Humans have two copies of Survival of Motor Neuron (SMN) gene, SMN1 and SMN2. Loss of SMN1 leads to spinal muscular atrophy (SMA), a debilitating disease of infants and children. SMN2 fails to compensate for the loss of SMN1 due to skipping of exon 7 resulting in the synthesis of a truncated protein, which is unstable. Presence of SMN2 in most SMA patients provides a rare opportunity to restore SMN levels by correcting the aberrant splicing of exon 7. Using a novel method of in vivo selection, we previously reported that a weak 5'splice site (51 ss) serves as the limiting factor for exon 7 inclusion in SMN2. Based on this observation, we have recently discovered that a unique intronic inhibitory element contributes towards the weak 5'ss of exon 7. We call this element Intronic Splicing Silencer N1 (abbreviated as ISS-N1). Interestingly, ISS-N1 appears to be unique to humans. Based on our preliminary results, ISS-N1 plays an important role in pathogenesis of SMA. Most importantly, we discovered that Antisense Oligonucleotides (abbreviated as ASOs) that targeted ISS-N1 corrected aberrant splicing of SMN2 in all cell types tested including SMA patient cells. Consequently, ASO against ISS-N1 fully restored SMN levels in patient cells. Significantly, the ASO-mediated stimulatory effect was observed even at low ASO doses, suggesting that ISS-N1 is a highly accessible antisense target. The antisense effect was very specific to ISS-N1 as two or more mutations within ISS-N1 completely eliminated the ASO-mediated stimulatory effect. Based on these results we believe that we have discovered an ideal target-site for the ASO-mediated therapy of SMA. In this grant proposal, we will (1) characterize ISS-N1, its RNA structure and interacting factors in details;(2) develop efficient ASOs against ISS-N1 to correct SMN2 splicing in patient cells;and finally (3) conduct in vivo studies, using mice models of SMA to validate ASOs against ISS-N1 as the possible drug candidates. The most frequent cause of spinal muscular atrophy (SMA) is the loss of SMN1 gene accompanied by the inability of SMN2 gene to compensate due to aberrant splicing. Here, we will characterize a novel intronic element that plays a critical role in pathogenesis of SMA. In addition, we will use this element as a target for the antisense-mediated correction of aberrant splicing in SMA.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Research Project (R01)
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Cell Death in Neurodegeneration Study Section (CDIN)
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Porter, John D
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Iowa State University
Veterinary Sciences
Schools of Veterinary Medicine
United States
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Seo, Joonbae; Ottesen, Eric W; Singh, Ravindra N (2014) Antisense methods to modulate pre-mRNA splicing. Methods Mol Biol 1126:271-83
Howell, Matthew D; Singh, Natalia N; Singh, Ravindra N (2014) Advances in therapeutic development for spinal muscular atrophy. Future Med Chem 6:1081-99
Seo, Joonbae; Howell, Matthew D; Singh, Natalia N et al. (2013) Spinal muscular atrophy: an update on therapeutic progress. Biochim Biophys Acta 1832:2180-90
Sivanesan, Senthilkumar; Howell, Matthew D; Didonato, Christine J et al. (2013) Antisense oligonucleotide mediated therapy of spinal muscular atrophy. Transl Neurosci 4:
Singh, Natalia N; Lawler, Mariah N; Ottesen, Eric W et al. (2013) An intronic structure enabled by a long-distance interaction serves as a novel target for splicing correction in spinal muscular atrophy. Nucleic Acids Res 41:8144-65
Singh, Natalia N; Singh, Ravindra N (2011) Alternative splicing in spinal muscular atrophy underscores the role of an intron definition model. RNA Biol 8:600-6
Singh, Natalia N; Seo, Joonbae; Ottesen, Eric W et al. (2011) TIA1 prevents skipping of a critical exon associated with spinal muscular atrophy. Mol Cell Biol 31:935-54
Singh, Natalia N; Hollinger, Katrin; Bhattacharya, Dhruva et al. (2010) An antisense microwalk reveals critical role of an intronic position linked to a unique long-distance interaction in pre-mRNA splicing. RNA 16:1167-81
Singh, Natalia N; Shishimorova, Maria; Cao, Lu Cheng et al. (2009) A short antisense oligonucleotide masking a unique intronic motif prevents skipping of a critical exon in spinal muscular atrophy. RNA Biol 6:341-50
Papp, Laura V; Wang, Junning; Kennedy, Derek et al. (2008) Functional characterization of alternatively spliced human SECISBP2 transcript variants. Nucleic Acids Res 36:7192-206

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