Spinal Muscular Atrophy Flashcards
What is the function of the SMN1 gene?
It encodes survival motor neuron protein (SMN) which is a critical part of the complex that interacts with small nuclear ribonucleoproteins (snRNPs)
What are snRNPs and what do they do?
Small Nuclear Ribonucleoproteins
U1, U2, U4, U5, U6
They are a key part of the spliceosome, which carries out splicing
What type of mutation in the SMN1 gene is usually the cause of Spinal Muscular Atrophy?
Deletion in exon 7 or exon 8
How is SMA inherited?
It is autosomal recessive, as it is a loss of function mutation
What is the prevalence of SMA?
Affects 1 in every 6,000-10,000
It is the second most common autosomal recessive disorder, behind Cystic Fibrosis
What is the pathophysiology behind SMA?
No/less abundance of Survival Motor Neuron (SMN) protein leads to atrophy of the alpha-motor neurons in the anterior horn of the spinal cord
Muscles innervated by these neurons receive no stimulation, so undergo atrophy
SMA has phenotypic heterogeneity: what does this mean?
The phenotype of the disease varies depending on the specific genetic make-up
In the case of SMA, the severity depends on the copy number of the SMN2 gene
What is the function of the SMN2 gene?
The SMN2 gene is almost identical to SMN1, except it undergoes alternative splicing to miss out exon 7, so only codes a functional SMN protein 10-20% of the time
Features of Type 1 SMA
Most severe form of SMA
Signs and symptoms appear shortly after birth
Patients do not survive past 2 years of age
Patients have 1 or 2 copies of the SMN2 gene
Features of Type 2 SMA
Develops around age 1
Can shorten life expectancy, but most survive into adulthood
Patients usually have 3 copies of the SMN2 gene
Features of Type 3 SMA
May not appear until late childhood or adulthood
Life expectancy not affected
Patients usually have 3 copies of the SMN2 gene
Features of Type 4 SMA
The least severe form of SMA Symptoms do not occur until adult life Symptoms are much milder Life expectancy not affected Patients have 4 copies of the SMN2 gene
What are the general symptoms of SMA?
Problems swallowing
Increased incidence of respiratory illnesses due to difficulty coughing
Weak arms and legs
Shaking
How is SMA diagnosed (after birth)?
Multiplex Ligation-Dependent Probe Amplification Assay (MLPA)
Blood sample taken, look for common deletions in exon 7 and exon 8
How to interpret the results of MLPA?
Peaks form for all the exons of a gene on a graph
Full peak = both copies of gene functioning normally
Reduced height peak = one copy of the gene has the exons deleted
No peaks = both copies of the gene have the exons deleted
3 possible methods by which fetal DNA can be obtained for prenatal testing for SMA
Amniocentesis
Chorionic Villus sampling
Cell-free fetal DNA
What happens during amniocentesis?
Cells taken from amniotic fluid by a needle inserted through the abdominal wall
Chance of miscarriage or damaging placenta
What happens during chorionic villus sampling?
Cells taken from the placenta by a needle inserted through the abdominal wall or cervix
Chance of miscarriage
Only offered if there is family history of a severe genetic disorder
What happens during cffDNA testing?
Cell free fetal DNA circulates in the mothers blood
Much less invasive but has a low PPV
How is fetal DNA analysed for SMA?
Sequenced using NGS
OR
Amplified using qPCR with primers for SMN1 exon 7. Compare the fluorescence over cycles against a control gene
What is constitutive splicing?
Splicing of sites that are always used (as opposed to alternative splicing)
What percentage of genes undergo alternative splicing?
95%
What are the 3 important binding sites in an intron and what sequence do they contain?
5’ Splice site: GU
Branch point: A
3’ Splice site: AG
Which snRNP binds to which splice site?
U1 binds 5’ splice site
U2 bind branch point
The tri-snRNP (U4, U5, U6) binds the region in between
What is hnRNA?
Heterogenous nuclear RNA
The term for the mRNA transcript before it has undergo splicing
Also know as pre-mRNA
RNA splicing is a form of genomic plasticity. What does this mean?
The ability of the genome to change and adapt
How is alternative splicing regulated?
Splicing regulatory proteins and Exon/Intron Enhancers/Silencers
What are the splicing regulatory proteins?
Serine Arginine rich (SR) proteins which bind to enhancers
Heterogenous nuclear ribonucleoparticles (hnRNPs) which bind to silencers
What determines whether or not a splice site is used?
The balance of enhancer and silencer proteins
Where are enhancer/silencer elements located?
They can be located far away from the splice site, but are brought into proximity by looped 3D structures of RNA molecules
