The role of nutrition in DNA replication, DNA damage prevention and DNA repair - PowerPoint Presentation

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The role of nutrition in DNA replication, DNA damage prevention and DNA repair

 

Author: Michael Fenech

Affiliation: Genome Health Foundation, North Brighton, SA, 5048, Australia

Email:

mf.ghf@outlook.com

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Introduction

Life as we know it depends entirely on the capacity of cells to utilize energy and molecules in the environment for cellular function and reproduction.

Multicellular animal organisms, including humans, acquire energy and essential nutrients from foods.

Some of these essential nutrients are required for DNA synthesis, maintenance of normal chromosome structure, repair of DNA damage caused by nutrient deficiency and/or environmental genotoxins, and for the control of gene expression by epigenetic mechanisms.

This review provides a brief outline of the role of nutrition in DNA replication, DNA damage prevention and DNA repair.

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Role of Nutrition in DNA replication, DNA damage prevention and DNA repair

At the most basic level nutrition plays an important role by providing essential precursor molecules for the

de novo

synthesis of purine and pyrimidine nucleotides that determine the genetic code in DNA [1].

Examples of precursor molecules provided by nutrition that are required for nucleotide synthesis are methyl donors such as folate, vitamin B12 and methionine.

Folate plays a critical role in the

de novo

synthesis of purines as 10-formyl tetrahydrofolate, and in the synthesis of pyrimidines as 5,10-methylenetetrahydrofolate by donating formyl and methyl moieties respectively (

Figure 1, next slide

).

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De Novo Nucleotide Synthesis

Purines

Pyrimidines

IMP

UMP

UTP

CTP

dUMP

dTTP

AMP

GMP

GTP

ATP

Ribose-5-P

10-formyl THF

5,10-meTHF

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Furthermore,

5-methyltetrahydrofolate is required for synthesis of methionine.

Methionine is essential for the synthesis of S-adenosyl methionine (SAM) which is the common methyl donor

SAM is required for the conversion of cytosine to 5-methylcytosine, the fifth nucleotide in DNA.

5-methylcytosine plays a critical role in:

structural chromosome stability, particularly in the pericentromeric region; and maintenance of DNA methylation patterns that control normal cellular gene expression and phenotype in response to environmental cues.

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Vitamin B12 is vital in DNA metabolism because it determines the availability of folate for nucleotide and methionine synthesis due to its role as an essential cofactor for the enzyme methionine synthase, which enables the transfer of a methyl group from 5-methyltetrahdrofolate to homocysteine to generate methionine and tetrahydrofolate (THF).

Tetrahydrofolate (THF) is the form of folate that can be stored in cells after

polyglutamation

.

THF is required as a precursor to generate (

i

) 10-formyl tetrahydrofolate essential for purine nucleotide (ATP, GTP) synthesis; and (ii) 5,10-methylenetetrahydrofolate, required for pyrimidine nucleotide synthesis (TTP, CTP).

When vitamin B12 and/or folate are deficient the cell cannot generate enough nucleotides to properly replicate DNA, leading to DNA replication stress, DNA strand breaks and chromosome aberrations.

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Minerals from foods, such as zinc and magnesium, are essential as cofactors for DNA polymerases required for nuclear and mitochondrial DNA synthesis .

Furthermore, it was discovered that nuclear iron-

sulphur

(Fe–S) cluster proteins conduct functions in DNA replication processes involving the enzymes POLD1, PRIM2, and DNA2.

Deficiencies in these minerals may also cause DNA replication stress and result in DNA breaks, deletions and point mutations.

The role of minerals in DNA metabolism

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Further examples of micronutrients involved in various genome stability processes and the genomic consequences of deficiency are given in Table 1 (below).

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Micronutrient/s

Role in genomic stability

Consequence of deficiency

Vitamin C, Vitamin E, antioxidant polyphenols

(e.g. caffeic acid)

 

Prevention of DNA and lipid oxidation

 Increased base-line level of DNA strand breaks, chromosome breaks, oxidative DNA lesions and lipid peroxide adducts on DNA

Folate and Vitamins B2, B6 and B12Maintenance methylation of DNA; synthesis of nucleotides including dTTP from dUMP and efficient recycling of folate.

DNA replication stress. Uracil mis-incorporation in DNA, increased chromosome breaks and DNA hypomethylation. Telomere shortening and dysfunction.

Table 1

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Niacin

(also known as Nicotinic acid and nicotinamide, which are precursors of nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP))

Required as substrate for poly[ADP-ribose] polymerases (PARP) which detect single-stranded DNA breaks (SSBs) and recruit DNA repair complexes to the site of SSBs. PARP activity is also required for telomere length maintenance

Increased level of SSBs in DNA, increased chromosome breaks and rearrangements, and sensitivity to mutagens. Impaired telomere length regulation.

 

Micronutrient/s

Role in genomic stability

Consequence of deficiency

Table 1 (continued)

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Micronutrient/s

Role in genomic stability

Consequence of deficiency

Zinc

 

Required as a co-factor for Cu/Zn superoxide dismutase, endonuclease IV, function of p53,

Fapy

glycosylase and in Zn finger proteins required for genome maintenance such as PARP in DNA damage recognition, hOGG1 for repair of oxidized guanine and

PrimPol, a primase-polymerase involved in nuclear and mitochondrial DNA replication.

DNA replication stress. Increased DNA oxidation , DNA breaks and elevated chromosome damage rate  

Iron Fe–S cluster proteins conduct important functions in DNA replication (POLD1, PRIM2, DNA2) as well as in DNA repair processes (XPD) or the regulation of telomere length (RTEL1). Also required as component of ribonucleotide reductase and mitochondrial cytochromes

Increased DNA replication stress. Reduced DNA repair capacity and increased propensity for oxidative damage to mitochondrial DNA. Impaired telomere length control.

Table 1 (continued)

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Micronutrient/s

Role in genomic stability

Consequence of deficiency

Magnesium

 

Required as co-factor for a variety of DNA polymerases, in nucleotide excision repair, base excision repair and mismatch repair. Essential for microtubule polymerization and chromosome segregation.

Reduced fidelity of DNA replication. Reduced DNA repair capacity. Chromosome segregation errors

 

Manganese

Required as a component of mitochondrial Mn superoxide dismutase.

Increased susceptibility to superoxide damage to mitochondrial DNA and reduced resistance to radiation-induced damage to nuclear DNA.

CalciumRequired as cofactor for regulation of the mitotic process

Mitotic dysfunction

SeleniumSelenoproteins involved in methionine metabolism and antioxidant metabolism (e.g. selenomethionine, glutathione peroxidase I)

Increase in DNA strand breaks, DNA oxidation and telomere shortening

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Some of the various possible mechanisms by which micronutrient deficiency could cause DNA damage, accelerate senescence and chromosomal instability are illustrated in Figure 2 (below).

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Folate/B12

Methionine

deficiency

Uracil

in DNA

Cytosine

Hypome-

thylation

OxidisedDNAbases

DNA breakmisrepair

UnrepairedDNA breaks

UnrepairedDNA adducts

Dicentric

chromosomes

Acentric Chromosomefragments

Telomeredysfunction

Centromere

dysfunction

Telomere

shortening

Telomere

end fusion

Base

Sequence

mutationor deletion

ChromosomeLoss orMalsegregation, Micronucleus

formation

mtDNA

deletion

Micronucleus

formation

Anaphase

bridge

formation

BFB

CYCLES

CHROMOSOME

INSTABILITY

PHENOTPYE

&

ABERRANT

KARYOTYPE

ACCELERATED

SENESCENCE

Deficiency

of antioxidant

Vitamins and

Cofactors for

Antioxidant

enzymes

Deficiency

in Cofactors

for DNA

Repair

enzymes

Deficiency in

Cofactors for

DNA replication

enzymes

DNA

replication

stress

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A key point is that micronutrient deficiency or excess can cause genome damage of the same order of magnitude – if not greater – than the genome damage caused by exposure to significant doses of environmental genotoxins, such as chemical carcinogens, ultra-violet radiation and ionizing radiation.

For example, chromosomal damage in cultured human lymphocytes caused by reducing folate concentration from 120 nmol/L to 12 nmol/L is equivalent to that induced by an acute exposure to 0.2

Gy

of low linear energy transfer (LET) ionizing radiation (e.g., X-rays), a dose of radiation which is approximately ten times greater than the annual allowed safety limit of exposure for the general population [8].

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Example of results from a population study

Results from a population study suggest that at least nine micronutrients affect genome stability in humans in vivo [10].

This cytogenetic epidemiological study on 190 healthy individuals (mean age 47.8 years, 46% males) was designed to determine the association between dietary intake, estimated using a food frequency questionnaire, and genome damage (chromosome breakage and/or loss) in lymphocytes, measured using the cytokinesis-block micronucleus assay.

Multivariate analysis of baseline data showed that:

the highest tertile of intake of vitamin E, retinol, folate, nicotinic acid (preformed) and calcium is associated with significant reductions in micronucleus (MN) frequency (i.e., -28%, -31%, -33%, -46%, and -49% respectively (all P < 0.005) relative to the lowest tertile of intake; and

(b) the highest tertile of intake of riboflavin, pantothenic acid and biotin was associated with significant increases in MN frequency (i.e., +36% (P =0.054), +51% (P = 0.021), and +65% (P = 0.001), respectively, relative to the lowest tertile of intake).

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Combinatorial interactive effects 

It is also important to consider the combined effects of micronutrients such as calcium or riboflavin with folate, because epidemiological evidence suggests that these dietary factors may interact in modifying the risk of cancer [8,12].

Interactive additive effects were observed, including the protective (-46%) effect of increased calcium intake, and the exacerbating (+42%) effect of higher riboflavin consumption on increased genome damage caused by low folate intake.

The results from this study illustrate the strong impact of a wide variety of micronutrients and their interactions on genome integrity, depending on level of intake. The effects of these interactions highlight the need to consider not only individual micronutrients, but also micronutrient combinations at varying dosages.

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The

Nutriome

concept

The term “

nutriome

” was introduced to define the multi-nutrient composition of diets and supplements as well as nutritional requirements for optimal health [13].

The ultimate goal is to define, for each individual, the nutriome

that matches their genome to allow optimal DNA replication, genome stability and cell function to be achieved.

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The need to consider carefully dietary pattern design

The amounts of micronutrients that appear to be protective against genome damage vary greatly between foods, and careful choice is needed to design dietary patterns optimized for genome health maintenance.

Because dietary choices vary between individuals, due to taste preferences (which may be genetically determined) or cultural or religious constraints, several options are required, and supplements may be needed to cover gaps in micronutrient requirements.

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Nutrient-dense foods and nutritional landscape of foods

Clearly, the development or identification of nutrient-dense foods and ingredients that are rich in micronutrients required for DNA replication and repair and for prevention of genome-damaging events is essential in making it feasible for individuals to achieve their daily nutrient requirements for genome integrity maintenance without intake of excess calories.

It was recently shown that bioinformatic, data-driven analysis methods, including network-based approaches, can also be applied to food and nutrition to determine the “nutritional landscape” of foods to design healthy diets that meet specific nutritional requirements [14]. A similar approach might be used to identify the minimum sets of foods required for prevention of DNA damage.

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Intervention studies for DNA damage prevention

An important development in recent years is the observation that, although DNA damage measured by both molecular and cytogenetic biomarkers tends to increase with age [8], appropriate dietary changes or supplementation by specific micronutrient combinations can attenuate the rate of increase, or even reduce the level of these biomarkers.

A limitation of most these intervention studies is that they are usually performed over brief periods of time (3-6 months) and limited to single tissues, usually blood cells and single assays of DNA damage.

A more robust approach should include:

measurements performed in easily accessible multiple tissues, such as blood lymphocytes and neutrophils, as well as buccal cells, the latter being representative of epithelial cells, which comprise the bulk of the body; anda comprehensive set of complementary biomarkers of genome damage. These should measure both chromosomal instability events – readily performed using micronucleus

cytome assays – as well as molecular lesions – such as DNA strand breaks (comet assay or γH2AX assay), DNA hypo- or hypermethylation, telomere length/dysfunction, DNA oxidation and mitochondrial DNA deletions.

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Future directions

Given this burgeoning knowledge on the association of micronutrients with well-validated DNA damage biomarkers (e.g., micronuclei, telomere length), it has become feasible to define Dietary Reference Values based on requirements to prevent the DNA damaging effects of nutritional deficiency.

The earliest evidence of DNA damage induced by malnutrition was that reported by

Armendares

et al in 1971, showing a 5.5-fold increase in chromosome aberrations in children with protein-calorie malnutrition compared to well-nourished children [15]. In contrast a 2.4-fold increase in micronuclei and 6.4-fold increase in DNA strand breaks was observed in children who are overweight and obese [16]. Thus, determining Dietary Reference Values for macronutrients for DNA damage prevention should also be an important and feasible future goal .

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Future directions

In addition, data from both in vitro models and cross-sectional in vivo data indicate the possibility of significant nutrient-genotype interactions that can modify nutritional requirements for DNA damage prevention.

Although it appears feasible to define personalized nutritional requirements for prevention of DNA damage using genotype information, the level of evidence available remains inadequate, at this stage, to be actionable based on recently published guidelines [17].

A research road map is required to determine the type and quality of data necessary to start defining personalized nutritional advice for DNA damage prevention, preferably focused, initially, on well-studied nutrients such as folate and vitamin B12.

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Conclusions

Nutrition plays an important role in providing essential molecules required for DNA synthesis and DNA repair.

The extent of DNA damage induced by nutrient deficiency and excess is as high as that induced by known chemical and physical mutagens.

For this reason and, given the known consequences of developmental defects and increased risk of degenerative diseases and accelerated aging associated with increased genomic instability, much more attention should be given to defining the Dietary Reference Values for DNA damage prevention.

The prospect of personalized nutrition for DNA damage prevention exists, but more data are required to reliably translate this concept into practice.

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