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An antisense oligonucleotide splicing modulator to treat spinal muscular atrophy

Figure adapted with permission from Rigo, F. et al. J. Cell Biol. 199, 21–25 (2012)

On 23 December 2016, the United States Food and Drug Administration (FDA) approved the antisense oligonucleotide (ASO) drug nusinersen (Spinraza) to treat spinal muscular atrophy (SMA), a fatal genetic disease that can affect children and adults. The approval was the culmination of a successful collaboration between researchers in academia and industry, with support and assistance from patient advocacy groups and regulatory agencies.

SMA is a devastating neuromuscular disease that affects 1 in 10,000 people and is caused by mutations in the gene survival of motor neuron 1 (SMN1). Without functional SMN protein, the motor neurons in the spinal cord and brain stem degenerate, resulting in muscle weakness and atrophy. Of the infants born with SMA, 60% show symptoms before six months of age, with median life expectancy of less than two years. A paralog of SMN1 in the human genome, SMN2, encodes an identical SMN protein. However, its pre-mRNA undergoes aberrant splicing, with 90% of mature SMN2 transcripts lacking exon 7 and producing a truncated, unstable polypeptide. Some individuals with SMA carry multiple copies of SMN2 and can thus produce higher levels of full-length SMN protein, which reduces the severity and delays the onset of the disease.

The molecular basis of SMN2 exon 7 skipping was elucidated by several groups, including those of Ravendra Singh at University of Massachusetts Medical School and Adrian Krainer at the Cold Spring Harbor Laboratory, in the late 1990s to early 2000s. SMN2 contains a synonymous C‑to‑T substitution in exon 7 that weakens the binding of splicing activators, thereby reducing the efficiency of the 3ʹ splice site. In 2003, Cartegni and Krainer engineered bifunctional ASOs that operate as synthetic splicing activators: a peptide mimicking a splicing activator was covalently linked to an ASO that hybridized to exon 7. This chimeric effector was able to promote exon 7 inclusion in cell extracts. Those findings prompted C. Frank Bennett, from Isis (later Ionis) Pharmaceuticals, to contact Krainer and initiate a collaboration, as recounted by Rigo et al. in 2012.

Over the next years, the strategy to control exon 7 inclusion was optimized for use in cells and animal models. ASOs targeting a site near the 5ʹ splice site in SMN2 intron 7 could efficiently promote exon 7 inclusion without the need of an appended peptide moiety. They acted by preventing binding of the splicing repressors HNRNPA1 and HNRNPA2. In addition, chemical modifications in the backbone (phosphorothioate) and nucleotides (2ʹ‑O‑methoxyethyl, or 2ʹ‑MOE) of the ASOs improved their pharmacological properties.

With promising results in preclinical studies, the ASO nusinersen entered clinical trial phase I and II studies in 2011 and 2013–2014, respectively. A multi-centre, randomized, double-blind phase III study took place in 2014–2016 and included 121 infants up to seven months of age who had been diagnosed with SMA before they were six months old (infantile onset). Participants received the drug injected intrathecally (that is, through a lumbar puncture for delivery into the cerebrospinal fluid, to reach targets in the central nervous system). A control group was treated with a mock procedure (skin prick). An interim analysis conducted with 82 patients showed that 40% of those treated with nusinersen showed improvements in motor function milestones, such as head control, sitting, rolling, crawling, standing and walking, compared to none in the control group. These results led to early termination of the trial in August 2016, so that infants in the control group could start receiving the drug. Beneficial effects observed in another trial, with children aged 2–12 with later-onset SMA, also prompted its early termination in November 2016.

The FDA approved nusinersen only three months after the new drug application (NDA) was filed by Biogen. This occurred with fast-track designation and priority review, and without an advisory committee, as outside expertise was not deemed necessary given the lack of controversial issues, as noted in the agency’s summary report. Nusinersen was approved by the European Medicines Agency in May 2017, and it is currently available for treating SMA in more than 40 countries.

Further reading

Lefebvre, S. L. et al. Identification and characterization of a spinal muscular atrophy-determining gene. Cell 80, 155–165 (1995)

Hofmann, Y. et al. Htra2-b1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 (SMN2). Proc. Natl. Acad. Sci. USA 97, 9618–9623 (2000).

Cartegni, L. & Krainer, A. R. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat. Genet. 30, 377–394 (2002).

Cartegni, L & Krainer, A. R. Correction of disease-associated exon skipping by synthetic exon-specific activators. Nat. Struct. Biol. 10, 120–125 (2003).

Singh, N. K. et al. Splicing of a critical exon of human Survival Motor Neuron is regulated by a unique silencer element located in the last intron. Mol. Cell. Biol. 26, 1333–1346 (2006).

Hua, Y. et al. Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am. J. Hum. Genet. 82, 834–848 (2008).

Singh, N. K. et al. A short antisense oligonucleotide masking a unique intronic motif prevents skipping of a critical exon in spinal muscular atrophy. RNA Biol. 6, 341–350 (2009).

Hua, Y. et al. Peripheral SMN restoration is essential for long-term rescue of a severe SMA mouse model. Nature 478, 123–126 (2011).

Rigo, F. et al. Antisense-based therapy for the treatment of spinal muscular atrophy. J. Cell Biol. 199, 21–25 (2012).

Chiriboga, C. A. et al. Results from a phase 1 study of nurinersen (ISIS-SMNRx) in children with spinal muscular atrophy. Neurology 86, 890–897 (2016).

Wadman, M. Updated: FDA approves drug that rescues babies with fatal neurodegenerative disease. Science (2016).

Finkel, R. S. et al. Treatment of infantile-onset spinal muscular atrophy with nusinersen: a phase 2, open-label, dose-escalation study. The Lancet 388, 3017–3026 (2017).

Finkel, R. S. et al. Nusinersen versus sham control in infantile-onset spinal muscular atrophy. N. Engl. J. Med. 377, 1723–1732 (2017).

Mercuri, E. et al. Nusinersen versus sham control in later-onset spinal muscular atrophy. N. Engl. J. Med. 378, 625–635 (2018).

Bastings, E. Division Director Summary Review (FDA, 2016);

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