Studies on mammalian ribosomal protein S7

http://www.ester.ee/record=b1163838~S1*es

Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression

<p>Abstract</p> <p>Background</p> <p>Mammalian transcriptome contains a large proportion of diverse and structurally complex noncoding RNAs. One class of such RNAs, natural antisense transcripts (NATs), are derived from the opposite strand of many protein-coding genes. Although the exact structure and functional relevance of most of the NATs is unknown, their emerging role as gene expression regulators raises the hypothesis that NATs might contribute to development of complex human disorders. The goal of our study was to investigate the involvement of NATs in regulation of candidate genes for blood pressure.</p> <p>Results</p> <p>First we analysed blood pressure candidate genes for the presence of natural antisense transcripts. <it>In silico </it>analysis revealed that seven genes (<it>ADD3</it>, <it>NPPA</it>, <it>ATP1A1</it>, <it>NPR2</it>, <it>CYP17A1</it>, <it>ACSM3</it>, <it>SLC14A2</it>) have an antisense partner transcribed from the opposite strand. We characterized <it>NPPA </it>and its antisense transcript (<it>NPPA-AS</it>) in more detail. We found that <it>NPPA-AS </it>is expressed in a number of human tissues as a collection of alternatively spliced isoforms and that <it>NPPA-AS </it>and <it>NPPA </it>can form RNA duplexes <it>in vivo</it>. We also demonstrated that a specific <it>NPPA-AS </it>isoform is capable of down-regulating the intron-retained <it>NPPA </it>mRNA variant. We studied the evolutionary conservation of <it>NPPA-AS </it>and were able to detect the presence of <it>Nppa-as </it>transcript in mouse.</p> <p>Conclusion</p> <p>Our results demonstrate functional interaction of <it>NPPA-AS </it>with <it>NPPA </it>at the RNA level and suggest that antisense transcription might be an important post-transcriptional mechanism modulating <it>NPPA </it>expression.</p

Cis-epistasis at the LPA locus and risk of cardiovascular diseases

AIMS Coronary artery disease (CAD) has a strong genetic predisposition. However, despite substantial discoveries made by genome-wide association studies (GWAS), a large proportion of heritability awaits identification. Non-additive genetic-effects might be responsible for part of the unaccounted genetic variance. Here we attempted a proof-of-concept study to identify non-additive genetic effects, namely epistatic interactions, associated with CAD. METHODS AND RESULTS We tested for epistatic interactions in ten CAD case-control studies and UK Biobank with focus on 8,068 SNPs at 56 loci with known associations with CAD risk. We identified a SNP pair located in cis at the LPA locus, rs1800769 and rs9458001, to be jointly associated with risk for CAD (odds ratio OR=1.37, p = 1.07 $\times$ 10-11), peripheral arterial disease (OR = 1.22, p = 2.32 $\times$ 10-4), aortic stenosis (OR = 1.47, p = 6.95 $\times$ 10-7), hepatic lipoprotein(a) (Lp(a)) transcript levels (beta = 0.39, p = 1.41 $\times$ 10-8), and Lp(a) serum levels (beta = 0.58, p = 8.7 $\times$ 10-32), while individual SNPs displayed no association. Further exploration of the LPA locus revealed a strong dependency of these associations on a rare variant, rs140570886, that was previously associated with Lp(a) levels. We confirmed increased CAD risk for heterozygous (relative OR = 1.46, p = 9.97 $\times$ 10-32) and individuals homozygous for the minor allele (relative OR = 1.77, p = 0.09) of rs140570886. Using forward model selection, we also show that epistatic interactions between rs140570886, rs9458001, and rs1800769 modulate the effects of the rs140570886 risk allele. CONCLUSIONS These results demonstrate the feasibility of a large-scale knowledge-based epistasis scan and provide rare evidence of an epistatic interaction in a complex human disease. We were directed to a variant (rs140570886) influencing risk through additive genetic as well as epistatic effects. In summary, this study provides deeper insights into the genetic architecture of a locus important for cardiovascular diseases. TRANSLATIONAL PERSPECTIVE Genetic variants identified by GWAS studies explain about a quarter of the heritability of coronary artery disease by additive genetic effects. Our study demonstrates that non-additive effects contribute to the genetic architecture of the disease as well and identifies complex interaction patterns at the LPA locus, which affect LPA expression, Lp(a) plasma levels and risk of atherosclerosis. This proof-of-concept study encourages systematic searches for epistatic interactions in further studies to shed new light on the aetiology of the disease

Methylation Markers of Early-Stage Non-Small Cell Lung Cancer

Despite of intense research in early cancer detection, there is a lack of biomarkers for the reliable detection of malignant tumors, including non-small cell lung cancer (NSCLC). DNA methylation changes are common and relatively stable in various types of cancers, and may be used as diagnostic or prognostic biomarkers.We performed DNA methylation profiling of samples from 48 patients with stage I NSCLC and 18 matching cancer-free lung samples using microarrays that cover the promoter regions of more than 14,500 genes. We correlated DNA methylation changes with gene expression levels and performed survival analysis.We observed hypermethylation of 496 CpGs in 379 genes and hypomethylation of 373 CpGs in 335 genes in NSCLC. Compared to adenocarcinoma samples, squamous cell carcinoma samples had 263 CpGs in 223 hypermethylated genes and 513 CpGs in 436 hypomethylated genes. 378 of 869 (43.5%) CpG sites discriminating the NSCLC and control samples showed an inverse correlation between CpG site methylation and gene expression levels. As a result of a survival analysis, we found 10 CpGs in 10 genes, in which the methylation level differs in different survival groups.We have identified a set of genes with altered methylation in NSCLC and found that a minority of them showed an inverse correlation with gene expression levels. We also found a set of genes that associated with the survival of the patients. These newly-identified marker candidates for the molecular screening of NSCLC will need further analysis in order to determine their clinical utility

Mutation analysis and copy number alterations of KIF23 in non-small-cell lung cancer exhibiting KIF23 over-expression

KIF23 was recently suggested to be a potential molecular target for the treatment of lung cancer. This proposal is based on elevated expression of KIF23 in several tumors affecting breast, lung, brain, and liver, and also on the presence of KIF23 mutations in melanoma and colorectal cancer. Recently, we identified a mutation in the KIF23 gene causing a rare hereditary form of dyserythropoietic anemia (CDA III) with predisposition to blood cancer. We suggested that KIF23 overexpression in tumors might be due to the presence of activating somatic mutations, and therefore, mutation screening of the KIF23 in 15 non-small-cell lung cancer (NSCLC) cases with elevated expression level of KIF23 was undertaken. Eight sequence variants were found in all samples. Furthermore, one variant was present in two cases, and one variant was case specific. Nine variants were previously reported while one variant lacks frequency information. Nine of ten cases available for single nucleotide polymorphism-array analysis demonstrated aberrant karyotypes with additional copy of entire chromosome 15. Thus, no activating somatic mutations in coding regions of the KIF23 were found. Furthermore, no mutations were detected in cell cycle genes homology region in KIF23 promoter responsible for p53-dependent repression of KIF23 expression. We showed that the elevated level of KIF23 could be due to additional copy of chromosome 15 demonstrated in 90% of NSCLC cases analyzed in this study. Considering the crucial role of KIF23 in the final step of mitosis, the gene is a potential molecular marker, and for better understanding of its role in cancer development, more tumors should be analyzed

Graphs depicting miRNA-SNP-mRNA associations.

<p>Shown is an example subset of filtered associations supported by AGO-CLIP data (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.s005" target="_blank">S4 Fig</a> for full data). The color of miRNA-SNP links shows miRNA targeting probability, assessed by TargetScan context+ score change (grey, context+ score change > 0; the gradient from yellow to red shows the magnitude of context+ score change) and the line type indicates concordance with the mechanism of miRNA-mediated regulation: a continuous line is concordant (C-type), and a dashed line is unconcordant (U-type). In the case of SNP-gene links, the concordance type is indicated by the color: a red line is C-type, a blue line is U-type, and the intensity of the color indicates the <i>cis</i>-eQTL effect size (overall Z-score) from the Westra <i>et al</i>. meta-analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.ref021" target="_blank">21</a>], averaged over all detected SNPs in the LD block (R² = 1). Multiple interactions between one SNP and one gene show several Illumina probes detecting the same transcript. Outlined genes are validated targets of a targeting miRNA, as reported by miRTarBase, TarBase, or miRecords.</p

Analysis strategy for the identification of miRNA-mediated <i>cis</i>-eQTL effects.

<p>(a) <i>Cis</i>-eQTL SNPs and their perfect proxies (R² = 1, 1000G CEU population) were mapped to the 3' UTRs of <i>cis</i>-affected ENSEMBL transcripts. Next, the SNPs that were located within the <i>in silico</i> miRNA binding sites were identified from public databases PolymiRTS, miRSNP, and webtool mrSNP, each utilizing a different <i>in silico</i> target prediction algorithm. The direction of allelic trends was assessed for concordance with the logic of miRNA-mediated regulation. (b) Associations between Illumina expression probes, MRE-SNPs, and miRNAs. An MRE-SNP-probe association consists of an MRE-SNP and an Illumina probe, detecting the corresponding <i>cis</i>-affected gene. An miR-SNP-probe association adds the miRNA, for which the predicted MRE is either disrupted or created by the MRE-SNP.</p

Top 30 filtered SNP-miR-probe associations, sorted based on their context+ scores.

<p>SNPs shown in bold are in experimentally validated MREs.</p><p>^a SNP effect on miRNA binding: D disrupts an MRE and C creates an MRE.</p><p>^b MAF is based on 1000G pilot 1 CEU population.</p><p>^c Number of <i>cis</i>-eQTL SNPs from the LD block (R² = 1, 1000G pilot 1, CEU)</p><p>^d Z-scores from a recent meta-analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.ref021" target="_blank">21</a>] are averaged for LD block (R² = 1); FDR < 0.05 for all associations.</p><p>^e Association type: C-concordant; U-unconcordant.</p><p>Top 30 filtered SNP-miR-probe associations, sorted based on their context+ scores.</p

MRE-SNPs from the filtered set of associations that overlap with validated miRNA-target interactions.

<p>* SNP has been experimentally shown to influence MRE.</p><p>^a SNP effect on miRNA binding: D disrupts an MRE and C creates an MRE.</p><p>^b MAF is based on 1000G pilot 1 CEU population.</p><p>^c Z-scores from a recent eQTL meta-analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141351#pone.0141351.ref021" target="_blank">21</a>] are averaged for LD block (R² = 1, 1000G pilot 1, CEU); FDR < 0.05 for all associations.</p><p>^d Conservation shows in which species a corresponding MRE is present (polymiRTS v3.0 database).</p><p>^e Supported by AGO-CLIP data.</p><p>^f Validation method: LU- luciferase reporter assay; IM- immunoprecipitation; EX- target expression profiling; CL- CLASH; QP- qRT-PCR; SE- sequencing; PS- pSiLAC; and WE- Western blot.</p><p>^g Association type: C-concordant; U-unconcordant.</p><p>MRE-SNPs from the filtered set of associations that overlap with validated miRNA-target interactions.</p

Regional LD plots for the four C-type MRE-SNPs overlapping with the GWAS Catalog.

<p>Regional LD plots for the four C-type MRE-SNPs overlapping with the GWAS Catalog.</p