More targets, more pathways and more clues for mutant p53.

Mutations in the transcription factor p53 are among the most common genetic alterations in human cancer, and missense p53 mutations in cancer cells can lead to aggressive phenotypes. So far, only few studies investigated transcriptional reprogramming under mutant p53 expression as a means to identify deregulated targets and pathways. A review of the literature was carried out focusing on mutant p53-dependent transcriptome changes with the aims of (i) verifying whether different p53 mutations can be equivalent for their effects, or whether there is a mutation-specific transcriptional reprogramming of target genes, (ii) understanding what is the main mechanism at the basis of upregulation or downregulation of gene expression under the p53 mutant background, (iii) identifying novel candidate target genes of WT and/or mutant p53 and (iv) defining cellular pathways affected by the mutant p53-dependent gene expression reprogramming. Nearly 600 genes were consistently found upregulated or downregulated upon ectopic expression of mutant p53, regardless of the specific p53 mutation studied. Promoter analysis and the use of ChIP-seq data indicate that, for most genes, the expression changes could be ascribed to a loss both of WT p53 transcriptional activation and repressor functions. Pathway analysis indicated changes in the metabolism/catabolism of amino acids such as aspartate, glutamate, arginine and proline. Novel p53 candidate target genes were also identified, including ARID3B, ARNT2, CLMN, FADS1, FTH1, KPNA2, LPHN2, PARD6B, PDE4C, PIAS2, PRPF40A, PYGL and RHOBTB2, involved in the metabolism, xenobiotic responses and cell differentiation

Determining the effectiveness of High Resolution Melting analysis for SNP genotyping and mutation scanning at the TP53 locus

<p>Abstract</p> <p>Background</p> <p>Together single nucleotide substitutions and small insertion/deletion variants are the most common form of sequence variation in the human gene pool.</p> <p>High-resolution SNP profile and/or haplotype analyses enable the identification of modest-risk susceptibility genes to common diseases, genes that may modulate responses to pharmaceutical agents, and SNPs that can affect either their expression or function. In addition, sensitive techniques for germline or somatic mutation detection are important tools for characterizing sequence variations in genes responsible for tumor predisposition. Cost-effective methods are highly desirable. Many of the recently developed high-throughput technologies are geared toward industrial scale genetic studies and arguably do not provide useful solutions for small laboratory investigator-initiated projects. Recently, the use of new fluorescent dyes allowed the high-resolution analysis of DNA melting curves (HRM).</p> <p>Results</p> <p>Here, we compared the capacity of HRM, applicable to both genotyping and mutation scanning, to detect genetic variations in the tumor suppressor gene <it>TP53 </it>with that of mutation screening by full resequencing. We also assessed the performance of a variety of available HRM-based genotyping assays by genotyping 30 <it>TP53 </it>SNPs. We describe a series of solutions to handle the difficulties that may arise in large-scale application of HRM to mutation screening and genotyping at the <it>TP53 </it>locus. In particular, we developed specific HRM assays that render possible genotyping of 2 or more, sometimes closely spaced, polymorphisms within the same amplicon. We also show that simultaneous genotyping of 2 SNPs from 2 different amplicons using a multiplex PCR reaction is feasible; the data can be analyzed in a single HRM run, potentially improving the efficiency of HRM genotyping workflows.</p> <p>Conclusion</p> <p>The HRM technique showed high sensitivity and specificity (1.0, and 0.8, respectively, for amplicons of <400 bp) for mutation screening and provided useful genotyping assays as assessed by comparing the results with those obtained with Sanger sequencing. Thus, HRM is particularly suitable for either performing mutation scanning of a large number of samples, even in the situation where the amplicon(s) of interest harbor a common variant that may disturb the analysis, or in a context where gathering common SNP genotypes is of interest.</p

Estrogen-like activity of seafood related to environmental chemical contaminants

BACKGROUND: A wide variety of environmental pollutants occur in surface waters, including estuarine and marine waters. Many of these contaminants are recognised as endocrine disrupting chemicals (EDCs) which can adversely affect the male and female reproductive system by binding the estrogen receptor and exhibiting hormone-like activities. In this study the estrogenic activity of extracts of edible marine organisms for human consumption from the Mediterranean Sea was assayed. METHODS: Marine organisms were collected in two different areas of the Mediterranean Sea. The estrogenic activity of tissues was assessed using an in vitro yeast reporter gene assay (S. cerevisiae RMY 326 ER-ERE). Concentrations of polychlorinated biphenyls (PCBs) (congeners 28, 52, 101, 118, 138, 153, 180) in fish tissue was also evaluated. RESULTS: Thirty-eight percent of extracts showed a hormone-like activity higher than 10% of the activity elicited by 10 nM 17b-estradiol (E2) used as control. Total PCB concentrations ranged from 0.002 up to 1.785 ng/g wet weight. Chemical analyses detected different levels of contamination among the species collected in the two areas, with the ones collected in the Adriatic Sea showing concentrations significantly higher than those collected in the Tyrrhenian Sea (p < 0.01). CONCLUSION: The more frequent combination of chemicals in the samples that showed higher estrogenic activity was PCB 28, PCB 101, PCB 153, PCB 180. The content of PCBs and estrogenic activity did not reveal any significant correlation

Re-sequencing TP53: seeking new polymorphisms and haplotypes

The p53 tumor suppressor serves as one of the major cellular barriers against cancer development. Indeed, as many as 50% of all human tumors contain p53 mutants whereas the other half maintain a wild-type TP53 gene but acquire other genetic or epigenetic alterations that compromise the p53 response. Most of the mutations within the TP53 gene are missense mutations (75%) that results in the expression of full-length mutant p53 (mutp53) proteins lacking its specific DNA-binding activity and accumulating in the nucleus of tumor cells. TP53 germline mutations are seen in 70-80% of patients with Li-Fraumeni syndrome (LFS), a familial cancer predisposition syndrome. Though most of germline mutations occur in one of the six hotspots, a rare germline TP53 mutation at codon 337 (R337H) has been found in a number of apparently unrelated cancer-prone families in Southern Brazil. Moreover, recent studies associated the common polymorphisms, intron3 16bp-duplication, Arg72Pro, and the MspI RFLP in intron 6, with the risk of various types of cancer. Nevertheless, TP53 haplotypic structure is still poorly known. According to this view, it would be desirable to characterize the haplotypic structure of TP53 and find other genetic variants that have not yet been used in association studies. Thus, in the present study we undertook a complete mutation screening of TP53, in order to find new polymorphisms, and finely reconstruct the common haplotypes of TP53. We identified 18 new variants along the gene. After the screening of 192 control samples, we classified these into mutations (i.e., allelic frequency 0.01, n=6). We determined the haplotypes across the whole gene and we selected 29 tagSNP out of 182 SNPs.Using these 29 tagSNPs we demonstrated that some R337H Brazilian carriers shared the same uncommon haplotype, supporting the hypothesis of founder effect for this mutation

A Novel Collection of snRNA-Like Promoters with Tissue-Specific Transcription Properties

We recently identified a novel dataset of snRNA-like trascriptional units in the human genome. The investigation of a subset of these elements showed that they play relevant roles in physiology and/or pathology. In this work we expand our collection of small RNAs taking advantage of a newly developed algorithm able to identify genome sequence stretches with RNA polymerase (pol) III type 3 promoter features thus constituting putative pol III binding sites. The bioinformatic analysis of a subset of these elements that map in introns of protein-coding genes in antisense configuration suggest their association with alternative splicing, similarly to other recently characterized small RNAs. Interestingly, the analysis of the transcriptional activity of these novel promoters shows that they are active in a cell-type specific manner, in accordance with the emerging body of evidence of a tissue/cell-specific activity of pol III

Monitoring of polychlorinated biphenyl contamination and estrogenic activity in water, commercial feed and farmed seafood

We evaluated the concentration and congener distribution of seven "target" polychlorinated biphenyls (PCBs) present in water collected in different aquaculture farms of the Mediterranean area, commercial feeds, and farmed seafood. PCBs were present in feed and in tissues of all the analysed organisms at levels ranging from 1.96 ng g(-1) to 124.00 ng g(-1) wet weight, and in 10.5% of the water samples, at levels from under detection limit to 33.0 ng l(-1) with total PCB concentrations significantly higher in samples from the Tyrrhenian Sea than the Adriatic Sea. PCB congener distribution in tissues resembled that of feed, suggesting that commercial feed is an important source of PCBs. The estrogenicity of organic extracts of the samples was also evaluated by using an in vitro yeast reporter assay. Estrogenic activity higher than 10% of the activity induced by 10 nM 17 beta-estradiol was observed in 20.0% of seafood samples and 15.8% of water samples. Seafood and water samples from the Tyrrhenian Sea were more frequently estrogenic than the Adriatic ones (16.45 versus 4.08%). A significant correlation of total PCB concentrations on biological activity was observed for sea bass and mussels from the Adriatic Sea (p < 0.045 and p < 0.04, respectively), and for sea bass of the Tyrrhenian Sea (p=0.05). These results indicate the need of an integral approach in the exposure assessment to potential toxic compounds for human via food