Pieter J. Pretorius

Circulating DNA:its origin and fluctuation

Circulating DNA is present in the blood of all individuals, but it has been found that cancer patients and patients with a variety of other conditions have increased amounts of these circulating DNA fragments in their blood. Even though more than 30 years of research have been done on this subject, the origin of these nucleic acid molecules is still not clear. We present evidence that does not support the general notion that apoptosis or necrosis is the major source of circulating free DNA. Active release of free circulating DNA by living cells may be a plausible mechanism. Disturbance of the equilibrium between the release of DNA by living cells and the mechanisms used for clearing this DNA may play the main role in the appearance of increased amounts of circulating DNA in the blood of individuals with different ailments. Elucidating the origin and the mechanism that cells use to release free circulating DNA into the blood may enhance the diagnostic and prognostic value of these nucleic acid molecules.

Is the role of circulating DNA as a biomarker of cancer being prematurely overrated

BACKGROUND Circulating DNA is utilized widely as a genetic biomarker in a variety of pathological conditions, mainly in cancerous conditions. Quantification of circulating DNA and identifying the frequencies of a variety of mutations, microsatellite alterations and gene promoter methylation are the main foci of research on circulating DNA. CONTENT A compilation of research reports available to us were reviewed to highlight the rather great variety of methods presently used to isolate circulating DNA, the lack of uniformity in presenting and interpreting quantitative research data as well as the virtual absence of information regarding the structure and function of circulating DNA. CONCLUSIONS The information compelled us to conclude that the application of circulating DNA as an unambiguous biomarker is currently overrated. We therefore emphasize the need for elucidating the prevailing questions regarding the origin, function and significance of these nucleic acid molecules before utilizing circulating DNA as a biomarker.

DNA damage and repair detected by the comet assay in lymphocytes of African petrol attendants : a pilot study

Petrol attendants are exposed to petrol volatile organic compounds (VOCs) which may have genotoxic and carcinogenic effects. The single-cell gel electrophoresis assay (comet assay) is a method highly sensitive to DNA damage induced by environmental and occupational exposure to carcinogenic and mutagenic agents. The aim of this study was to evaluate the level of exposure of petrol attendants to petrol VOCs and also to determine their effect on DNA damage and repair in lymphocytes of African petrol attendants. The exposed group consisted of 20 subjects, randomly selected from three petrol stations. A control group of 20 unexposed subjects was also chosen and matched for age and smoking habits with the exposed group. Sorbent tubes were used to assess personal exposure of petrol attendants. The comet assay was used to investigate the basal DNA damage and repair capacity in isolated lymphocytes of petrol attendants and unexposed subjects. Blood samples were taken from the petrol attendants at the end of their 8-h working shift and also from the unexposed subjects. The petrol attendants were found to be exposed to levels of petrol VOCs lower than the South African occupational exposure limit for constituent chemicals. A significant relationship was found between the volume of petrol sold during the shift and the average concentrations of benzene, toluene and the total VOCs measured. However, relative humidity had a negative correlation with the average concentrations of benzene, toluene, xylene and the total VOCs. Significantly higher basal DNA damage was observed with the exposed group compared to the unexposed group. The period of exposure influenced the level of DNA damage and the calculated repair capacity. Smoking and age had a significant influence on the level of DNA damage. DNA repair capacity was delayed in smokers of both exposed and unexposed group.

Assessing the DNA methylation status of single cells with the comet assay.

The comet assay (single cell gel electrophoresis) is a cost-effective, sensitive, and simple technique that is traditionally used for analyzing and quantifying DNA damage in individual cells. The aim of this study was to determine whether the comet assay could be modified to detect changes in the levels of DNA methylation in single cells. We used the difference in methylation sensitivity of the isoschizomeric restriction endonucleases HpaII and MspI to demonstrate the feasibility of the comet assay to measure the global DNA methylation level of individual cells. The results were verified with the well-established cytosine extension assay. We were able to show variations in DNA methylation after treatment of cultured cells with 5-azacytidine and succinylacetone, an accumulating metabolite in human tyrosinemia type I.

A method for characterization of total circulating DNA.

Although much work has been done in the field of circulating DNA, no definitive information on sequencing data of total circulating DNA is available. Characterization of total circulating DNA by sequence analysis may give valuable information about the origin and function of these nucleic acid molecules. Circulating DNA was isolated from plasma of one healthy individual and one cancer patient with various methods and was cloned into a blunted cloning vector. Resulting colonies were sequenced and analyzed. The majority of the DNA that ligated into the vector was about 200 bp in length. Sequence analysis revealed that circulating DNA consists partly of currently uncharacterized human genomic sequences and when human repeats were masked it matched with sequences present in contigs containing known genes situated at various distances from the identified targets. In addition to the presence of large repeats, a variety of Alu repeat sequences were observed. Preliminary results showed that more Alu repeats are present in the plasma of normal individuals than in patient material. None of the gene sequences reported in the literature to be part of circulating DNA (e.g., P53, the Ras family, β‐globin, or β‐actin) was observed. Cloning and sequencing of free circulating DNA was successful and this first attempt on characterizing sequence data of free circulating DNA not only confirmed previous results, but also revealed a large variety of sequences. Further characterization of circulating DNA may be beneficial in diagnosis and prognosis and may also contribute to determining the source and function of circulating DNA.

Hereditary tyrosinemia type 1 metabolites impair DNA excision repair pathways

Hereditary tyrosinemia type 1 is an autosomal recessive metabolic disorder, which is caused by a defective fumarylacetoacetate hydrolase enzyme, and consequently metabolites such as succinylacetone and p-hydroxyphenylpyruvate accumulate. We used a modified comet assay to determine the effect of these metabolites on base- and nucleotide excision repair pathways. Our results indicate that the metabolites affected the repair mechanisms differently, since the metabolites had a bigger detrimental effect on BER than on NER.

In vitro antioxidant, antimutagenic and genoprotective activity of Rosa roxburghii fruit extract

The antioxidant properties of the fruit of the Rosa roxburghii (RR) plant have been associated with several putative health promoting effects. The possible cytotoxic, mutagenic/antimutagenic and genotoxic effects of RR fruit extract were investigated. The effect on antioxidant status and protection against induced oxidative stress were also investigated using primary rat hepatocytes. A RR fruit extract containing 45 g/L total ascorbic acid and 65 g/L total polyphenols was used in this study. Dilutions up to 0.08% (v/v) increased significantly the antioxidant status in primary rat hepatocytes. The glutathione redox state was decreased with RR treatment but was increased in Chang liver cells and MT‐2 lymphoblast. No cyto‐ or genotoxicity were observed at levels of up to 5% (v/v) of the fruit extract. In addition, a significant protection against t‐BHP induced oxidative stress was observed in primary rat hepatocytes. The Ames test revealed no mutagenic activity using the Salmonella typhimurium strains TA98, TA100 and TA102. A significant antimutagenic effect of the extract was observed against the metabolic activated mutagens 2‐acetylaminofluorene and aflatoxin B1 and to a lesser extent against methyl methanesulfonate. It is concluded that these results support the associated health promoting potential of Rosa Roxburghii fruit and in particular against oxidative stress. Copyright

Using a medium-throughput comet assay to evaluate the global DNA methylation status of single cells

The comet assay is a simple and cost effective technique, commonly used to analyze and quantify DNA damage in individual cells. The versatility of the comet assay allows introduction of various modifications to the basic technique. The difference in the methylation sensitivity of the isoschizomeric restriction enzymes HpaII and MspI are used to demonstrate the ability of the comet assay to measure the global DNA methylation level of individual cells when using cell cultures. In the experiments described here, a medium-throughput comet assay and methylation sensitive comet assay are combined to produce a methylation sensitive medium-throughput comet assay to measure changes in the global DNA methylation pattern in individual cells under various growth conditions.

8-Oxo-7,8-dihydro-2’-deoxyguanosine, reactive oxygen species and ambulatory blood pressure in African and Caucasian men: The SABPA study

Abstract Various studies indicate a relationship between increased oxidative stress and hypertension, resulting in increased DNA damage and consequent excretion of 8-oxo-7,8-dihydro-2’-deoxyguanosine (8-oxodG). The aim of this study was to compare urinary 8-oxodG levels in African and Caucasian men and to investigate the association between ambulatory blood pressure (BP) and pulse pressure (PP) with 8-oxodG in these groups. We included 98 African and 92 Caucasian men in the study and determined their ambulatory BP and PP. Biochemical analyses included, urinary 8-oxodG, reactive oxygen species (ROS) (measured as serum peroxides), ferric reducing antioxidant power (FRAP), total glutathione (GSH), glutathione peroxidase (GPx) and glutathione reductase (GR) activity. The African men had significantly higher systolic (SBP) and diastolic blood pressure (DBP) (both p < 0.001). Assessment of the oxidative stress markers indicated significantly lower 8-oxodG levels (p < 0.001) in the African group. The African men also had significantly higher ROS (p = 0.002) with concomitant lower FRAP (p < 0.001), while their GSH levels (p = 0.013) and GR activity (p < 0.001) were significantly higher. Single and partial regression analyses indicated a negative association between urinary 8-oxodG levels with SBP, DBP and PP only in African men. These associations were confirmed in multiple regression analyses (SBP: R2 = 0.41; β = −0.25; p = 0.002, DBP: R2 = 0.30; β = −0.21; p = 0.022, PP: R2 = 0.30; β = −0.19; p = 0.03). Our results revealed significantly lower urinary 8-oxodG in African men, accompanied by a negative association with BP and PP. We propose that this may indicate a dose-response relationship in which increased oxidative stress may play a central role in the up-regulation of antioxidant defence and DNA repair mechanisms.

Impaired DNA repair and genomic stability in hereditary tyrosinemia type 1.

The autosomal recessive disorder, hereditary tyrosinemia type 1 (HT1), is caused by a defective fumarylacetoacetate hydrolase enzyme. Consequently intermediate metabolites such as fumarylacetoacetate, succinylacetone and p-hydroxyphenylpyruvic acid accumulate. Characteristic to HT1 is the development of hepatocellular carcinoma, irrespective of dietary intervention or pharmacological treatment. Carcinogenesis may occur through a chromosomal instability mutator phenotype or a microsatellite instability phenotype, and deficient DNA repair may be a contributing factor thereof. The purpose of this study was to investigate the expression of DNA repair proteins, and the possible occurrence of microsatellite instability in HT1. Gene expression analyses show low expression of hOGG1 and ERCC1 in HT1 patient lymphocytes. Results from microsatellite instability analyses show allelic imbalance on chromosome 7 of the fah(-/-) mouse genome, and instability of the D2S123, D5S346 and (possibly) D17S250 microsatellite markers, in HT1 patient lymphocytes.