Mutations and Disease - No lectures with this module, but looking at the questions, this is one of the PDF

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Summary

Genetic Diseases: Phenylketonuria: Phenylketonuria (PKU) is a germinal disease of the metabolism. It is a decrease in metabolism of phenylalanine, leading to a of said amino acid in the body. Symptoms: Intellectual disability Seizures Behavioural problems Mental disorders Musty smell Lighter skin Ba...

Description

Genetic Diseases: Phenylketonuria: Phenylketonuria (PKU) is a germinal disease of the metabolism. It is a decrease in metabolism of phenylalanine, leading to a build-up of said amino acid in the body. Symptoms: -

Intellectual disability Seizures Behavioural problems Mental disorders Musty smell Lighter skin Babies born to PKU mothers may have heart problems, small head and low birth weight

Genetics: Autosomal recessive metabolic genetic disorder, hence two PKU alleles required for an individual to express symptoms. Same inheritance as cystic fibrosis, 25% for child to be completely unaffected, 50 chance to be a carrier and 25% chance to be a sufferer. PKU is characterised by homozygous or compound heterozygous mutations in the gene for the hepatic enzyme Phenylalanine Hydroxylase (PAH) rendering it non-functional. PAH metabolises Phe to Tyr. When this activity is reduced Phe accumulates and is converted to phenylpyruvate. PAH gene is located on chromosome 12 in bands 12q22-q24.1. There’s been more than 400 diseasecausing mutations discovered in the PAH gene. Pathophysiology: In classical PKU sufferers, a diet that would be healthy for people without PKU causes abnormally high levels of Phe to accumulate in the blood, which is toxic in the brain and can cause nervous system damage. Because PAH is non-functioning in PKU sufferers, Tyr becomes a conditional essential amino acid, Tyr is necessary for the production of neurotransmitters such as epinephrine, norepinephrine and dopamine. Phe is a Large Neutral Amino Acid (LNAA). LNAAs compete for transport across the bloodbrain barrier via Large Neutral Amino Acid Transporters (LNAATs). If Phe is present in excessive amount in the blood, it saturates the LNAATs and outcompetes other LNAAs for transport across the blood-brain barrier. This is harmful as these other LNAAs are necessary for protein and neurotransmitter synthesis, hence Phe build-up hinders brain development. Diagnosis and Treatment: Most people are diagnosed soon after birth due to the regular newborn screening procedures. Usually done via a heel prick. PKU is not curable, but if diagnosed at the newborn stage, a child can grow up with normal brain development simply by managing Phe levels through a strictly controlled diet or a combination of diet and medication. People that follow the prescribed diet may have no symptoms and PKU

would only be detectable through a blood test. Optimal health ranges are between 120 and 30 Micromol/L. Tyrosine supplements can be prescribed.

Colour-Blindness: This is a visual disorder characterised by the decreased ability to see colour or determine the differences between colours. Common cause is an inherited fault in development of one or more of the three sets of colour sensing cones in the eye. It’s a sex-linked disorder as the genes responsible for the most common forms of colour blindness are located on the X chromosome and as females have 2 chromosomes, a defect in one is usually compensated for by the other. Genetics: Generally considered as an inherited genetic disease but there can be some acquired causes such as diseases and some drugs may cause colour blindness. The most commonly inherited mutations are on the X chromosome but mapping of the human genome has shown many causative mutations, originating from at least 19 different chromosomes and 56 different genes. The most common inherited forms are protanomaly and deuteranomaly. These are both known as red-green colour blindness, which is present in ~8% of males and 0.6% of females of Northern European ancestry.

Cystic Fibrosis: Cystic Fibrosis is one of the most discussed and researched genetic disorders of modern times. It’s a disorder that affects the lungs mainly but also the pancreas, liver, kidneys and intestine. Long term issues include difficulty breathing and coughing up mucus due to frequent lung infections. CF is inherited in an autosomal recessive manner meaning that it is caused by the presence of mutations in both copies of the gene for cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is involved in production of sweat, digestive fluids and mucus. When it’s not functional, secretions which are usually thin and not viscous become thick. Cause: CF is caused by a mutation in CFTR. There are many different disease causing mutations, but the most common one by far is the DeltaF508, which is the deletion of three nucleotides encoding for a phenylalanine at the 508 position. This mutation accounts for 66-70% of CF cases worldwide and 90% in the US, however, there are over 1500 mutations known to cause CF. Only one functioning copy of CFTR is needed to negate the effects of one defective allele. CFTR is found at the q31.2 locus on chromosome 7, is 230,000 bp long and creates a protein that is 1,480 amino acids long. Structurally CFTR is known as an ABC gene (ATP-Binding Casette). The product of this gene is the CFTR protein which is a chloride ion channel important in synthesising sweat, digestive juices and mucus. It contains two ATP-hydrolysing domains, which allows the protein to use energy in the form of ATP. It also contains two domains comprising of six alpha helices apiece, which allow the protein to cross the cell membrane. A regulatory binding site on the protein allows it to be activated by phosphorylation. The C-terminus of the protein is anchored to the cytoskeleton by a PDZ domain interaction.

Pathophysiology: Different mutations cause different defects in CFTR protein, sometimes giving a milder or more severe phenotype. These proteins are hence the targets for drugs that can sometimes restore their function. DeltaF508 creates a protein that mis-folds and as such is not appropriately transported to the cell membrane, resulting in its untimely degradation via the Unfolded Protein Response. Other mutations result in truncations due to premature termination of protein synthesis. Other mutations produce proteins that don’t use energy in the form of ATP normally, do not allow chloride, iodide and thiocyanate to cross the membrane appropriately, and are degraded at a faster rate than normal. Mutations may also lead to fewer copies of the CFTR protein being produced. CFTR is a protein anchored in the outer membrane of many exocrine cells all around the body as well as in the lungs. It spans the membrane and acts as a channel connecting the cytoplasm to the surrounding fluid. The channel is primarily responsible for controlling the movement of halogens from inside to the outside of the cell; however in sweat glands it facilitates the movement of chloride from the sweat duct into the cytoplasm. Most of the damage in CF is due to blockage of the narrow passages of affected organs with thickened secretions. These blockages lead to remodelling and infection in the lung, damage by accumulated digestive enzymes in the pancreas, blockage of the intestines by thick faeces etc. The widely accepted theory suggests that defective ion transport leads to dehydration in the airway epithelia, thickening mucus. In airway epithelial cells, the cilia exist in between the cell’s apical surface and mucus in a layer known as the airway surface layer. The flow of ions from the cell and into this layer is determined by channels such as CFTR. CFTR not only allows chloride ions to be drawn from the cell into the ASL, but it also regulates another channel called ENac, which allows sodium ions to leave the ASL and enter the respiratory epithelium. CFTR normally inhibits ENac, but if the CFTR is defective then sodium flows freely from the ASL and into the cell. As water follows the sodium by osmosis, the depth of ASL will be depleted and the cilia will be left in the mucus layer. As cilia cannot effectively move in this kind of thick, viscous environment, mucociliary clearance is deficient and a build-up of mucus occurs, clogging small airways. The accumulation of more viscous nutrient-rich mucus in the lungs allows bacteria to hide from the body’s immune system, causing repeat respiratory infections. Management: There are currently no known cures for CF, but there are several treatment methods currently in practice. The cornerstones of management are proactive treatment of airway infections and encouragement of good nutrition and active lifestyle. Many CF sufferers are on one or more antibiotics at all times, even when healthy, to prophylactically suppress infection. Prolonged therapy often requires hospitalisation and insertion of a more permanent IV. Inhaled therapy with antibiotics such as tobramycin is often given for months at a time to improve lung function by impeding the growth of colonised bacteria. Antibiotics can also be given orally. Research: Gene therapy has been explored as a potential cure for CF. This is where there is an attempt to restore genetic normality in the afflicted cells of the patients’ body, hence restoring the normal

production of CFTR. So far, little benefit has been seen from this kind of therapy. Most CF gene research is based around trying to place a normal copy of the CFTR gene into the affected cells. To prevent symptoms found in the lungs, only 5-10% of normal CFTR expression is needed. Multiple approaches for delivering this gene have been tested, such as liposomes and viral vectors in animal models and clinical trials. However, both were found to be inefficient treatment methods, mainly because of poor vector uptake. Small molecules are another potential treatment for CF. These molecules aim at compensating various mutations in the CFTR gene. One approach is to develop drugs that get the ribosome to overcome the stop codon of truncation mutations and synthesise a full-length CFTR protein (around 10% f CF is down to a protein truncation). These drugs target mutations such as G542X, which consists of the amino acid glycine in position 542 being replaced with a stop codon. Aminoglycoside antibiotics interfere with protein synthesis and error-correction. In some cases, they can cause the cell to overcome a premature stop codon by inserting a random amino acid, thereby allowing expression of the full-length protein. Precision Medicine Approaches: Subclasses of CF are defined according to the functional effects of specific genetic variants of CFTR. 6 subclasses are defined: - I = No functional protein (G542x) - II = Trafficking defect (DeltaF508) - III = Defective regulation (G551D) - IV = Decreased conductance (R117H) - V = Reduced synthesis (3120+1G>A) - VI = Reduced stability (Q1412x) The first drug approved for a subclass of CF was Ivacaftor, which increases the opening probability of channels on the cell surface. It was initially approved for class III CF, for which the trafficking of CFTR is fine, but the regulation is defective. The most comment variant, DeltaF508, results in the destruction of a misfolded CFTR protein (Class II). For this a combination of Lumacaftor (to enhance intracellular processing and trafficking) and Ivacaftor may be optimal. In this, Lumacaftor aids in the correct trafficking of mutant CFTR by providing a proteasomal escape. However, when the defective CFTR reaches the cell surface, it has a gating abnormality similar to G551D and hence Ivacaftor, as it does in G551D patients, aids by increasing channel opening times.

Down Syndrome: A genetic disorder also known as Trisomy 21 caused by the presence of all or part of a copy of chromosome 21. It’s associated with physical growth delays, characteristic facial features and mild to moderate intellectual disability, with an average young adult IQ being around 50, that of an 8-9 year old. Genetics:

The cause of the syndrome is the presence of 3 copies of chromosome 21, rather than the usual two. Parents of a Down syndrome individual are usually genetically normal; the presence of the third chromosome is down to chance. The possibility of having a child born with DS increases from 0.1% in 20-year old mothers to 3% in those aged 45. Most commonly, sufferers have a complete extra copy of chromosome 21 (92-95% of cases). In 1-2.5% of cases, some cells in the body are normal and others have trisomy 21, known as mosaic down syndrome. Other mechanisms by which it can occurs are Robertsonian translocation, isochromosome or ring chromosome. Trisomy 21 is caused by a failure of chromosome 21to split during egg or sperm cell development, resulting in a germinal cell with an extra copy of Chromosome 21. The extra chromosome 21 material may also be due to a Robertsonian translocation in 2-4% of cases. In this way, the long arm of chromosome 21 is attached to another chromosome, often chromosome 14. Mechanism: The extra genetic material means there is an increased expression of the 310 genes on chromosome 21. Some research suggests that there is an area on the chromosome that is specific to down syndrome that encodes genes for amyloid, superoxide dismutase and likely the EST2 protooncogene (however there has been other research that disputes these findings). Dementia occurs in DS sufferers at a much earlier stage and a much more frequent rate. Alzheimer’s that occurs is due to an excess of amyloid beta peptide produced in the brain. The gene for said protein is located on, surprise surprise, chromosome 21. Senile plaques and neurofibrillary tangles are seen in nearly all DS individuals by 35 years of age. The candidate for the dosage-sensitive gene contributing to the AD phenotype is Amyloid Precursor Protein (APP), because proteolysis of said protein produces amyloid-B, the main constituent of senile plaques. Degeneration of basal forebrain cholinergenic neurons (BFCNs) has been seen in humans with AD and in the Ts65Dn mouse. Neurons in the mouse model have a defect in retrograde transport of the neurotrophic factor Nerve Growth Factor (NGF) to the cell soma which might contribute to their degeneration. The reduction of APP from 3 to 2 copies partially rescues defective NGF retrograde transport and BFCN degeneration in the Ts65Dn mouse. In contrast, overexpression of APP alone causes defective NGF transport but not BFCN degeneration in DS, implying the involvement of other genes. Around 40-60% of DS individuals have congenital heart defects (CHDs), a major cause of the high morbidity or infant mortality associated with DS. The most common defect is the atrioventricular septal defect (AVSD), which is considered a hallmark of DS as the incidence of AVSD is 1000-fold in DS individuals compared to non-DS population.

Spinal Muscular Atrophy: SMA is a rare neuromuscular disorder characterised by a loss of motor neurons and progressive muscle wasting, often leading to early death. It’s caused by a genetic defect in SMN1 which encodes Survival of Motor Neuron (SMN), a protein widely expressed in all eukaryotic cells and funnily enough, necessary for the survival of motor neurons. Decreased levels of SMN result in the loss of function of neuronal cells in the anterior horn of the spinal cord and subsequent system-

wide muscle wasting (atrophy). SMA has 4 classifications dependent on severity, age of onset or with the highest attained milestone of motor development. SMA1: Infantile, 0-6 months, quick and unexpected onset (floppy baby syndrome). Rapid motor neuron death causes inefficiency of major organs, especially the respiratory system and pneumonia-induced respiratory failure is the most-frequent cause of death. Unless placed on mechanical ventilation, babies diagnosed with SMA1 don’t generally live past 2 years, with death occurring as early as weeks after diagnosis in most severe cases (sometimes called SMA type 0). SMA2: Intermediate, 6-18 months, affected children aren’t able to walk or stand but can maintain a sitting position. Scoliosis may also be present in these children and correction with a brace may improve respiration. Life expectancy is reduced but most survive well into adulthood. SMA3: Juvenile, >12 months, Able to walk without support at some time, but lose this ability later. Less adverse respiratory effects, life expectancy normal or near-normal. SMA4: Adullt-onset, usually manifests after the 3rd decade of life with gradual weakening of the muscles, mainly effects proximal muscles of the extremities, frequently requiring use of a wheel chair. Other complications are rare and life expectancy is unaffected. Causes: SMA is linked to SMN1 gene. Chromosome 5 has two nearly identical genes at location 5q13, a telomeric copy SMN1 and a centromeric copy SMN2. In healthy individuals, SMN1 codes the survival of motor neuron protein. The SMN2 gene however, because of variation in a single nucleotide undergoes alternative splicing, with only 10-20% of SMN2 transcripts coding a fully functional SMN protein. In SMA individuals, the SMN1 gene undergoes a mutation, due to either a deletion at exon 7 or other point mutations which frequently result in the functional conversion of SMN1 to SMN2. Reduced availability of SMN results in gradual death of motor neuron cells in the anterior horn of the spinal cord and the brain. Muscles that depend on these neurons for neural input now have decreased innervation and therefore have decreased input from the central nervous system. Decreased impulse transmission through motor neurons leads to decreased contractile activity of the denervated muscle. Consequently these muscles undergo progressive atrophy. Severity of SMA seems to be associated somewhat with how well the remaining copies of SMN2 make up for the loss of function of SMN1. This is related to the number of SMN2 gene copies present on the chromosome. Most individuals have 1-2 copies but some can have up to and above 4 copies. As you might expect SMA1 individuals have 1-2 copies, SMA2 and 3 have 3 copies usually and SMA4 has 4 or above. The correlation is not absolute as there appear to be other factors influencing.

Somatic Mutations...