Computational strategies for analyzing data in gene expression microarray experiments

Microarray analysis has become a widely used method for generating gene expression data on a genomic scale. Microarrays have been enthusiastically applied in many fields of biological research, even though several open questions remain about the analysis of such data. A wide range of approaches are available for computational analysis, but no general consensus exists as to standard for microarray data analysis protocol. Consequently, the choice of data analysis technique is a crucial element depending both on the data and on the goals of the experiment. Therefore, basic understanding of bioinformatics is required for optimal experimental design and meaningful interpretation of the results. This review summarizes some of the common themes in DNA microarray data analysis, including data normalization and detection of differential expression. Algorithms are demonstrated by analyzing cDNA microarray data from an experiment monitoring gene expression in T helper cells. Several computational biology strategies, along with their relative merits, are overviewed and potential areas for additional research discussed. The goal of the review is to provide a computational framework for applying and evaluating such bioinformatics strategies. Solid knowledge of microarray informatics contributes to the implementation of more efficient computational protocols for the given data obtained through microarray experiments.     

Exome Sequencing of Uterine Leiomyosarcomas Identifies Frequent Mutations in TP53, ATRX,and MED12

Uterine leiomyosarcomas (ULMSs) are aggressive smooth muscle tumors associated with poor clinical outcome. Despite previous cytogenetic and molecular studies, their molecular background has remained elusive. To examine somatic variation in ULMS, we performed exome sequencing on 19 tumors. Altogether, 43 genes were mutated in at least two ULMSs. Most frequently mutated genes included tumor protein P53 (TP53; 6/19; 33%), alpha thalassemia/mental retardation syndrome X-linked (ATRX; 5/19; 26%), and mediator complex subunit 12 (MED12; 4/19; 21%). Unlike ATRX mutations, both TP53 and MED12 alterations have repeatedly been associated with ULMSs. All the observed ATRX alterations were either nonsense or frameshift mutations. ATRX protein levels were reliably analyzed by immunohistochemistry in altogether 44 ULMSs, and the majority of tumors (23/44; 52%) showed clearly reduced expression. Loss of ATRX expression has been associated with alternative lengthening of telomeres (ALT), and thus the telomere length was analyzed with telomere-specific fluorescence in situ hybridization. The ALT phenotype was confirmed in all ULMSs showing diminished ATRX expression. Exome data also revealed one nonsense mutation in death-domain associated protein (DAXX), another gene previously associated with ALT, and the tumor showed ALT positivity. In conclusion, exome sequencing revealed that TP53, ATRX, and MED12 are frequently mutated in ULMSs. ALT phenotype was commonly seen in tumors, indicating that ATR inhibitors, which were recently suggested as possible new drugs for ATRX-deficient tumors, could provide a potential novel therapeutic option for ULMS.     

Differential Predictive Roles of A- and B-Type Nuclear Lamins in Prostate Cancer Progression

Background

Prostate cancer (PCa) is the most common cancer among men in western countries. While active surveillance is increasingly utilized, the majority of patients are currently treated with radical prostatectomy. In order to avoid over-treatment, there is an indisputable need for reliable biomarkers to identify the potentially aggressive and lethal cases. Nuclear intermediate filament proteins called lamins play a role in chromatin organization, gene expression and cell stiffness. The expression of lamin A is associated with poor outcome in colorectal cancer but to date the prognostic value of the lamins has not been tested in other solid tumors.

Methods

We studied the expression of different lamins with immunohistochemistry in a tissue microarray material of 501 PCa patients undergoing radical prostatectomy and lymph node dissection. Patients were divided into two staining categories (low and high expression). The correlation of lamin expression with clinicopathological variables was tested and the association of lamin status with biochemical recurrence (BCR) and disease specific survival (DSS) was further analyzed.

Results

Low expression of lamin A associated with lymph node positivity (p<0.01) but not with other clinicopathological variables and low expression had a borderline independent significant association with DSS (HR = 0.4; 95% CI 0.2–1.0; p = 0.052). Similarly, low lamin C expression associated with poorer survival (HR = 0.2; 95% CI 0.1–0.6; p = 0.004). Lamin B1 expression did not associate with clinicopathological variables but high expression independently predicted BCR in multivariable Cox regression analysis (HR = 1.8; 95% CI 1.1–2.9; p = 0.023). Low expression of lamin B2 correlated with lymph node positivity (p<0.01) and predicted unfavorable DSS (HR = 0.4; 95% CI 0.2–1.0; p = 0.047).

Conclusions

These results suggest differential roles for lamins in PCa progression. Reduced amounts of lamin A/C and B2 increase risk for lymph node metastasis and disease specific death possibly through increased nuclear deformability while high expression of lamin B1 predicts disease recurrence.     

Dynamics and interactions of parvoviral NS1 protein in the nucleus

Nuclear positioning and dynamic interactions of viral proteins with nuclear substructures play essential roles during infection with DNA viruses. Visualization of the intranuclear interactions and motility of the parvovirus replication protein (NS1) in living cells gives insight into specific parvovirus protein-cellular structure interactions. Confocal analysis of highly synchronized infected Norden Laboratory Feline Kidney cells showed accumulation of nuclear NS1 in discrete interchromosomal foci. NS1 fused with enhanced yellow fluorescence protein (NS1-EYFP) provided a marker in live cells for dynamics of NS1 traced by photobleaching techniques. Fluorescence Recovery after Photobleaching suggested that the NS1 protein is not freely diffusing but undergoes transient interactions with nuclear compartments. Fluorescence Loss in Photobleaching demonstrated for the first time the shuttling of a parvoviral protein between the nucleus and the cytoplasm as assayed with NS1-EYFP. Finally, time-lapse imaging of infected cells revealed that the intranuclear distribution of NS1-EYFP evolves dramatically starting from the formation of NS1 foci and proceeding to a homogenous distribution extending throughout the nucleus.     

GENERA ARE OFTEN BETTER THAN SPECIES FOR DETECTING EVOLUTIONARY CHANGE IN THE FOSSIL RECORD: A REPLY TO SALESA ET AL.

In their technical comment Salesa et al. (2011) raise several issues, including an important topic affecting most, or perhaps all, paleoecological studies—the difficulty of determining a reasonable way to deal with taxonomy. Specifically, Salesa et al. draw our attention to a taxonomic revision of Iberian Anchitherium ( Sánchez et al. 1998 ), that we failed to follow in our study ( Eronen et al. 2010 ), and express concerns that a different handling of Anchitherium taxonomy would have affected our results and conclusions.     

Egg-harvesting allows large scale rearing ofAmblyseius finlandicus (Acari: Phytoseiidae) in the laboratory

An improved method to rearAmblyseius finlandicus (Oudemans) in the laboratory is described that allows large numbers to be produced. Mites developed faster and had a higher ovipositional rate when fed on pollen and reared on a bean (Phaseolus vulgaris L.) leaf substrate than when fed on pollen on an artificial arena. Two-spotted spider mites (Tetranychus urticae Koch) were an inferior food source forA. finlandicus mainly because of their profuse webbing.A. finlandicus was able to develop and reproduce on all 11 types of pollen tested although immature mortality was high on cedar (Cedrus sp.) pollen. Total number of mites increased almost 100-fold in three weeks on bean leaf substrate when eggs were collected and transferred (=egg-harvesting) in cotton tufts from the base colonies every two or three days to initiate new colonies. Only about a 13-fold population increase occurred when egg-harvesting was not employed, probably due to a combination of cannibalism and reduced fecundity. Egg-harvesting using cotton tufts is especially suitable for large scale rearing of species likeA. finlandicus that are cannibalistic and/or lay fewer eggs with increasing population density. In addition, the phytoseiidsAmblyseius reductus Wainstein andAnthoseius rhenanus (Oudemans) were reared successfully on pollen and spider mites using either leaf or artificial arenas. This is the first record of successful rearing ofA. rhenanus in the laboratory and ofA. reductus in the laboratory on pollen.     

Comparing priority setting in integrated hazardous substance assessment and in life cycle impact assessment

Purpose  

The purpose of the study was to compare three recent Life Cycle Impact Assessment (LCIA) models in prioritizing substances and products from national emission inventories. The focus was on ecotoxic and human toxic impacts. The aim was to test model output against expert judgment on chemical risk assessment.