Quantitative analysis of mRNA expression levels and DNA methylation profiles of three neighboring genes: FUS1, NPRL2/G21 and RASSF1A in non-small cell lung cancer patients

Background

Tumor suppressor gene (TSG) inactivation plays a crucial role in carcinogenesis. FUS1, NPRL2/G21 and RASSF1A are TSGs from LUCA region at 3p21.3, a critical chromosomal region in lung cancer development. The aim of the study was to analyze and compare the expression levels of these 3 TSGs in NSCLC, as well as in macroscopically unchanged lung tissue surrounding the primary lesion, and to look for the possible epigenetic mechanism of TSG inactivation via gene promoter methylation.

Methods

Expression levels of 3 TSGs and 2 DNA methyltransferases, DNMT1 and DNMT3B, were assessed using real-time PCR method (qPCR) in 59 primary non-small cell lung tumors and the matched macroscopically unchanged lung tissue samples. Promoter methylation status of TSGs was analyzed using methylation-specific PCRs (MSP method) and Methylation Index (MI) value was calculated for each gene.

Results

The expression of all three TSGs were significantly different between NSCLC subtypes: RASSF1A and FUS1 expression levels were significantly lower in squamous cell carcinoma (SCC), and NPRL2/G21 in adenocarcinoma (AC). RASSF1A showed significantly lower expression in tumors vs macroscopically unchanged lung tissues. Methylation frequency was 38–76 %, depending on the gene. The highest MI value was found for RASSF1A (52 %) and the lowest for NPRL2/G21 (5 %). The simultaneous decreased expression and methylation of at least one RASSF1A allele was observed in 71 % tumor samples. Inverse correlation between gene expression and promoter methylation was found for FUS1 (rs = −0.41) in SCC subtype. Expression levels of DNMTs were significantly increased in 75–92 % NSCLCs and were significantly higher in tumors than in normal lung tissue. However, no correlation between mRNA expression levels of DNMTs and DNA methylation status of the studied TSGs was found.

Conclusions

The results indicate the potential role of the studied TSGs in the differentiation of NSCLC histopathological subtypes. The significant differences in RASSF1A expression levels between NSCLC and macroscopically unchanged lung tissue highlight its possible diagnostic role in lung cancer in situ recognition. High percentage of lung tumor samples with simultaneous RASSF1A decreased expression and gene promoter methylation indicates its epigenetic silencing. However, DNMT overexpression doesn’t seem to be a critical determinate of its promoter hypermethylation.     

The Assessment of Science: The Relative Merits of Post-Publication Review,the Impact Factor,and the Number of Citations

The assessment of scientific publications is an integral part of the scientific process. Here we investigate three methods of assessing the merit of a scientific paper: subjective post-publication peer review, the number of citations gained by a paper, and the impact factor of the journal in which the article was published. We investigate these methods using two datasets in which subjective post-publication assessments of scientific publications have been made by experts. We find that there are moderate, but statistically significant, correlations between assessor scores, when two assessors have rated the same paper, and between assessor score and the number of citations a paper accrues. However, we show that assessor score depends strongly on the journal in which the paper is published, and that assessors tend to over-rate papers published in journals with high impact factors. If we control for this bias, we find that the correlation between assessor scores and between assessor score and the number of citations is weak, suggesting that scientists have little ability to judge either the intrinsic merit of a paper or its likely impact. We also show that the number of citations a paper receives is an extremely error-prone measure of scientific merit. Finally, we argue that the impact factor is likely to be a poor measure of merit, since it depends on subjective assessment. We conclude that the three measures of scientific merit considered here are poor; in particular subjective assessments are an error-prone, biased, and expensive method by which to assess merit. We argue that the impact factor may be the most satisfactory of the methods we have considered, since it is a form of pre-publication review. However, we emphasise that it is likely to be a very error-prone measure of merit that is qualitative, not quantitative.

Author summary

Subjective assessments of the merit and likely impact of scientific publications are routinely made by scientists during their own research, and as part of promotion, appointment, and government committees. Using two large datasets in which scientists have made qualitative assessments of scientific merit, we show that scientists are poor at judging scientific merit and the likely impact of a paper, and that their judgment is strongly influenced by the journal in which the paper is published. We also demonstrate that the number of citations a paper accumulates is a poor measure of merit and we argue that although it is likely to be poor, the impact factor, of the journal in which a paper is published, may be the best measure of scientific merit currently available.     

Genetic selection for protein solubility enabled by the folding quality control feature of the twin-arginine translocation pathway

One of the most vexing problems facing structural genomics efforts and the biotechnology enterprise in general is the inability to efficiently produce functional proteins due to poor folding and insolubility. Additionally, protein misfolding and aggregation has been linked to a number of human diseases, such as Alzheimer's. Thus, a robust cellular assay that allows for direct monitoring, manipulation, and improvement of protein folding could have a profound impact. We report the development and characterization of a genetic selection for protein folding and solubility in living bacterial cells. The basis for this assay is the observation that protein transport through the bacterial twin-arginine translocation (Tat) pathway depends on correct folding of the protein prior to transport. In this system, a test protein is expressed as a tripartite fusion between an N-terminal Tat signal peptide and a C-terminal TEM1 beta-lactamase reporter protein. We demonstrate that survival of Escherichia coli cells on selective medium expressing a Tat-targeted test protein/beta-lactamase fusion correlates with the solubility of the test protein. Using this assay, we isolated solubility-enhanced variants of the Alzheimer's Abeta42 peptide from a large combinatorial library of Abeta42 sequences, thereby confirming that our assay is a highly effective selection tool for soluble proteins. By allowing the bacterial Tat pathway to exert folding quality control on expressed target protein sequences, we have generated a powerful tool for monitoring protein folding and solubility in living cells, for molecular engineering of solubility-enhanced proteins or for the isolation of factors and/or cellular conditions that stabilize aggregation-prone proteins.     

Nonlinear acoustics in pant hoots of common chimpanzees (Pan troglodytes): frequency jumps, subharmonics, biphonation, and deterministic chaos

The pant hoot calls produced by common chimpanzees (Pan troglodytes) are multi-call vocalizations that have figured prominently in investigations of acoustic communication in this species. Although pant hoots are predominantly harmonically structured, they can exhibit an acoustic complexity that has recently been linked to nonlinearity in the vocal-fold dynamics underlying typical mammalian sound production. We examined the occurrence of these sorts of nonlinear phenomena in pant hoot vocalizations, contrasting quieter and lower-pitched "introduction" components with loud and high-pitched "climax" calls in the same bouts. Spectrographic evidence revealed four kinds of nonlinear phenomena, including discrete frequency jumps, subharmonics, biphonation, and deterministic chaos. While these events were virtually never observed during the introduction, they occurred in more than half of the climax calls. Biphonation was by far the most common phenomenon, followed by subharmonics, chaos, and frequency jumps. Individual callers varied in the degree to which their climax calls exhibited nonlinear phenomena, but were consistent in showing more biphonation than other forms. These outcomes show that nonlinear phenomena are routinely present in chimpanzee pant hoots, and help lay the foundation for investigating the function of such events.     

Combined molecular and morphological data provide insights into the evolution and classification of Chilocorini ladybirds (Coleoptera: Coccinellidae)

Ladybirds of the cosmopolitan tribe Chilocorini prey mainly on coccids and include several important biocontrol agents. The phylogenetic relationships of Chilocorini are poorly known. In this paper, we provide a phylogenetic reconstruction of Chilocorini containing all 27 genera based on five molecular markers and 86 adult morphological characters. Morphological character states were mapped on the combined data tree from Bayesian inference to analyse morphological traits of each genus. Sixteen morphological characters were selected to reconstruct the ancestral states using maximum parsimony and maximum likelihood methods. Divergence times were estimated based on the relaxed molecular clock approach. Our results indicate that Chilocorini, excluding Chilocorellus Miyatake, is monophyletic and closely related to Plotinini. The crown group Chilocorini was estimated to date back to the Middle Cretaceous. Anisorcus Crotch, Egius Mulsant, Phaenochilus Weise and Simmondsius Ahmad & Ghani are synonymized here with Chilocorus Leach ( syn.n. ). The genus Chilocorellus is excluded from Chilocorini. The split of current genera was estimated to have occurred during the Middle Paleogene to Late Paleogene.     

Spread and population structure of <Emphasis Type=Italic>Cryphonectria parasitica</Emphasis> in a young chestnut orchard in Slovakia

The chestnut blight pathogen Cryphonectria parasitica was studied in a chestnut collection composed of both seedlings and grafts derived from selected Castanea sativa and C. sativa × C. crenata trees located in south-east Slovakia, near village Príbelce on an area of approximately 3.5 ha. The study was conducted during eight years (2003–2010). During this period 133 trees were infected, which represents 59.82% of chestnut trees of all chestnut accessions. Based on the phenotype of the fungus culture and the type of cankers in the field, all isolates were determined to be virulent. No hypovirulent strains were found. No vegetative compatibility (vc) type diversity was observed. More than 130 isolates were analyzed for vc and all were in single vc type, which was identical with EU 12. All isolates assayed for mating type were MAT-1. No perithecia were observed. No significant differences were found between the proportion of cankered and dead cankered trees in seedlings and grafts of hybrid origin (C. sativa × C. crenata) and of C. sativa origin. However, particular seedlings and grafts of hybrid origin seemed to exhibit certain resistance to chestnut blight.