L5 Genetics Genome damage and repair

Overview

This lecture covers gene-environment interaction at the level of the genome: what damages DNA, how much damage happens, and how cells repair it. It works through three sections: (A) radiation, (B) chemical mutagens from diet and environment, and (C) DNA damage checkpoints and the four major repair pathways, with the inherited diseases that arise when each pathway fails. Two framing ideas run through it: most DNA variation is inherited and most of it has no pathological consequence, and mutagens damage DNA constantly but most damage is either repaired or the cell undergoes apoptosis. Objectives are to describe the types of radiation and chemical mutagens that raise mutation rates, to outline strategies for reducing mutagenesis and cancer through reduced exposure, diet and lifestyle, and to outline the four major repair mechanisms with examples of genetic diseases in which they are dysfunctional. It links to the Genetics lectures on mechanisms and types of mutations, to the Cancer module (carcinogens, genome instability and mutation as an enabling characteristic of cancer) and to Metabolism (free radicals and antioxidants).

Baseline human genetic variation

• The genome has about 20,000 protein-coding genes, roughly 1% of the genome, and possibly more noncoding RNA genes.
• Variation within an individual influences traits, which can be a good thing, and may affect disease risk.
• Inherited variation (most variation): about 10,000 non-synonymous variants across 5,000 genes, of which 50 to 100 are associated with disease (usually common variants, each with a small effect); 25,000 to 50,000 rare variants in genes; many are Variants of Uncertain Significance (VUS).
• De novo variation (not inherited from parents): about 75 variations, of which only 1 to 5 are non-synonymous, including 3 to 7 Copy Number Variants (CNV) of around 500 kb of DNA.
• During cell division, DNA replication errors accumulate and may contribute to somatic cell mutations and cancer, but most of these variations have no pathological consequence.

Replication errors and the per-division mutation rate

• Errors in DNA replication occur at roughly 1 in $10^7$.
• DNA polymerase proofreading plus other repair reduces this to 1 in $10^{10}$.
• With a genome of $2\times (3\times 10^9)$ base pairs, this gives about 1 new mutation per genome per cell division.
• When and where the mutation arises matters: most new mutations are unlikely to have an effect, and most are in somatic cells so are not transmitted.

Mutational hot spots

• Some genomic locations are more prone to mutation because of genomic context, particularly CpG or CG-rich regions where C can be methylated.
• Mechanism: methylated C (meC) is mutated to T, and the mismatched G then becomes an A after repair.
• Disease-related hotspot example: achondroplasia, FGFR3 c.1138G>A transition.
• The rate is higher in male spermatogenesis because there are more cell divisions.
• New-mutation rates for hot-spot disease loci:
  • Achondroplasia, FGFR3 (fibroblast growth factor receptor 3): $1.4\times 10^{-5}$
  • Aniridia, PAX6 (Pax6): $2.9$ to $5\times 10^{-6}$
  • Duchenne muscular dystrophy, DMD (dystrophin): $3.5$ to $10.5\times 10^{-5}$
  • Haemophilia A, F8 (factor VIII): $3.2$ to $5.7\times 10^{-5}$
  • Haemophilia B, F9 (factor IX): $2$ to $3\times 10^{-6}$
  • Neurofibromatosis type 1, NF1 (neurofibromin): $4$ to $10\times 10^{-5}$
  • Polycystic kidney disease type 1, PKD1 (polycystin): $6.5$ to $12\times 10^{-5}$
  • Retinoblastoma, RB1 (Rb1): $5$ to $12\times 10^{-6}$

Mutagens: the general picture

• Mutagens are environmental agents that cause mutations, in two groups: A, radiation; B, chemicals.
• $10^4$ to $10^6$ nucleotides are damaged per cell per day.
• Different agents cause different types of damage: nucleotide damage versus strand break.
• Three possible results: repair (within hours), cell death, or failure to repair leading to mutation.
• Free radicals are a common intermediate: UV light, smoking, ionising radiation and air pollution converge on DNA damage via free radicals, as do metabolism/mitochondria and inflammation/white blood cells.

A. Radiation: types and how it reaches DNA

• Electromagnetic radiation: X-rays and gamma rays, with high penetration of tissues.
• High energy particles: alpha and beta particles, with limited penetration, so the major risk is following ingestion. In tissue, alpha is stopped near the surface, beta penetrates further, and gamma passes through.
• Direct action: a photon strikes the DNA helix directly.
• Indirect action: a photon interacts with water or oxygen to generate radicals which then act on DNA. Water radiolysis yields e${}_{aq}^{-}$, H$\bullet$, HO$\bullet$, HO${}_2\bullet$, OH${}^{-}$, H${}_3$O${}^{+}$, H${}_2$ and H${}_2$O${}_2$; oxygen “fixes” damage via $R\bullet +O_2\to R{O}_2\bullet$. Indirect action is dominant for X-rays.
• Either route produces base-pair change, single-strand breaks (SSB), double-strand breaks (DSB), and reactions with DNA and proteins.

A. Radiation: doses and exposure

• Typical New Zealand exposure is about 2.3 mSv/year (Sv = sievert), and exposure should be As Low As Reasonably Achievable (ALARA).
• Average per caput radiation dose in New Zealand, by source (E, µSv/y): natural 1800; medical 500; fallout 5; air travel 6; occupational 0.5; luminous dials less than 2.
• Examples that increase exposure, as printed on the slide: moving 35 m up a hill 10 mSv/y; moving to a brick house 100 mSv/y; medical diagnostic X-ray 500 mSv/y on average; USA average 1.5 mSv/y from CT scan; flight New York to Los Angeles 50 mSv; chest X-ray 100 mSv; CT scan 1 to 3 mSv (comparable to typical NZ); USA 6.2 mSv; Denver 13 mSv.

Warning

The transcript flags that the mSv figures for moving 35 m up a hill (10 mSv/y), a brick house (100 mSv/y), diagnostic X-ray (500 mSv/y), the NY to LA flight (50 mSv) and a chest X-ray (100 mSv) are far larger than typical real-world values and inconsistent with the ~2.3 mSv/y NZ baseline given on the same slide. They are transcribed exactly as printed; there is a possible unit error (µSv versus mSv) on the source slide.

A. Radiation: dose-response and the linear no-threshold model

• Effects on the genome are proportional to dose, described by the Linear No Threshold model (LNT): additional risk above natural/background risk rises linearly with additional dose, with most imaging and interventional procedures sitting in the low-dose region near the origin.
• The damage caused is breaks, base damage and cross-linking.
• Effects are cumulative.
• There are “permissible” doses, but the principle remains ALARA.
• Certain conditions carry a higher risk of effects. [slide does not elaborate]

Non-ionising UV radiation

• UV also causes damage, through pyrimidine dimers and through indirect effects via radicals.
• Pyrimidines (C and T) form dimers through new bonds.
• Dimers distort the structure of DNA and require repair.
• Free radicals are produced, for example OH from H${}_2$O, which can cause indirect effects on DNA.

Radon and lung cancer risk

• Radon gas is produced as uranium in soil decays, and leaks into houses from bricks and/or soil.
• It is a significant preventable risk in some countries, for example lung cancer in the USA.
• Mitigation: ventilation, and sealing gaps in basements.
• EPA estimate of US deaths per year for comparison: radon 21,000; drunk driving 17,400; falls in the home 8,000; drownings 3,900; home fires 2,800.
• Radon is the second greatest environmental risk after tobacco for smokers, and the greatest for non-smokers. The lifetime risk of lung cancer due to radon is greatest for smokers.
• Lifetime lung cancer risk by indoor radon level (Bq m${}^{-3}$) and smoking status:

Indoor radon level	Non-smoker	Ex-smoker, gave up at 30	Ex-smoker, gave up at 50	Current smoker
20	less than 1 in 200	1 in 60	1 in 18	1 in 7
200	1 in 190	1 in 48	1 in 14	1 in 5
800	1 in 100	1 in 28	1 in 8	1 in 3

• Risk rises with radon level across every smoking category, and at any given radon level risk runs non-smoker < ex-smoker who quit at 30 < ex-smoker who quit at 50 < current smoker. The slide gives these figures by quit-age without offering an explanation for the ordering.

Aside: nuclear energy accidents (not examinable)

• Chernobyl (1986), northern Ukraine: a disaster poorly handled by the Russian authorities; 134 people exposed to 800 to 16,000 mSv, of whom 28 died within 6 months; more than 5,000 deaths due to cancer, mainly thyroid, from food containing radioactive iodine.
• Fukushima (2011): a tsunami led to the accident; no deaths directly due to the reactors; initial exclusion zone 20 to 30 km (with a wider 80 km zone recommended by the US), mainly to prevent ingestion of short-lived isotopes; no measurable effect on morbidity is likely.
• Coal for comparison: deaths due to coal mining reduced to 245 in China and 10 in the USA in 2022, plus many additional deaths (millions) due to pollution and the effect on climate.

B. Chemical mutagens: sources and testing

• Chemical mutagens come from food and the environment. Some act through DNA damage, for example folate deficiency.
• The Ames test detects mutagens as mutation induced in bacteria exposed to the chemical: high counts of reverse mutations on special bacterial strains reveal mutagenicity, and extracts from barbequed meats show mutagenic properties in this assay.
• Mutagenic activity of beef patties increases with both frying temperature and frying time: over 0 to 10 minutes, activity at 230 °C is highest (reaching about 1,100 revertants per gram of fried beef), 190 °C is moderate (about 250), and 150 °C is lowest and near flat.
• Related epidemiology: well-done red meat has been linked to aggressive prostate cancer.

B. Chemical mutagens: the four classes

1. Base analogues, for example bromouracil and aminopurine, causing transitions (A<>G, T<>C) in the DNA sequence.
2. Base pairing agents, for example nitrous acid, causing point mutations.
3. Intercalating agents, for example proflavin, causing frameshifts.
4. Other alterations in DNA structure, for example psoralens causing crosslinks, and peroxides causing DNA breaks.

These classes trigger different repair pathways in the cell. The slide poses the question of when such mutations could be useful. [slide does not elaborate]

Epidemiology, diet and lifestyle as cancer risk factors

• Epidemiology is now commonly used for risk identification. The World Cancer Research Fund reports are the reference source: the Third Expert Report, “Diet, Nutrition, Physical Activity and Cancer: a Global Perspective”, and the fourth report (April 2025), “Dietary and lifestyle patterns for cancer prevention: evidence and recommendations from CUP Global”, which focuses on breast and colorectal cancer, builds on the prior reports, and works in terms of Diet and Lifestyle Patterns (DLP).
• Some of these dietary factors relate to genome instability and mutation, for example processed food, while others relate to other hallmarks of cancer.

Interactive Cancer Risk Matrix

• The matrix plots factors by strength of evidence, and can be viewed per cancer or per risk factor. It shows both increased and decreased risk.
• Evidence bands for decreasing risk: convincing decrease, probable decrease, limited-suggestive decrease, and substantial effect on risk unlikely. Bands for increasing risk: limited-suggestive increase, probable increase, convincing increase.
• Risk-decreasing factors: physical activity, walking, wholegrains, non-starchy vegetables and fruit, lactation, dairy products, foods containing carotenoids, foods containing dietary fibre, foods containing isoflavones, fish, tea.
• Risk-increasing factors: adult body fatness, dairy products (in some contexts), red meat, processed meat, alcoholic drinks, refined grains, fast foods, sedentary behaviour and screen time, “Western-type” diet, high-dose beta-carotene supplements, arsenic in drinking water, sugar-sweetened drinks, adult height, low blood selenium and vitamin E.
• Note that dairy products appear on both sides of the matrix: among the risk-decreasing bubbles, and also among the risk-increasing bubbles qualified as “in some contexts”.

The 10 cancer prevention recommendations

Limit consumption of red and processed meat; limit consumption of sugar-sweetened drinks; limit alcohol consumption; do not use supplements for cancer prevention; for mothers, breastfeed your baby if you can; after a cancer diagnosis, follow the recommendations if you can; be a healthy weight; be physically active; eat a diet rich in wholegrains, vegetables, fruit and beans; limit consumption of “fast foods” and other processed foods high in fat, starches or sugars. Not smoking or avoiding tobacco, and avoiding excess sun, are also important, and following the recommendations is likely to reduce intakes of salt, saturated fats and trans fats.

Strength of evidence versus size of risk

These are different things. The evidence that processed meat causes cancer is as strong as the evidence for tobacco, but the risk from tobacco is much higher: tobacco causes 72% of lung cancers and 15% of all cancers, whereas processed meat causes 13% of bowel cancers and 1.5% of all cancers. In the UK, about 54,300 cases per year are preventable by not smoking, versus about 5,400 by cutting down on processed meat.

Mechanisms linking diet, nutrition, physical activity and height to genome instability

Details are not examinable, but the point is that there is some understanding of mechanism and pathophysiology, and that these exposures lead to genome instability. The exposure, systemic impact, cell-signalling route and consequence run as follows.

• Greater body fatness: hyperinsulinaemia via mTOR/PI3K/AKT/MAPK gives reduced apoptosis, increased proliferation and genome instability; increased oestradiol via MAPK/ERK/PI3K gives increased proliferation in ER-positive tissues and genome instability; inflammation via STAT3/NF-$\kappa$B gives reduced apoptosis, increased cell division, altered macrophage function and genome instability; also WNT and P53, affecting cellular energetics.
• Lower fruit and vegetable intake: folate deficiency causes DNA uracil misincorporation and genome instability; low dietary fibre intake gives low butyrate, with reduced apoptosis and increased proliferation; low levels of carotenoids and vitamins A, C and E give oxidative stress and inflammation, with increased inflammation, genomic instability, reduced apoptosis and increased proliferation.
• Greater intake of red and processed meat: elevated exposure to nitrites and endogenous N-nitroso compound formation causes DNA adduct formation, then mutations in p53, KRAS and similar genes, giving reduced apoptosis, increased proliferation and genomic instability; oxidative stress and inflammation give increased inflammation and genomic instability.
• Greater intake of dairy foods: higher IGF-I via mTOR/PI3K/AKT/MAPK gives reduced apoptosis and increased proliferation.
• Greater alcohol intake: elevated acetaldehyde causes oxidative stress and lipid peroxidation, with increased inflammation and genomic instability; increased oestradiol via MAPK/ERK/PI3K increases proliferation in ER-positive tissues; inflammation via STAT3/NF-$\kappa$B gives reduced apoptosis, increased cell division and altered macrophage function; folate deficiency and interference with 1-carbon metabolism cause DNA uracil misincorporation and genome instability.
• Greater physical activity (the protective counterpart): reduction in insulin via mTOR/PI3K/AKT/MAPK gives increased apoptosis, reduced proliferation and less genome instability; reduction in oestradiol and testosterone via MAPK/ERK/PI3K gives reduced proliferation in ER-positive tissues and reduced genome instability; reduced long-term inflammation and improved immune function act via STAT3/NF-$\kappa$B with reduced genome instability; also WNT and P53, affecting cellular energetics.
• Greater height: higher IGF-I via mTOR/PI3K/AKT/MAPK gives reduced apoptosis and increased proliferation.

C. DNA damage checkpoints, and why repair failure causes cancer

• Cells with DNA damage should arrest in the cell cycle and then go into apoptosis (programmed cell death).
• TP53/p53 is a gatekeeper, the guardian of the genome, and part of the critical DNA damage sensor at cell cycle checkpoints.
• Genome instability and mutation is an enabling characteristic of cancer. Two hallmarks of cancer cells are that they resist cell death and evade growth suppressors, for example through mutations in TP53 or RB that would otherwise arrest the cell cycle.
• Most damage is repaired, so DNA repair is the default outcome rather than mutation.

The four major repair pathways: damaging agent to lesion to pathway

Damaging agent	Lesion	Repair pathway
X-rays, oxygen radicals, alkylating agents, spontaneous reactions	uracil, abasic site, 8-oxoguanine, single-strand break	Base excision repair (BER)
UV light, polycyclic aromatic hydrocarbons	(6-4)PP, bulky adduct, CPD	Nucleotide excision repair (NER)
X-rays, anti-tumour agents (cis-Pt, MMC)	interstrand cross-link, double-strand break	Recombinational repair (HR, EJ)
Replication errors	A-G mismatch, T-C mismatch, insertion, deletion	Mismatch repair (MMR)

How the repair pathways differ

Different damage requires different repair pathways, and the pathways differ in:

• the number of proteins and steps required;
• the length of DNA excised;
• whether they use a template (the other strand) or another copy;
• when in the cell cycle the pathway is active.

Approximate number of genes involved: BER 40; NER 37; MMR 26; NHEJ 10; HR 20. Note that a double-strand-break lesion can be handled by either NHEJ or HR.

Examples of relevant genes mutated in human cancer: BER, MYH; NER, XPA, XPC, ERCC4; MMR, MLH1, PMS1, EXO1; NHEJ, Lig IV; HR, NBS1, MRE11, BRCA1.

Diseases associated with errors in repair

Variants in repair genes increase disease risk, and hereditary genetic diseases associated with mutations in repair genes include familial cancers.

• BER, base excision repair: MYH, colorectal cancer.
• NER, nucleotide excision repair of TT dimers: XP genes, Xeroderma pigmentosum (presenting with extensive sun-damaged, pigmented skin lesions).
• Recombinational repair and ligation: BRCA1/2 breast cancer, a germline risk, autosomal dominant (the basis of the widely publicised preventive mastectomy case in 2013); also rare growth disorders, autosomal recessive.
• Mismatch repair: MSH, MSL, colorectal cancer.

Congenital disorders related to repair genes

Growth delay and primordial dwarfism, with many subtypes, are congenital genetic disorders related to repair genes. The slide raises other complications and the question of cancer risk, and shows cohort pictograms of two groups, n=128 with a x7 multiple and n=32 with a x5 multiple, illustrating relative representation or risk multiples in a cohort. [slide does not elaborate]

Consequences of DNA damage

Three outcomes follow damage:

1. Cell cycle checkpoints (acting on the G1, S, G2 and M circuit) produce transient cell cycle arrest, allowing repair.
2. Inhibition of transcription, replication or chromosome segregation leads to apoptosis, cell death.
3. Mutations and chromosome aberrations lead to cancer, ageing and inborn disease.

Sporadic cancer and chromosomal instability

Most mutations observed in sporadic cancer are not due to mutations in the repair genes. Most of these mutations result from Chromosomal INstability (CIN), seen as multiple abnormal and rearranged chromosomes on spectral karyotyping.

Self-test

1. State roughly how many protein-coding genes the human genome contains and what proportion of the genome they represent.
2. Distinguish the amount and type of inherited variation from de novo variation in a single individual, using the figures given.
3. Explain how the raw DNA replication error rate, proofreading and genome size combine to give the number of new mutations per genome per cell division.
4. Describe the mechanism by which a CpG site becomes a mutational hot spot.
5. Predict what happens to the new-mutation rate at a CpG hot spot in male gametes compared with female gametes, and explain why.
6. State the mutation rate for FGFR3 in achondroplasia and name the specific transition involved.
7. List the three possible outcomes for a damaged nucleotide, and state how many nucleotides are damaged per cell per day.
8. Distinguish electromagnetic radiation from high energy particle radiation in terms of tissue penetration and the circumstances in which each poses the major risk.
9. Describe the difference between direct and indirect action of radiation on DNA, and state which dominates for X-rays.
10. List the types of DNA lesion produced by radiation acting through either route.
11. State the typical annual New Zealand radiation exposure and the four largest contributing sources with their doses.
12. Explain what the linear no-threshold model asserts and what practical principle follows from it.
13. Describe how UV radiation damages DNA by both of the mechanisms given.
14. Explain where radon comes from, how it enters houses, and two measures that reduce exposure.
15. Using the radon risk table, state the lifetime lung cancer risk at 800 Bq m${}^{-3}$ for a non-smoker, an ex-smoker who quit at 50, and a current smoker.
16. Explain how the Ames test detects a chemical mutagen, and describe how frying temperature and time affect the mutagenic activity of beef patties.
17. List the four classes of chemical mutagen with an example agent and the type of sequence change each produces.
18. Explain the difference between strength of evidence and size of risk, using the tobacco versus processed meat comparison with figures.
19. Explain why dairy products are an unusual entry on the cancer risk matrix, and give the mechanism the lecture offers for greater dairy intake.
20. Describe the proposed mechanistic chain linking greater intake of red and processed meat to genomic instability.
21. Describe the mechanism by which folate deficiency causes genome instability, and name two exposures through which it arises.
22. Match each of the following lesions to its repair pathway: 8-oxoguanine; a CPD following UV exposure; an interstrand cross-link from cis-Pt; a T-C mismatch from a replication error.
23. List four ways in which the repair pathways differ from one another.
24. List the four major repair pathways with a genetic disease or cancer predisposition caused by their dysfunction.
25. Describe the role of TP53 in the response to DNA damage, and predict the consequence for a cell in which TP53 is mutated.
26. Explain why most mutations in sporadic cancer are not attributable to repair gene mutations, and state what they are attributed to instead.
27. Integrative: trace the route from a well-done barbequed steak eaten regularly through to a cancer-causing mutation, naming the damage, the repair pathway that would normally handle it, and the consequences if repair fails.

Answers

Reveal answers

1. About 20,000 protein-coding genes, roughly 1% of the genome, with possibly more noncoding RNA genes.
2. Inherited: about 10,000 non-synonymous variants in 5,000 genes (50 to 100 disease-associated, usually common variants of small effect), plus 25,000 to 50,000 rare variants in genes, many of uncertain significance. De novo: only about 75 variations, of which 1 to 5 are non-synonymous, including 3 to 7 CNVs of around 500 kb.
3. Replication errors occur at about 1 in $10^7$; polymerase proofreading and other repair reduce this to 1 in $10^{10}$; with $2\times (3\times 10^9)$ base pairs per genome that gives about 1 new mutation per genome per cell division.
4. In CpG or CG-rich regions the C can be methylated; the methylated C is mutated to T, and the mismatched G then becomes an A after repair.
5. Higher in male spermatogenesis, because there are more cell divisions.
6. $1.4\times 10^{-5}$; the mutation is FGFR3 c.1138G>A, a transition.
7. Repair within hours, cell death, or failure to repair leading to mutation; $10^4$ to $10^6$ nucleotides are damaged per cell per day.
8. Electromagnetic radiation (X-rays, gamma rays) has high penetration of tissues; alpha and beta particles have limited penetration, so their major risk follows ingestion. Alpha is stopped near the tissue surface, beta penetrates further, gamma passes through.
9. Direct action is a photon striking the DNA helix itself; indirect action is a photon interacting with water or oxygen to generate radicals (for example e${}_{aq}^{-}$, H$\bullet$, HO$\bullet$, HO${}_2\bullet$, H${}_2$O${}_2$, and $R\bullet +O_2\to R{O}_2\bullet$ which fixes the damage) that then attack DNA. Indirect action is dominant for X-rays.
10. Base-pair change, single-strand break, double-strand break, and reaction with DNA and proteins.
11. About 2.3 mSv per year. By source, in µSv/y: natural 1800, medical 500, air travel 6, fallout 5 (with occupational 0.5 and luminous dials less than 2).
12. That additional risk rises linearly with additional dose with no threshold below which there is no risk, effects being cumulative; therefore, although there are “permissible” doses, exposure should be As Low As Reasonably Achievable (ALARA).
13. Pyrimidines (C and T) form dimers through new bonds, which distort DNA structure and require repair; and UV generates free radicals such as OH from H${}_2$O, which act indirectly on DNA.
14. Radon is produced as uranium in soil decays and leaks into houses from bricks and/or soil; ventilation and sealing gaps in basements reduce exposure.
15. Non-smoker 1 in 100; ex-smoker who gave up at 50, 1 in 8; current smoker 1 in 3.
16. Bacteria are exposed to the chemical and mutation is scored as reverse (revertant) mutations on special bacterial strains, with high counts indicating mutagenicity. Mutagenic activity of fried beef patties increases with both frying temperature and frying time: over 10 minutes, 230 °C reaches about 1,100 revertants per gram, 190 °C about 250, and 150 °C stays near flat.
17. Base analogues (bromouracil, aminopurine) causing transitions A<>G and T<>C; base pairing agents (nitrous acid) causing point mutations; intercalating agents (proflavin) causing frameshifts; other alterations in DNA structure, with psoralens causing crosslinks and peroxides causing DNA breaks.
18. Strength of evidence is how certain we are that a factor causes cancer; size of risk is how much cancer it actually causes. The evidence that processed meat causes cancer is as strong as that for tobacco, but tobacco causes 72% of lung cancers and 15% of all cancers versus 13% of bowel cancers and 1.5% of all cancers for processed meat; in the UK about 54,300 cases per year are preventable by not smoking versus about 5,400 by cutting down on processed meat.
19. Dairy products appear on both sides of the matrix, among the risk-decreasing factors and also among the risk-increasing factors where they are qualified as “in some contexts”. The mechanism given is that greater dairy intake raises IGF-I, signalling through mTOR/PI3K/AKT/MAPK to reduce apoptosis and increase proliferation.
20. Elevated exposure to nitrites and endogenous N-nitroso compound formation leads to DNA adduct formation, then mutations in genes such as p53 and KRAS, giving reduced apoptosis, increased proliferation and genomic instability; in parallel, oxidative stress and inflammation increase inflammation and genomic instability.
21. Folate deficiency causes DNA uracil misincorporation, which produces genome instability; it arises from lower fruit and vegetable intake and from greater alcohol intake through interference with 1-carbon metabolism.
22. 8-oxoguanine, base excision repair; CPD from UV, nucleotide excision repair; cis-Pt interstrand cross-link, recombinational repair (HR or EJ); T-C mismatch from replication error, mismatch repair.
23. The number of proteins and steps required; the length of DNA excised; whether a template (the other strand) or another copy is used; and when in the cell cycle the pathway is active.
24. BER, MYH, colorectal cancer; NER of TT dimers, XP genes, xeroderma pigmentosum; recombinational repair and ligation, BRCA1/2 breast cancer (autosomal dominant germline risk) and rare autosomal recessive growth disorders; mismatch repair, MSH and MSL, colorectal cancer.
25. TP53/p53 is a gatekeeper, the guardian of the genome, and part of the critical DNA damage sensor at cell cycle checkpoints, so that damaged cells arrest and then undergo apoptosis. If TP53 is mutated the cell resists cell death and evades growth suppression, so damaged cells continue through the cycle, which is an enabling step towards cancer.
26. Because most sporadic cancer mutations do not arise from defective repair genes; they result instead from Chromosomal INstability (CIN), visible as multiple abnormal and rearranged chromosomes on spectral karyotyping.
27. Frying or barbequing meat at high temperature and for longer generates mutagens (demonstrated by revertant counts in the Ames test); red and processed meat intake also raises exposure to nitrites and endogenous N-nitroso compounds, producing DNA adducts, along with oxidative stress and inflammation. Bulky adducts are handled by nucleotide excision repair, while oxidative lesions such as 8-oxoguanine are handled by base excision repair. If repair succeeds the cell arrests transiently and continues, or undergoes apoptosis if damage is too great; if repair fails, mutations in genes such as p53 and KRAS accumulate, giving reduced apoptosis, increased proliferation and genome instability, and ultimately cancer, ageing or inborn disease.