Spinal Muscular Atrophy

Spinal Muscular Atrophy (SMA) describes several different diseases that are characterised by degeneration of alpha motoneurons in the brainstem and spinal cord. Autosomal recessive SMA associated with chromosome 5 is molecularly the best understood. It is characterised by progressive paralysis caused by the loss of alpha-motor neurons in the spinal cord.

The incidence is 1:6,000 to 1:10,000 for live births and the carrier frequency is 1 in 40. SMA is the second most common autosomal recessive disorder and is the most frequent genetic cause of infantile death.

Molecular cause and consequences

SMA is caused by the loss of the SMN1 gene that encodes the SMN protein, which regulates snRNP assembly. Humans posses an almost identical gene, SMN2, that was generated through a recent duplication.

Although both genes are almost identical in sequence, due to a translationally silent C->T change at position 6 in exon 7, they have different splicing patterns and exon 7 is predominantly excluded in SMN2. This exon-skipping event generates a truncated, less stable and probably non-functional protein. Therefore, SMN2 cannot compensate the loss of SMN1. At least one copy of SMN2 is retained in humans with SMA, as lack of SMN2 and SMN1 is embryonic lethal.

Although, in SMA patients the SMN protein is almost completely absent from all cells, for unknown reasons, alpha motoneurons are most severely affected and die, which causes the muscular atrophy. The disease can manifest in four phenotypes (type I to IV) that differ in onset and severity. The phenotypes correlate roughly with the number of SMN2 copies in the genome, most likely because more SMN2 copies produce more SMN protein.

Gene's structure and Alternative Splicing (AS) events

View the full gene diagram and AS pattern of SMN1 on the Fast DB website.

Molecular approaches to diagnoses and therapy

Since stimulation of SMN2 exon7 usage would increase SMN protein levels and potentially cure the disease, work has concentrated on understanding the regulation of exon 7. Mice have only one SMN gene where exon 7 is constitutively spliced. A homozygous knock out of this gene is lethal. To study the splicing regulation of the human gene in mice, transgenic animals that contain the human gene were developed.

Typical for the combinatorial control of exon regulation, multiple factors determine the regulation, including a suboptimal polypyrimidine tract, a central tra2-beta1-dependent enhancer and the sequence around the C->T change at position 6. Recent large scale mutagenesis studies indicate that a composite regulatory exonic element termed EXINCT (extended inhibitory context) is responsible for the regulation of exon 7 inclusion.

The exon skipping event is caused by the C->T change at position 6 and currently two models are proposed for its mechanism. In one model, the Base Exchange destroys and exonic enhancer that normally binds to SF2/ASF and in the other model, the mutation creates an hnRNPA1 binding site that acts as a silencer. Both models can explain the predominant skipping of exon 7. Inclusion of exon 7 depends on a central tra2-beta1 enhancer sequence. Tra2-beta1 is an SR-related protein. Its activity is regulated by dephosphorylation mediated by protein phosphatase 1 and not surprisingly, exon 7 usage depends on cellular PP1 activity.

Bifunctional oligonucleotide approach has been recently tested for treating SMA. Bifunctional oligomers use a 2’-Ome-modified binding domain and an effector domain, which is composed of RNA that contains binding sites for known splicing trans-acting factors. It acts as an ESE and promotes inclusion of the SMN2 exon 7 in fibroblasts from SMA patients leading to partial restoration of the SMN function.

EURASNET contacts:

Stefan Stamm: stefan@stamms-lab.net
Daniel Schümperli: daniel.schuemperli@izb.unibe.ch
Ian Eperon: eci@le.ac.uk

Based on ‘Alternative splicing and disease’ Tazi, J., Bakkour, N., Stamm, S. Biochimica et Biophysica Acta. 2009 Jan;1792(1):14-26. Epub 2008 Oct 17.