Inter-individual variation in nucleotide excision repair pathway is modulated by non-synonymous polymorphisms in ERCC4 and MBD4 genes

Inter-individual differences in DNA repair capacity (DRC) may lead to genome instability and, consequently, modulate individual cancer risk. Among the different DNA repair pathways, nucleotide excision repair (NER) is one of the most versatile, as it can eliminate a wide range of helix-distorting DNA lesions caused by ultraviolet light irradiation and chemical mutagens. We performed a genotype-phenotype correlation study in 122 healthy subjects in order to assess if any associations exist between phenotypic profiles of NER and DNA repair gene single nucleotide polymorphisms (SNPs). Individuals were genotyped for 768 SNPs with a custom Illumina Golden Gate Assay, and peripheral blood mononuclear cells (PBMCs) of the same subjects were tested for a NER comet assay to measure DRC after challenging cells by benzo(a)pyrene diolepoxide (BPDE). We observed a large inter-individual variability of NER capacity, with women showing a statistically significant lower DRC (meanSD: 6.684.76; p=0.004) than men (meanSD: 8.895.20). Moreover, DRC was significantly lower in individuals carrying a variant allele for the ERCC4 rs1800124 non-synonymous SNP (nsSNP) (p=0.006) and significantly higher in subjects with the variant allele of MBD4 rs2005618 SNP (p=0.008), in linkage disequilibrium (r(2)=0.908) with rs10342 nsSNP. Traditional in silico docking approaches on protein-DNA and protein-protein interaction showed that Gly875 variant in ERCC4 (rs1800124) decreases the DNA-protein interaction and that Ser273 and Thr273 variants in MBD4 (rs10342) indicate complete loss of protein-DNA interactions. Our results showed that NER inter-individual capacity can be modulated by cross-talk activity involving nsSNPs in ERCC4 and MBD4 genes, and they suggested to better investigate SNP effect on cancer risk and response to chemo- and radiotherapie

An Overview of the genetic structure within the Italian population from genome-wide data

In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise FST statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies

Identity-by-state (IBS) sharing between and within populations.

<p>Density estimates for empirical distributions of genome-wide mean proportions of alleles sharing identity-by-state between subjects from different population or within the same populations, are shown for A) Northern Europe (CEU and French), B) Middle East (Bedouin, Palestinian and Druze), C) Northern Africa (Mozambite), D) within Italian populations. Color code as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone-0043759-g001" target="_blank">Figures 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone-0043759-g002" target="_blank">2</a>.</p

SNP-Based PC of 1,262 individuals from 10 sub-populations.

<p>The Italian population plotted onto the first two principal components defined by the European HGDP-CEPH populations and CEU HapMap data. Scatter plot of the first two principal components, obtained using R software (<i>prcomp</i>). Analysis based on 125,799 autosomal SNPs. Individuals included belong to Northern Italy (N-IT): black dots, Central Italy (C-IT): red dots, Southern Italy (S-IT): green dots, Sardinian (SAR): blue dots, CEU HapMap (CEU); light blue dots, Beduoin (BED): purple dots, Druze (DRU): yellow dots, Mozabite (MOZ): black triangles, Palestinian (PAL): red triangles, French (FRE): green triangles. The top 100 Eigenvectors and associated Eigenvalues for this plot are given in Supplementary Material: <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone.0043759.s002" target="_blank">Figure S2</a> (panel a).</p

Datasets and individuals number from each population.

<p>Individuals included were filtered for individual call rate >98% and Identity By State (IBS) >0.05. Individuals included belong to Northern Italian (N-IT), Central Italian (C-IT), Southern Italian (S-IT), Sardinian (SAR), CEU HapMap (CEU), French (FRE), Palestinian (PAL), Bedouin (BED), Druze (DRU), and Mozabite (MOZ).</p

Clustering of the European, Northern African and Middle Eastern individuals by the Structure software.

<p>Model-based ancestry analysis based on a subset of HGDP-CEPH and HapMap CEU data using the merged data of 126K autosomal SNPs. Ancestry for each individual was inferred using ADMIXTURE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone.0043759-Alexander1" target="_blank">[50]</a> at K = 4. Abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone-0043759-g001" target="_blank">Figure 1</a>.</p

SNP-Based PC of 1,014 individuals from the Italian dataset.

<p>A. A Scatter Plot of the Italian population of the first two principal components obtained via R software (<i>prcomp</i>). Individuals included belong to Northern Italy : black dots, Central Italy : red dots, Southern Italy : green dots, Sardinian: blue dots. B. Italian population without the Sardinian-projected scatter plot of the first two principal components obtained via the R software (<i>prcomp</i>). Both analyses were based on 125,799 autosomal SNPs and 1,014 individuals for the Italian dataset and 746 individuals for the Italian dataset without Sardinia. Top 100 Eigenvectors and associated Eigenvalues for this plot are given in Supplementary Material: <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone.0043759.s002" target="_blank">Figure S2</a> (panel b and c, respectively).</p

F_st values and genomic control inflation factor (λ_GC) between National areas.

<p>F_st values above the diagonal; λ<b>_GC</b> below. Individuals included belong to Northern Italian (N-IT), Central Italian (C-IT), Southern Italian (S-IT), Sardinian (SAR), CEU HapMap (CEU), Bedouin (BED), Druze (DRU), Mozabite (MOZ), Palestinian (PAL), and French (FRE) populations.</p