Gene Mutations and Pathogenesis

Gene Mutations

Mutation Types

Several types of mutations can occur, including:

• Missense mutations: These result in a change in the amino acid sequence.
• Insertions and deletions: These involve the addition or removal of nucleotides, potentially causing frameshift mutations.
• Silent mutations: These do not alter the amino acid sequence due to the redundancy of the genetic code.
• Splice site mutations: These affect the splicing of pre-mRNA, leading to altered mRNA and protein products.
• Nonsense mutations: These introduce a premature stop codon, resulting in a truncated protein.
• Dynamic mutations: Involve the expansion of short tandem repeats within a gene.

Dynamic Mutations

Dynamic mutations occur due to the expansion of short tandem repeats. If the number of repeats exceeds a certain threshold, the sequences become unstable.
Dynamic mutations in untranslated regions (UTRs) or coding sequences can be associated with disease. Here are some examples:

Huntington's Disease

• Huntington's disease is an autosomal dominant disorder caused by the expansion of CAG repeats in the HTT gene, which codes for huntingtin.
• The repeat expansion can be detected using PCR and polyacrylamide gel electrophoresis.
• The mutant huntingtin protein contains an expanded poly-glutamine tract, leading to protein aggregation.
• These aggregates interfere with neurotransmitter secretion and can induce apoptosis.

Correlation of CAG Length and Age of Motor Onset

The age of onset of motor symptoms in Huntington's disease is inversely correlated with the length of the CAG repeat. Longer CAG repeats are associated with earlier onset.

Somatic Expansion over Time

CAG repeats within the genome tend to expand over time, potentially influencing the progression of Huntington's disease.

Anticipation

Anticipation is a phenomenon where a disease manifests earlier or increases in severity in successive generations.
Fragile X syndrome is an example of a disease exhibiting anticipation.
It is suspected when a mild disorder is observed in a parent or relative after diagnosis in the child (index patient).
This can be linked to clinical diagnosis and expanded $(CGG)_n$ repeats in the 5' UTR of FMR1. Borderline genotypes in parents might be identified retrospectively and offspring might be affected.

Pathogenesis

Gain/Loss of Function

Mutations produce cellular responses by altering protein function, potentially leading to either a loss of function or a gain of function.

• Loss of function mutations: These are mainly recessive because a single gene copy that generates active products is generally sufficient.
• Haploinsufficiency: In some cases, the product amount from one gene copy isn't sufficient. Mutations causing haploinsufficiency are usually dominant.

Gene/Protein Dosage

Disease manifestation depends on the amount (dosage) of normal gene product.

• In dominant mutations, 50% of the normal amount of active product can lead to disease.
• In recessive mutations, less than 50% of the normal amount of protein can lead to disease.

PAX3 Loss of Function

Truncating mutations in PAX3 indicate a loss-of-function mechanism.
Waardenburg syndrome exhibits allelic heterogeneity, where multiple different mutations in the same gene can cause the same phenotype. This is typical for loss-of-function mutations.
Truncating mutations or point mutations at various positions in PAX3 can cause Waardenburg syndrome type 1.

Waardenburg syndrome also shows gene association with facial features in normal populations.

Gain of Function

• Monogenic diseases can be caused by gain of function, although loss of function is more common.
• Gain of function is a common mechanism in tumor cells.
• Gain of function can be associated with:
  • Gross overexpression of certain genes.
  • Acquisition of a novel function and production of chimeric genes.
  • Modification of cellular signaling responses.

Examples of Gain of Function Mutations

Activation of Oncogenes by Chromosomal Rearrangements

In chronic myeloid leukemia (CML), a translocation between chromosomes 9 and 22 results in the Philadelphia chromosome (Ph1).
Ph1 contains a fusion gene, BCR-ABL1, which encodes a constitutively active tyrosine kinase.

Genotype to Phenotype Correlation

Protein Aggregation

The sickle cell anemia mutation, a missense mutation in HBB (c.20A>T), leads to the exchange p.Glu6Val.
Changes in the physical surface properties result in protein aggregation.

Protein Folding: Collagens

Mutations in genes for connective tissue proteins such as collagens can explain normal protein assembly and disease mechanisms caused by protein misfolding.

Type I Collagen Biosynthesis

Collagen type I consists of two α1-chains and one α2-chain.
These chains must align to initiate the folding of procollagen type I into a triple helix.
Post-translational modifications and collagen trimming occur after this folding process.
Mutations in collagen genes or genes coding for modifying proteins can lead to osteogenesis imperfecta.

Protein Dimers

Normal Condition

Normal active products (protein dimers) are produced from two alleles.

Heterozygous Mutant (Mild Disease)

If only products from one allele are expressed in a heterozygous mutant, it can possibly lead to a mild disease. Protein misfolding can cause mild disease by loss of interaction.
Single protein chains are degraded.

Heterozygous Mutant (Severe Disease)

If a heterozygous mutant has active product from one allele and inactive product from the second allele, it can possibly lead to a severe disease. Protein misfolding can cause severe disease by dominant negative activity. The protein dimer is stable but inactive.

Genotype/Phenotype Correlation: Osteogenesis Imperfecta (OI)

OI is caused by different collagen mutations.
The genotype/phenotype correlation for OI is based on the trimerization of collagens.

• Dominant negative mutations.
• C-terminal mutation, severe disease.
• N-terminal mutation, moderate disease.
• Heterozygous null mutation, mild disease.

Mutations in N-terminal domains lead to milder diseases than mutations in central and C-terminal domains.
This is because mutations in the central and C-terminal domains are dominant negative. The disease severity depends on the position of the mutation in the protein.
Mutations are mostly tolerated for assembly in the N-terminal, while central and C-terminal mutations are dominant negative within the triple helix domain.

Genotype/Phenotype Correlation in OI

OI can be caused by mutations in COL1A1 and COL1A2 (and several other genes).
The severity of the disease depends on the type and position of the mutation.
Dominant negative mutations that impair the coordinated assembly of collagen fibers explain the strong genotype/phenotype correlation.

Genetic Diseases

Genetic diseases can be associated with mutations in a single gene (monogenic), variants in several genes (polygenic), or a mix of genetic variants and exposure to certain environmental factors (multifactorial).

• Monogenic (Mendelian)
• Polygenic
• Multifactorial

Polygenic Inheritance

In polygenic inheritance, individuals whose liability is above a threshold are affected.
Combinations of different variants contribute to the risk. If relatives are closer, there is familial recurrence risk.
The distance between the liability in the population and the increased liability in relatives of affected persons indicates the strength of the genetic component for the disease.

Multifactorial Diseases

Multifactorial diseases involve combinations of genetic and environmental factors. These can be detrimental or beneficial factors.

Summary

• Mutations can cause a loss or a gain of protein function.
• Mutant proteins can cause a disease because of aggregation or misfolding.
• Osteogenesis imperfecta caused by collagen mutations is an example for dominant negative mutations and demonstrates a genotype/phenotype correlation.
• Changes in gene or protein dosage are involved in many diseases.
• Most diseases are caused by the combined effects of multiple genes and environmental factors.