DNA damage and mutations part 2

Outline how UV light damages DNA

UV-C and UV-B induce the formation of pyrimidine dimers

Pyrimidine dimers block transcription and DNA replication

If not repaired, can result in T and C mutations

What are pyrimidine dimers?

Adjacent pyrimidine bases (c or t) on the SAME strand are covalently linked

Thymine dimers are the most common

if not repaired will result in c—> t mutations

How does radiation damage DNA?

Ionising radiation such as x-rays, radon, nuclear fallout generated ROS

Creates localised damage, with multiple hits including double strand breaks

How do intercalating agents work?

Damage DNA by causing base insertions or deletions (indels) resulting in frameshift mutations

What are base adducts?

Mutagens that add chemical groups to DNA bases

Ex: alkylating agents, add alkyl groups to bases such as EMS or nitrosamines

What are aflatoxins?

Base adducts that are produced by moulds that grow on foodstuffs

Lead to base loss and formation of an apurinic site

Aflatoxin and hepatitis exposure acts synergistically to increase risk of liver cancer

What are polyaromatic hydrocarbons?

Base adducts such as benzopyrene and polychlorinated biphenyls that are found in soot, exhaust gas, cigarette smoke and charred food

How does metabolism relate to toxicity?

Many chemicals only become toxic once metabolised

Metabolism of most foreign compounds leads to production of a less toxic substance which is excreted.

In a small number of cases, metabolism creates a more toxic compound

What are mutational signatures?

Exposure to different environmental agents can cause different types of mutations:

Specific base changes

Indels

Double mutations

Most agents produce complex signatures, whether a residue is mutated can depend on the neighbouring sequences

What are the mutational signatures of lung and skin cancer?

Lung cancer- PAHs (polycyclic aromatic hydrocarbond) predominantly cause G to T transversions

Malignant melanoma- if pyrimidine dimers are not repaired, they result in C to T and CC to TT transitions

What is the mutational signature of 1,2-DMH?

1,2-dimethylhydrazine is a DNA methylating agent

Causes C to T mutations and C deletions

C to T mutations are often flanked by a T or run of Ts on the 3’ side, eg ACT, GCT, CCT, TCT

C deletions tend to be flanked by Ts on the 3’ side

How can DNA damage be reversed?

Repair of pyrimidine dimers generated by UV light

• Photolyases use the energy of light to split pyrimidine dimers- photoreactivation

Methyltransferases can remove methyl groups from methylated bases

No new synthesis occurs

Outline base excision repair

1. damaged base excised by a DNA glycosylase

2. AP site repaired by AP endonuclease system

3. In eukaryotes DNAP beta replaces DNA phosphodiesterase

Basically: sugar-phosphate backbone (gums) kept, just base (tooth) cleaved (removed)

Outline the role of DNA glycosylase in BER

• DNA glycolases cleave the N-glycosidic bond, generating an AP site

• Different DNA glycosylases used to remove different damaged bases- DNA glycosylases specific to bases

• Uracil DNA glycosylase removes uracils generated by the oxidative deamination of cytosine

Outline the role of AP endonuclease in BER

• AP endonuclease cleaves DNA at the site of the damage

• Bacterial DNA: phosphodiesterase removes sugar-phosphate residue

• Eukaryote: DNA polymerase Beta removes sugar-phosphate residue

• DNA polymerase fills the gap and the nick in the DNA sealed by DNA ligase

When is BER used?

When the AP site or lesion has a specific DNA glycosylase

What is global nucleotide excision repair?

XPE and XPC (proteins) constantly scan the whole of the genome to detect and repair damage

Outline transcription coupled nucleotide excision repair

RNA polymerase stops at the damage during transcription and recruits CSA and CSB to repair it

How are double strand breaks repaired?

Non-homologous end joining

Homologous recombination

Outline xeroderma pigmentosum

XP: due to mutations within the NER system

extreme skin and eye sensitivity to sunlight, dry skin, areas of hypo and hyperpigmentation, predisposition to cancer, neurological defects, accelerated ageing

Outline cockayne syndrome

Due to defect in transcription-coupled repair pathway of NER

developmental+neurological disorder, inability to repair damage at stalled transcription sites leads to apoptosis

results in premature ageing, short stature, deafness and intellectual disability

no increased incidence of cancer- cell doesn’t get repaired, it dies

What happens if DNA damage is not repaired?

mutations- needed for evolution, but can lead to disease

somatic cells can obtain hundreds of mutations during the lifetime of an individual

What are driver mutations?

DNA sequence changes that cause cells to become cancerous

Affect cell-cycle control

Found within the 500 cancer genes within the human genome

Number of driver mutations varies between cancers (5-10s)

What are passenger mutations?

Do not confer growth advantage, were acquired before or after the cell became a cancer cell

What are germline mutations

• Individuals inherit 60-90 de novo mutations that arose in the germline of their parents

  • Paternal to maternal ratio 3:1

• Impact of de novo mutations on a disease depends on the number of genes linked to a particular disease- very low probability for single gene disorders, relatively common for diseases that are linked to many genes

How do de novo mutations relate to psychiatric disorders?

Mutations in over 100 genes linked to psychiatric disorders and developmental disorders