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Antisense oligonucleotide-mediated alternative splicing strategies to treat the type-1 fibrillinopathies

Cale, Jessica M. (2021) Antisense oligonucleotide-mediated alternative splicing strategies to treat the type-1 fibrillinopathies. PhD thesis, Murdoch University.

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The type-1 fibrillinopathies are a family of connective tissue disorders of which Marfan syndrome is the most common, affecting between 2-3 in 10,000 individuals. Marfan syndrome is a multisystem disorder characterised by ocular, skeletal and cardiovascular abnormalities and can be caused by any one of over 2800 unique mutations reported across the fibrillin-1 (FBN1) gene. FBN1 encodes the large extracellular glycoprotein, fibrillin-1; the fibrillin-1 monomers aggregate to form the backbone of microfibrils. Fibrillin-1 has both structural and regulatory roles, including the regulation of transforming growth factor-beta. This regulation is critical in maintaining extracellular matrix stability and dysregulation of this function is one of the keystones of the Marfan syndrome pathogenesis. Mutations in FBN1 can result in reduced fibrillin-1 expression, loss-of-function or the production of two different fibrillin-1 proteins that are unable to interact to form functional microfibrils. The result in all three cases is a lack of functional microfibrils and destabilisation of the extracellular matrix. The current standard of care relies heavily on surgical intervention and lifelong use of medications to slow disease progression, thus the need for new therapeutic options that target the cause of disease.

This thesis focused on developing a suite of short synthetic nucleic acid sequences, known as antisense oligonucleotides, to selectively manipulate FBN1 pre-mRNA splicing. We hypothesised that the removal of an amenable mutation-associated exon would result in one of the following scenarios. For missense mutations, removing the mutation-associated exon from affected and unaffected transcripts would eliminate the aberrant sequence and restore homogeneity between fibrillin-1 monomers. For splice-site and in-frame deletion mutations, excluding the mutation-associated exon from the remaining healthy transcripts would restore the domain periodicity and monomer homogeneity. Lastly, for mutations resulting in a premature termination codon, excluding the mutation-associated exon from the affected transcripts would restore the reading frame, rescuing transcript functionality. The mutation-associated exon would also need to be removed from the unaffected transcripts to maintain monomer homogeneity. For each of these scenarios, we hypothesised that the internally truncated proteins produced would be capable of forming functional microfibrils, thereby reducing the severity or slowing the progression of the Marfan syndrome phenotype.

As an initial proof-of-concept for this project, antisense oligonucleotide sequences targeting FBN1 exon 52 were assessed. A promising sequence induced dose-dependent exon skipping in healthy control cells allowing us to observe the formation of healthy fibrillin-1 fibres with 0% exon skipping, loss of extruded fibrillin-1 fibres with 50% skipping; mimicking the disease-like state, and subsequent re-appearance of extracellular fibrillin-1 fibres with greater than 80% skipping indicating that the internally truncated fibrillin-1 monomers are capable of forming aggregates. Similarly, we demonstrate that FBN1 exons 47 and 59 can be efficiently excluded, and sufficient skipping can result in fibrillin-1 fibre formation. However, many of the FBN1 exons targeted were not as readily excised from the mature mRNA.

Comparison of three antisense oligonucleotide chemistries revealed the promising efficacy of the newer thiophosphoramidate morpholino oligomer chemistry. Similar to the commonly used phosphorodiamidate morpholino oligomer, the thiophosphoramidate morpholino oligomer sequences resulted in efficient and consistent FBN1 exon 52 skipping. Both chemistries also had little effect on paraspeckle protein distribution, an indicator of toxicity, unlike the third, 2′OMe-PS, chemistry that caused gross paraspeckle protein disruption. Therefore, thiophosphoramidate morpholino oligomer should be included in the repertoire of chemistries routinely used in studies developing antisense therapeutics.

Lastly, while we demonstrate that >80% exon skipping can lead to fibrillin-1 microfibril-like formations in vitro, we could not confirm the functionality of these fibres nor the effect of exon skipping on the Marfan syndrome phenotype. Nevertheless, this study demonstrates proof-of-concept and lays a solid foundation for further development of antisense oligonucleotides to treat the type-1 fibrillinopathies.

Item Type: Thesis (PhD)
Murdoch Affiliation(s): Centre for Molecular Medicine and Innovative Therapeutics (CMMIT)
Health Futures Institute
United Nations SDGs: Goal 3: Good Health and Well-Being
Supervisor(s): Wilton, Steve and Fletcher, Sue
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