application of RNA therapeutics for splice site mutations

Precursor messenger RNA splicing is one of the most fundamental and complex mechanisms in eukaryotes. Over 90% of the human genes undergo alternative splicing, which is essential for the regulation of gene expression. A dynamic RNA-protein complex called the spliceosome catalyzes splicing. The spliceosome recognizes core splice site signals, and its function is furthermore regulated by other sequence elements that can either silence or enhance splicing in a cell-specific manner. These regulatory elements are recognized by trans-acting protein factors which modulate the function of the spliceosome. However, the fact that splicing is one of the most regulated mechanisms in the cell also makes it prone to dysfunctions caused by mutations. Mis-splicing diseases account for up to 30% of the inherited genetic diseases. They can be caused by mutations in the core splice sites as well as in the regulatory elements. Mutations that disrupt the splicing mechanism may result in RNA degradation, non-functional protein products, or toxic proteins that might alter the cellular environment. The understanding of mis-splicing disease mechanisms has been subject to various studies aiming at finding the appropriate therapeutics. In parallel with the development of gene therapy, where the classical aim is to introduce the corrected gene to cure a disease, another field has emerged; antisense oligonucleotide therapeutics. These RNA-DNA-based oligonucleotides can be designed to alter gene expression as well as to manipulate the splicing mechanism. Since their emergence during 1970s, antisense oligonucleotides have been extensively studied within the mis-splicing disease field, with several clinical trials ongoing. In this thesis, in paper I, we report a novel solid-phase synthesis method with a biological proof-of-concept. This synthesis method allows the conjugation of therapeutic oligonucleotides via a cleavable disulfide linker. The developed method can be applied to target several transcripts or different parts within the same transcript by allowing delivery of equimolar amounts of therapeutics. In paper II, we explore the possibility of using splicecorrection approach for restoring the aberrant splicing of the gene BTK. Lack of BTK causes a primary immunodeficiency disease called XLA, which is a B cell developmental disorder. For the first time, we show splice-correction in B cells by modified oligonucleotide therapeutics both ex vivo and in vivo. In paper III, we aim at developing methods to rescue the core splice site mutations in BTK by using bifunctional oligonucleotide therapeutics. These oligonucleotides have the ability to recruit splice factor proteins, improving the splicing of mutated sites. We show that rescuing of core splice site mutations is possible yet it has its own challenges, which need to be taken into account in the design process. The results in this thesis have provided new therapeutics for a genetic disease, and more generally explores new methods for improving the function and delivery of oligonucleotide therapeutics. LIST OF SCIENTIFIC PAPERS This thesis is based on the following articles: I. Bestas B*, McClorey G*, Tedebark U, Moreno PM, Roberts TC, Hammond SM, Smith CI, Wood MJ, and Andaloussi SE. Design and application of bispecific splice-switching oligonucleotides. Nucleic Acid Ther. 2014;24(1):13-24. II. Bestas B*, Moreno PM*, Blomberg KE, Mohammad DK, Saleh AF, Sutlu T, Nordin JZ, Guterstam P, Gustafsson MO, Kharazi S, Piatosa B, Roberts TC, Behlke MA, Wood MJ, Gait MJ, Lundin KE, El Andaloussi S, Månsson R, Berglöf A, Wengel J, and Smith CIE. Splice-correcting oligonucleotides restore BTK function in X-linked agammaglobulinemia model. The Journal of Clinical Investigation. 2014;124(9):4067-81. III. Turunen JJ*, Bestas B*, Tedebark U, Wengel J and Smith CIE. Parameters for correcting exon-skipping splicing defects in the BTK mRNA by the use of bifunctional oligonucleotides. (Manuscript) * Equal Contribution Other publications by the author not included in this thesis: I. Zaghloul EM, Madsen AS, Moreno PM, Oprea, II, El-Andaloussi S, Bestas B, Gupta P, Pedersen EB, Lundin KE, Wengel J, and Smith CIE. Optimizing anti-gene oligonucleotide 'Zorro-LNA' for improved strand invasion into duplex DNA. Nucleic Acids Res. 2011;39(3):1142-54. II. Jezowska M, Romanowska J, Bestas B, Tedebark U, and Honcharenko M. Synthesis of biotin linkers with the activated triple bond donor [p-(N-propynoylamino)toluic acid] (PATA) for efficient biotinylation of peptides and oligonucleotides. Molecules. 2012;17(12):14174-85. III. Moreno PM, Geny S, Pabon YV, Bergquist H, Zaghloul EM, Rocha CS, Oprea, II, Bestas B, Andaloussi SE, Jorgensen PT, Pedersen EB, Lundin KE, Zain R, Wengel J, and Smith CIE. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA. Nucleic Acids Res. 2013;41(5):3257-73. IV. Honcharenko M, Zytek M, Bestas B, Moreno P, Jemielity J, Darzynkiewicz E, Smith CIE, and Strömberg R. Synthesis and evaluation of stability of m3G-CAP analogues in serum-supplemented medium and cytosolic extract. Bioorganic & Medicinal Chemistry. 2013;21(24):7921-8. V. Berglöf A, Turunen JJ, Gissberg O, Bestas B, Blomberg KE, and Smith CIE. Agammaglobulinemia: causative mutations and their implications for novel therapies. Expert Rev Clin Immunol. 2013;9(12):1205-21. VI. Bestas B, Turunen JJ, Blomberg KE, Wang Q, Månsson R, El Andaloussi S, Berglöf A, and Smith CIE. Splice-correction strategies for treatment of x-linked agammaglobulinemia. Curr Allergy Asthma Rep. 2015; 15(3): 510.