Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

Aberrant DNA methylation often occurs in colorectal cancer (CRC). In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions (DMRs) in 24 tumors and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. Using epigenetic data from human embryonic stem cells, we show that frequently hypermethylated regions coincide with bivalent loci in human embryonic stem cells. DNA methylation is commonly thought to lead to gene silencing; however, integration of publically available gene expression data indicates that 75% of the frequently hypermethylated genes were most likely already lowly or not expressed in normal tissue. Collectively, our study provides genome-wide DNA methylation maps of CRC, comprehensive lists of DMRs, and gives insights into the role of aberrant DNA methylation in CRC formation.     

Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases

The emerging structural information about allosteric kinase complexes and the growing number of allosteric inhibitors call for a systematic strategy to delineate and classify mechanisms of allosteric regulation and long-range communication that control kinase activity. In this work, we have investigated mechanistic aspects of long-range communications in ABL and EGFR kinases based on the results of multiscale simulations of regulatory complexes and computational modeling of signal propagation in proteins. These approaches have been systematically employed to elucidate organizing molecular principles of allosteric signaling in the ABL and EGFR multi-domain regulatory complexes and analyze allosteric signatures of the gate-keeper cancer mutations. We have presented evidence that mechanisms of allosteric activation may have universally evolved in the ABL and EGFR regulatory complexes as a product of a functional cross-talk between the organizing αF-helix and conformationally adaptive αI-helix and αC-helix. These structural elements form a dynamic network of efficiently communicated clusters that may control the long-range interdomain coupling and allosteric activation. The results of this study have unveiled a unifying effect of the gate-keeper cancer mutations as catalysts of kinase activation, leading to the enhanced long-range communication among allosterically coupled segments and stabilization of the active kinase form. The results of this study can reconcile recent experimental studies of allosteric inhibition and long-range cooperativity between binding sites in protein kinases. The presented study offers a novel molecular insight into mechanistic aspects of allosteric kinase signaling and provides a quantitative picture of activation mechanisms in protein kinases at the atomic level.     

Genetic diversity of tufted ducks (<Emphasis Type="Italic">Aythya fuligula</Emphasis>, Anatidae) in Eastern Europe

The tufted duck (Aythya fuligula, Anatidae) is widespread in the Palaearctic across Northern Eurasia. Birds breeding in Northern and Eastern Europe are highly migratory, while populations from Western Europe are partially migratory or resident. The aim of this study is to explore genetic variation within and between ducks breeding in Latvia and migrants sampled in North West Russia and Belarus. The technique of random amplified polymorphic DNA was applied using five random primers (ol-1, ol-9-12). Genetic variability was measured for all tufted ducks investigated and for different sub-populations from various regions. Individual genetic structure and genetic variability was higher in ducks collected from Latvia. Gene diversity of amplified DNA bands in birds of Latvian origin was 24% with 80% polymorphism. Means of gene diversity and polymorphism for tufted ducks sampled in other countries varied from 12 to 14% and from 27 to 40%, respectively. A high number of unique bands characterized ducks breeding in Latvia. The oligonucleotide primers used in this study were suitable to analyze differences among tufted ducks of different origin. Possible explanations for the variation observed among the studied ducks are discussed.     

Molecular sub-classification of renal epithelial tumors using meta-analysis of gene expression microarrays

Purpose

To evaluate the accuracy of the sub-classification of renal cortical neoplasms using molecular signatures.

Experimental Design

A search of publicly available databases was performed to identify microarray datasets with multiple histologic sub-types of renal cortical neoplasms. Meta-analytic techniques were utilized to identify differentially expressed genes for each histologic subtype. The lists of genes obtained from the meta-analysis were used to create predictive signatures through the use of a pair-based method. These signatures were organized into an algorithm to sub-classify renal neoplasms. The use of these signatures according to our algorithm was validated on several independent datasets.

Results

We identified three Gene Expression Omnibus datasets that fit our criteria to develop a training set. All of the datasets in our study utilized the Affymetrix platform. The final training dataset included 149 samples represented by the four most common histologic subtypes of renal cortical neoplasms: 69 clear cell, 41 papillary, 16 chromophobe, and 23 oncocytomas. When validation of our signatures was performed on external datasets, we were able to correctly classify 68 of the 72 samples (94%). The correct classification by subtype was 19/20 (95%) for clear cell, 14/14 (100%) for papillary, 17/19 (89%) for chromophobe, 18/19 (95%) for oncocytomas.

Conclusions

Through the use of meta-analytic techniques, we were able to create an algorithm that sub-classified renal neoplasms on a molecular level with 94% accuracy across multiple independent datasets. This algorithm may aid in selecting molecular therapies and may improve the accuracy of subtyping of renal cortical tumors.     

Fitness ranking of individual mutants drives patterns of epistatic interactions in HIV-1

Fitness interactions between mutations, referred to as epistasis, can strongly impact evolution. For RNA viruses and retroviruses with their high mutation rates, epistasis may be particularly important to overcome fitness losses due to the accumulation of deleterious mutations and thus could influence the frequency of mutants in a viral population. As human immunodeficiency virus type 1 (HIV-1) resistance to azidothymidine (AZT) requires selection of sequential mutations, it is a good system to study the impact of epistasis. Here we present a thorough analysis of a classical AZT-resistance pathway (the 41-215 cluster) of HIV-1 variants by fitness measurements in single round infection assays covering physiological drug concentrations ex vivo. The sign and value of epistasis varied and did not predict the epistatic effect on the mutant frequency. This complex behavior is explained by the fitness ranking of the variants that strongly depends on environmental factors, i.e., the presence and absence of drugs and the host cells used. Although some interactions compensate fitness losses, the observed small effect on the relative mutant frequencies suggests that epistasis might be inefficient as a buffering mechanism for fitness losses in vivo. While the use of epistasis-based hypotheses to make general assumptions on the evolutionary dynamics of viral populations is appealing, our data caution their interpretation without further knowledge on the characteristics of the viral mutant spectrum under different environmental conditions.     

Natural Variants of Photosystem II Subunit D1 Tune Photochemical Fitness to Solar Intensity

Photosystem II (PSII) is composed of six core polypeptides that make up the minimal unit capable of performing the primary photochemistry of light-driven charge separation and water oxidation in all oxygenic phototrophs. The D1 subunit of this complex contains most of the ligating amino acid residues for the Mn₄CaO₅ core of the water-oxidizing complex (WOC). Most cyanobacteria have 3–5 copies of the psbA gene coding for at least two isoforms of D1, whereas algae and plants have only one isoform. Synechococcus elongatus PCC 7942 contains two D1 isoforms; D1:1 is expressed under low light conditions, and D1:2 is up-regulated in high light or stress conditions. Using a heterologous psbA expression system in the green alga Chlamydomonas reinhardtii, we have measured growth rate, WOC cycle efficiency, and O₂ yield as a function of D1:1, D1:2, or the native algal D1 isoform. D1:1-PSII cells outcompete D1:2-PSII cells and accumulate more biomass in light-limiting conditions. However, D1:2-PSII cells easily outcompete D1:1-PSII cells at high light intensities. The native C. reinhardtii-PSII WOC cycles less efficiently at all light intensities and produces less O₂ than either cyanobacterial D1 isoform. D1:2-PSII makes more O₂ per saturating flash than D1:1-PSII, but it exhibits lower WOC cycling efficiency at low light intensities due to a 40% faster charge recombination rate in the S₃ state. These functional advantages of D1:1-PSII and D1:2-PSII at low and high light regimes, respectively, can be explained by differences in predicted redox potentials of PSII electron acceptors that control kinetic performance.     

In vivo bicarbonate requirement for water oxidation by Photosystem II in the hypercarbonate-requiring cyanobacterium Arthrospira maxima

While the presence of inorganic carbon in the form of (bi)carbonate has been known to be important for activity of Photosystem II (PSII), the vast majority of studies on this "bicarbonate effect" have been limited to in vitro studies of isolated thylakoid membranes and PSII complexes. Here we report an in vivo requirement for bicarbonate that is both reversible and selective for this anion for efficient water oxidation activity in the hypercarbonate-requiring cyanobacterium Arthrospira (Spirulina) maxima, originally isolated from highly alkaline soda lakes. Using a non-invasive internal probe of PSII charge separation (variable fluorescence), primary electron acceptor (Q(A)(-)/Q(A)) reoxidation rate, and flash-induced oxygen yield, we report the largest reversible bicarbonate effect on PSII activity ever observed, which is due to the requirement for bicarbonate at the water-oxidizing complex. Temporal separation of this donor side bicarbonate requirement from a smaller effect of bicarbonate on the Q(A)(-) reoxidation rate was observed. We expect the atypical way in which Arthrospira manages intracellular pH, sodium, and inorganic carbon concentrations relative to other cyanobacteria is responsible for this strong in vivo bicarbonate requirement.