Life expectancy in central-Eastern European countries is more than 10 years lower compared with Northern or Western countries which could be the result of complex factors including genetics, ...nutrition and life style. We conducted a molecular epidemiological study with the aim of investigating links between DNA instability, genetic polymorphisms in nucleotide excision repair genes and ageing. Two groups-151 young people (78 women and 73 men) aged 20-25, and 140 elderly subjects (101 women and 39 men), aged 65-70 have been investigated. Results show elevated levels of micronuclei and chromosome aberrations in elderly compared with young groups (P<0.001); women had more micronuclei than men (P<0.001). Micronucleus frequencies were influenced by age (P<0.001). In the group of elderly people those who were homozygous with C/C or A/A in XPC IVS11 had more aberrant cells compared with C/A heterozygotes (P=0.04). When the dependent variable was break per cell, elderly people A/A homozygous in XPC IVS11 had more breaks per cell compared with C/A heterozygous or C/C homozygous subjects (P=0.03). Significantly the most chromatid breaks were found in elderly people both Lys/Lys homozygous in the XPD Lys751Gln genotype and C/C or A/A homozygous in the XPC IVS11 genotype (P<0.05). A General Linear Model analysis shows a statistically significant effect of interactions between age, sex and genotype XPC IVS11 (P=0.001) and age, sex and genotype XPCin9 (P=0.007) on number of chromatid breaks. When we divided people into two subgroups (without mutant allele and with one or two mutant alleles) we found a significantly higher number of chromosome exchanges in people with one or two variant polymorphism XPCin9 (P=0.04), XPC IVS11 (P=0.004) or XPCex15 (P=0.001). Level of cells with micronuclei was influenced by polymorphisms XPD Lys751Gln (P=0.03). However, we did not find any relationship between XPA polymorphism and studied cytogenetic biomarkers.
Participants in a study of occupational exposure to mineral fibres in Slovakia were analysed for the polymorphism 23A→G in the DNA repair gene XPA. Of the 388 subjects, 239 were exposed to asbestos, ...stonewool or glass fibre; the rest were unexposed controls. Levels of DNA base alterations (oxidation and alkylation) in lymphocytes were measured using the comet assay with lesion-specific endonucleases. 8-oxoguanine DNA glycosylase (OGG1) DNA repair activity was measured, as incision activity of a lymphocyte extract on DNA containing the OGG1 substrate 8-oxoguanine. Presence of the A allele was associated with higher levels of DNA damage (sites sensitive to formamidopyrimidine DNA glycosylase, endonuclease III or 3-methyladenine DNA glycosylase II) as well as with higher activity of OGG1 repair enzyme. DNA base damage increased with age, showing highly significant correlations when the whole population or subgroups of the population were analysed. OGG1 repair activity also increased with age, but when analysed according to XPA genotype, the increase was observed only in those individuals with an A allele. Although XPA is known as a protein involved in nucleotide excision repair of UV-induced damage and bulky DNA adducts, it may also have a role in the repair of oxidized bases.
A set of 18 Y-chromosomal microsatellite loci was analysed in 568 males from Poland, Slovakia and three regions of Belarus. The results were compared to data available for 2,937 Y chromosome samples ...from 20 other Slavic populations. Lack of relationship between linguistic, geographic and historical relations between Slavic populations and Y-short tandem repeat (STR) haplotype distribution was observed. Two genetically distant groups of Slavic populations were revealed: one encompassing all Western-Slavic, Eastern-Slavic, and two Southern-Slavic populations, and one encompassing all remaining Southern Slavs. An analysis of molecular variance (AMOVA) based on Y-chromosomal STRs showed that the variation observed between the two population groups was 4.3%, and was higher than the level of genetic variance among populations within the groups (1.2%). Homogeneity of northern Slavic paternal lineages in Europe was shown to stretch from the Alps to the upper Volga and involve ethnicities speaking completely different branches of Slavic languages. The central position of the population of Ukraine in the network of insignificant AMOVA comparisons, and the lack of traces of significant contribution of ancient tribes inhabiting present-day Poland to the gene pool of Eastern and Southern Slavs, support hypothesis placing the earliest known homeland of Slavs in the middle Dnieper basin.
Established risk factors for cardiovascular diseases (CVD) may be moderated by genetic variants. In 2403 unrelated individuals from general practice (mean age 40.5 years), we evaluated the influence ...of 15 variants in 12 candidate genes on quantitative traits (QT) associated with CVD (body mass index, abdominal obesity, glucose, serum lipids, and blood pressure). Prior to multiple testing correction, univariate analysis associated APOE rs429358, rs7412 and ATG16L1 rs2241880 variants with serum lipid levels, while LEPR rs1137100 and ATG16L1 rs2241880 variants were linked to obesity related QTs. After taking into account confounding factors and correcting for multiple comparisons only APOE rs429358 and rs7412 variants remained significantly associated with risk of dyslipidemia. APOE rs429358 variant almost tripled the risk in homozygous subjects (OR = 2.97; 95% CI 1.09-8.10, p < 0.03) and had a lesser but still highly significant association also in heterozygous individuals (OR = 1.67; 95% CI 1.24-2.10; p < 0.001). Associations with hypertension, diabetes mellitus, and metabolic syndrome were not significant after Bonferroni correction. The influence of genetic variation is more evident in dyslipidemia than in other analyzed QTs. These results may contribute to strategic research aimed at including genetic variation in the set of data required to identify subjects at high risk of CVD.
Abstract
The COVID-19 pandemic has demonstrated the need for massively-parallel, cost-effective tests monitoring viral spread. Here we present SARSeq,
saliva analysis by RNA sequencing
, a method to ...detect SARS-CoV-2 and other respiratory viruses on tens of thousands of samples in parallel. SARSeq relies on next generation sequencing of multiple amplicons generated in a multiplexed RT-PCR reaction. Two-dimensional, unique dual indexing, using four indices per sample, enables unambiguous and scalable assignment of reads to individual samples. We calibrate SARSeq on SARS-CoV-2 synthetic RNA, virions, and hundreds of human samples of various types. Robustness and sensitivity were virtually identical to quantitative RT-PCR. Double-blinded benchmarking to gold standard quantitative-RT-PCR performed by human diagnostics laboratories confirms this high sensitivity. SARSeq can be used to detect Influenza A and B viruses and human rhinovirus in parallel, and can be expanded for detection of other pathogens. Thus, SARSeq is ideally suited for differential diagnostic of infections during a pandemic.
As part of a large human biomonitoring study, we conducted occupational monitoring in a glass fibre factory in Slovakia. Shopfloor workers (n = 80), with a matched group of administrators in the same ...factory (n = 36), were monitored for exposure to glass fibres and to polycyclic aromatic hydrocarbons (PAHs). The impact of occupational exposure on chromosomal aberrations, DNA damage and DNA repair, immunomodulatory markers, and the role of nutritional and lifestyle factors, as well as the effect of polymorphisms in metabolic and DNA repair genes on genetic stability, were investigated.
The (enzyme-modified) comet assay was employed to measure DNA strand breaks (SBs) and apurinic sites, oxidised and alkylated bases. Antioxidant status was estimated by resistance to H2O2-induced DNA damage. Base excision repair capacity was measured with an in vitro assay (based on the comet assay).
Exposure of workers to fibres was low, but still was associated with higher levels of SBs, and SBs plus oxidised bases, and higher sensitivity to H2O2. Multivariate analysis showed that exposure increased the risk of high levels of SBs by 20%. DNA damage was influenced by antioxidant enzymes catalase and glutathione S-transferase (measured in blood). DNA repair capacity was inversely correlated with DNA damage and positively with antioxidant status. An inverse correlation was found between DNA base oxidation and the percentage of eosinophils (involved in the inflammatory response) in peripheral blood of both exposed and reference groups. Genotypes of XRCC1 variants rs3213245 and rs25487 significantly decreased the risk of high levels of base oxidation, to 0.50 (p = 0.001) and 0.59 (p = 0.001), respectively.
Increases in DNA damage owing to glass fibre exposure were significant but modest, and no increases were seen in chromosome aberrations or micronuclei. However, it is of concern that even low levels of exposure to these fibres can cause significant genetic damage.
•Exposure of workers to glass fibres was associated with increased levels of DNA damage and higher sensitivity to H2O2.•DNA damage was influenced by catalase activity and glutathione S-transferase levels measured in peripheral blood.•XRCC1 variants rs3213245 and rs25487 were associated with a decrease in the risk of high DNA oxidation damage.•Glass fibre exposure did not affect the levels of chromosome aberrations or micronuclei in exposed workers.
Human cancers are often associated with numerical and structural chromosomal instability. Structural chromosomal aberrations (CAs) in peripheral blood lymphocytes (PBL) arise as consequences of ...direct DNA damage or due to replication on a damaged DNA template. In both cases, DNA repair is critical and inter-individual differences in its capacity are probably due to corresponding genetic variations. We investigated functional variants in DNA repair genes (base and nucleotide excision repair, double-strand break repair) in relation to CAs, chromatid-type aberrations (CTAs) and chromosome-type aberrations (CSAs) in healthy individuals. Chromosomal damage was determined by conventional cytogenetic analysis. The genotyping was performed by both restriction fragment length polymorphism and TaqMan allelic discrimination assays. Multivariate logistic regression was applied for testing individual factors on CAs, CTAs and CSAs. Pair-wise genotype interactions of 11 genes were constructed for all possible pairs of single-nucleotide polymorphisms. Analysed individually, we observed significantly lower CTA frequencies in association with XPD Lys751Gln homozygous variant genotype odds ratio (OR) 0.64, 95% confidence interval (CI) 0.48-0.85, P = 0.004; n = 1777. A significant association of heterozygous variant genotype in RAD54L with increased CSA frequency (OR 1.96, 95% CI 1.01-4.02, P = 0.03) was determined in 282 subjects with available genotype. By addressing gene-gene interactions, we discovered 14 interactions significantly modulating CAs, 9 CTAs and 12 CSAs frequencies. Highly significant interactions included always pairs from two different pathways. Although individual variants in genes encoding DNA repair proteins modulate CAs only modestly, several gene-gene interactions in DNA repair genes evinced either enhanced or decreased CA frequencies suggesting that CAs accumulation requires complex interplay between different DNA repair pathways.
We have investigated four X-chromosomal STR loci (a tetranucleotide repeat marker HPRTB, DXS7423 and trinucleotide repeat systems DXS101, DXS8377) in population samples of unrelated Belarusian and ...Slovak males (
N
=
180 and 116, respectively).
Markers were amplified in a multiplex PCR reaction with primers labeled with fluorescent dyes 5-FAM and 5-JOE (dye set F). The separation and detection of PCR products were performed by capillary electrophoresis on a 3130 Genetic Analyzer (Applied Biosystems), using positive controls (K562 and NA9947A) and the GeneScan-500 ROX internal lane standard. Allele designation was based on comparison with the constructed allelic ladder. We performed statistical analysis estimating power of discrimination for males (PD
male). Our data was compared with European populations from Poland and Germany. The obtained data are useful in forensic practice and they contribute to creation of national X-STR databases in Belarus and Slovakia.
Allelic frequencies of 15 short tandem repeat (STR) markers (AmpF
ISTR
® Identifiler™) were analyzed using AmpF
lSTR
® Identifiler™ PCR Amplification Kit in Belarusian (
N
=
176) and Slovak (
N
=
...164) individuals. No deviation from Hardy–Weinberg equilibrium was found for all loci. These results were compared with data available for northern Poland and Belarusian minority residing in northeastern Poland Z. Szczerkowska, E. Kapińska, J. Wysocka, L. Cybulska, Northern Polish population data and forensic usefulness of 15 autosomal STR loci, Forensic Sci. Int. 144 (2004) 69–71; W. Pepinski, A. Niemcunowicz-Janica, M. Skawrowska, E. Koc-Zorawska, J. Janica, I. Soltyszewski, Allele distribution of 15 STR loci in a population sample of Belarusian minority residing in the northeastern Poland, Forensic Sci. Int. 139 (2004) 265–267. Statistically significant differences were observed between Belarusian K. Rębała, J. Wysocka, E. Kapińska, L. Cybulska, A.I. Mikulich, I.S. Tsybovsky, Z. Szczerkowska, Belarusian population genetic database for 15 autosomal STR loci, Forensic Sci. Int. (2007), doi:10.1016/j.forsciint.2007.02.002 and Slovak populations and other compared populations.
The values of heterozygosity, polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), paternity index (PI) and matching probability (pM) were calculated. The results demonstrated the forensic usefulness of the analyzed loci.
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