12 Molecular Basis of Genetic Disease

Question 1

For Novel DNA disease variants we need to do what with teh variant?

Answer 1

Confirm the pathogenesis experimentally

Question 2

For known mutational variants we need to do what?

Answer 2

Explore the molecular basis, which is still ongoing for many diseases

Question 3

Why are disease mechanisms important?

Answer 3

To understand disease progression.
Predict disease progression and outcomes for patients. To guide disease management for patients. To identify drug targets for therapies (primary drive).

Question 4

What could be a drug target?

Answer 4

Literally anything. The variant is in the DNA instructions, so anything downstream of that, be it transcription, translation, protein folding, trafficking, subcellular organelles, cell signalling etc. are all potential targets.

Question 5

There are three things we can look at to determine disease mechanisms. And they all play into each other. What are they?

Answer 5

Types of DNA variants. Mode of inheritance. Functional consequences (e.g. LOF, GOF, DomNeg).

Question 6

What does LOF mean?

Answer 6

Loss of function is any reduced or abolish gene function

Question 7

What are the types of Loss of Function?

Answer 7

Quantitiative loss or protein product.
Qualitative loss fo protein product.
Regulatory mutations.
Large deletions and frameshifts.

Question 8

Name a disease caused by quantitative LOF

Answer 8

Thalassaemia

Question 9

What globins are there?

Answer 9

embryonic, fetal and adult globins.

Question 10

How is thalassaemia caused?

Answer 10

Mutations in HBA or HBB leading to reduced rate or no synthesis of one fo the chains making haemoglobin

Question 11

What is a common rare disease caused by a qualitative loss of function?

Answer 11

Sickle Cell Disease

Question 12

What’s the mode of inheritance of sickle cell anaemia?

Answer 12

AR

Question 13

What causes sickle cell disease?

Answer 13

an SNV in HBB. GAG>GTG. Glutamic acid>Valine

Question 14

How does an SNV in HBB lead to sickle cell disease?

Answer 14

Mutatnt beta globin makes haemoglobin tetramer stick together because of the hydrophobic properties of valine. So long chains of haemoglobin are made. This makes RBCs rigid. Microvascular thrombosis is where these rigid RBCs block blood flow.

Question 15

Name a blood disease that is caused by a regulatory mutation

Answer 15

Haemophilia B

Question 16

What type of inheritance of haemophilia B?

Answer 16

X-linked recessive

Question 17

What is the genetic cause and mechanism of haemophilia B?

Answer 17

A mutation in the promoter of the F9 gene encoding factor IX. There are two binding sites around the TSS. (The first form is called Haemophilia B Leyden?)

Question 18

Why does haemophilia B get milder at boys puberty?

Answer 18

There are two binding sites around the TSS of the F9 gene. One is ARE, which is androgen regulated, so at puberty androgen increases F9 experssion.

Question 19

Why type of haemophilia B is lifelong?

Answer 19

Haemophilia B Brandenburg, caused by mutations in the ARE (Androgen regulated element) of F9.

Question 20

Name a common rare disease caused by a large deletion or frameshifts

Answer 20

DMD and BMD

Question 21

What gene has mutations in DMD and BMD?

Answer 21

Dystrophin

Question 22

What is the inheritance of DMD and BMD?

Answer 22

X linked recessive

Question 23

1 in how many boys are affected by DMD?

Answer 23

1 in 3000

Question 24

What are the symptoms of DMD?

Answer 24

Muscle weakness, wheelchair use. Respiratory and cardiac involvement. Death in 20’s.

Question 25

1 in how many boys are affected by BMD?

Answer 25

1 in 20,000

Question 26

Clinically, what is BMD like?

Answer 26

The same as DMD but milder, can have a normal lifespan.

Question 27

Why is DMD more severe than BMD?

Answer 27

99% of the genomic DNA of Dystrophin is intronic. Large deletions are often in the introns. But deletions that cause frameshifts are more severe and cause DMD, those that don't just shorten the protein and lead to BMD.

Question 28

What does dystrophin do and why does it not matter hugely if it's shortened?

Answer 28

It's a long chain/rod reaching from the F-actin cytoskeleton to be anchored at the cell membrane. There are many repeats in the long chain structure. Large deletions can just shorten the chain in BMD so it can still do it's job.

Question 29

What's a common disease that is caused by a gain in function, and increased activity of the protien?

Answer 29

Familial Hypercholesterolaemia

Question 30

What's the inheritance pattern of FH caused by variants in PCSK9?

Answer 30

Autosomal dominant

Question 31

What does PCSK9 normally do?

Answer 31

Helps keep a homeostasis of cholesterol metabolism by surpressing LDL-R being recycled to the cell surface, so it get degraded instead.

Question 32

What are symptoms of FH?

Answer 32

High levels of LDL cholesterol, early atherosclerosis, xanthomas (cholesterol deposits on the skin).

Question 33

What normally happens to LDL in the body?

Answer 33

LDL gets degraded in the lysosome, and LDL-R that was bound to is it recycled back to the cell surface.

Question 34

Why do PCSK9 mutations lead to FH?

Answer 34

When there is too much PCSK9 activity, LDL-R is never recycled back to the surface, so LDL ends up in high amounts in the blood.

Question 35

What are some FH treatments?

Answer 35

PCSK9 inhibitors, mAbs, or siRNA.

Question 36

What is a dominant negative mechanism?

Answer 36

Where a mutant protein product disrupts the function adversely of the normal product in a heterozygote. Considered a specific type of LOF.

Question 37

How many genes for how many types of collagen in humans?

Answer 37

30 genes for 19 types...

Question 38

What motif in collagen is important to form a triple helix structure?

Answer 38

Gly-X-Y

Question 39

Where are the majority of mutations in collagen causing a dominant negative effect and why?

Answer 39

In the Gly of the Gly-X-Y motif as this dirsupts collagen processing, so the triple helix assembly is affected if there is one mutant chain and 2 normal chains in the same complex.

Question 40

Which collagens have mutations to lead to osteogenesis imperfecta type III

Answer 40

ColA1 and ColA2

Question 41

Which collagens have mutations to lead to stickler syndrome?

Answer 41

Col2A1 or Col11A1

Question 42

Which organs are affected in stickler syndrome?

Answer 42

Eye, bone, ear, face, heart

Question 43

What are the symptoms of Col4A1/A2 cerebral small vessel disease?

Answer 43

Strokes, seizures, migraines, leukoencephalopathy, vascular dementia

Question 44

The Genome is 50% repetitive seqeunces, these can be:

Answer 44

SINEs, LINEs, LTR, DNA transposons, satellites

Question 45

Satellites can be different sizes, named:

Answer 45

Micro, mini or mega satellites

Question 46

Micro satellites are how big?

Answer 46

1-4bp repeats

Question 47

What are dynamic mutations?

Answer 47

They are caused by expansion of polymorphic DNA repeats beyond a certain copy number threshold. Trinucleotide Repeat Disorders.

Question 48

Where can trinucleotide repeats occur?

Answer 48

Anywhere in a gene. the 5'UTR, intron, ORF, or 3'UTR.

Question 49

The majority of trinucleotide repeats in ORFs are what?

Answer 49

CAG glutamine repeats

Question 50

Name 9 polyglutamine diseases

Answer 50

HD, DRPLA, SBMA, and SCA1, 2, 3, 6, 7, and 17.

Question 51

Polyglutamine disorders are usually:

Answer 51

Neurodegenerative or neuromuscular. Dominant. Caused by protein aggregation GOF.

Question 52

What are the repeat ranges for HD?

Answer 52

<26 is normal 27-35 is premutation (not stable, likely to expand) >36 is pathogenic >60 is juvenile HD.

Question 53

What are we not sure about in HD?

Answer 53

Whether the neuronal intranuclear inclusions caused by protein aggregates are the cause of the disease or just a consequence of the mutation

Question 54

What might be the cause of HD?

Answer 54

Maybe blocking of vesicle trafficking, or inhibition of proteasome function, or cell apoptosis, toxic titration of chaperones, affected mitochondrial function, or aggregates sequestering other important proteins

Question 55

What are some non-polyglutamine repeat disorders in non-coding regions? (These repeats can generally be longer)

Answer 55

Fragile X syndrome, FXTAS, FRAXE, FXPOI DM1, DM2, SCA8, SCA12

Question 56

What are the main symptoms of Fragile X?

Answer 56

ID and autism

Question 57

What is the expansion in fragile X?

Answer 57

CGG in the 5'UTR

Question 58

What are the expansion ranges for fragile x?

Answer 58

6-54 normal 55-200 premutation >200 full mutation

Question 59

What gene is affected in fragile X and what protein does it encode?

Answer 59

FMR1 encoding FMRP

Question 60

What does the CGG repeat do in Fragile X syndrome?

Answer 60

Causes DNA methylation so there is a loss of FMRP leading to impaired synapse function

Question 61

What does FMRP do normally?

Answer 61

Binds to RNA, associated with the ribosome, leading to an increased expression of synaptic proteins

Question 62

Premutation FMR1 can lead to lots of RNAs that aggregate and trap lots of proteins involved in RNA binding, protein folding and nuclear integrity. What disease does this lead to?

Answer 62

Fragile X associated tremor/ataxia syndrome. Which also has memory loss and cognitive decline.

Question 63

FXTAS is what disease mechanism then?

Answer 63

an RNA gain of function

Question 64

What is anticipation?

Answer 64

Each generation repeat lengths get longer, leading to earlier symptoms and more severe disease

Question 65

How severe are haemoglobinopathies?

Answer 65

From life threatening anaemia to symptomless

Question 66

Sometimes multiple mutations lead to a disease. What is FHC caused by?

Answer 66

Two mutations in cis in MYH7. The low penetrance missense mutation makes the pathogenic variant more severe. Similar situation in CF, two milder missense variants make a more sever phenotype.

Question 67

How can a LOF mutation in SCN5A leading to SSS be rescued?

Answer 67

By another missense mutation at R558, to enhance cell surface targeting and improve steady state activation

Question 68

Deletion of 15q11 can cause what?

Answer 68

Either Angelman's syndrome or Prader Willi syndrome based on being inherited from the mother or father