Alternative Splicing and Human Disease

Abstract

Almost all human protein coding genes undergo alternative splicing, and an increasing number of diseases is associated with the selection of ‘wrong’ splice sites. Such missplicing can be caused by mutations in DNA (deoxyribonucleic acid), mutations in splicing factors and changes in the concentration of splicing factors. The effect of these mutations can be predicted using bioinformatic tools, but any prediction needs to be validated experimentally. Advances in understanding the molecular mechanisms regulating splice site selection resulted in the development of treatment options using RNA (ribonucleic acid) oligonucleotides as well as small molecules that inhibit or alter alternative splicing. Oligonucleotides for treatment of spinal muscular atrophy and Duchenne muscular dystrophy have advanced into clinical trials and serve as a paradigm for the treatment of other diseases caused by missplicing.

Key Concepts

  • Mechanism of alternative splice site selection.
  • Changes in alternative splicing caused by mutations that result in disease.
  • Mutations leading to a change in alternative splicing.
  • Analysis of mutations that change splice site selection.
  • Splicing‐changing oligonucleotides to treat diseases.
  • Small molecules as splicing inhibitors or modulators to treat diseases.

Keywords: alternative splicing; spinal muscular atrophy; Duchenne muscular dystrophy; genomic mutation; cancer; drug

Figure 1. Schematic overview over disease mechanisms. (a) Overview of exon recognition. A cassette exon flanked by two constitutive exon is shown. Exons are indicated as boxes and introns as lines. The exon contains enhancers (E) and silencers (S) that bind to proteins, SR proteins and hnRNPs. In general, SR proteins promote exon inclusion by stabilising the binding of U2 and U1 snRNPs to the branch point (bp) and 5′ splice site (5′), respectively, 3′: 3′ splice site. hnRNPs have in general the opposite effect. (b) General disease mechanism. Mutations on the DNA are indicated with a star. (i) Mutations in exon enhancers prevent SR proteins from binding, which inhibits exon usage; (ii) mutations in 5′ splice sites prevent U1 snRNP binding; (iii) intronic mutations generate cryptic exons; (iv) stable RNAs generated through repeat extensions sequester splicing proteins.
Figure 2. Therapeutic approaches. (a) Spinal muscular atrophy. A point mutation (star) in the SMN exon 7 generates a splicing silencer, leading to skipping, owing to the presence of other silencers, including an intronic silencer. An oligonucleotide binding to the silencer neutralises its action, leading to exon inclusion. (b) Duchenne muscular dystrophy. Exons a–d of the dystrophin gene are schematically indicated. The reading frame of the exons is indicated by the fitting shapes. Thus, a genomic deletion of exon b results in a reading frame change and truncated protein when a is spliced to c. An antisense oligonucleotide causing the skipping of exon c restores the reading frame between a and d.
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Further Reading

Chabot B and Shkreta L (2016) Defective control of pre‐messenger RNA splicing in human disease. The Journal of Cell Biology 212 (1): 13–27. PMID: 26728853.

Daguenet E, Dujardin G and Valcarcel J (2015) The pathogenicity of splicing defects: mechanistic insights into pre‐mRNA processing inform novel therapeutic approaches. EMBO Reports 16 (12): 1640–1655. PMID: 26566663.

Singh RK and Cooper TA (2012) Pre‐mRNA splicing in disease and therapeutics. Trends in Molecular Medicine 18 (8): 472–482. PMID: 22819011.

Stamm S, Smith C and Lührmann R (2012) Alternative Pre‐mRNA Splicing: Theory and Applications. Weinheim: Wiley‐Blackwell.

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Stamm, Stefan(Jan 2017) Alternative Splicing and Human Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021435.pub2]