CNAmet: an R package for integrating copy number, methylation and expression data

SUMMARY: Gene copy number and DNA methylation alterations are key regulators of gene expression in cancer. Accordingly, genes that show simultaneous methylation, copy number and expression alterations are likely to have a key role in tumor progression. We have implemented a novel software package (CNAmet) for integrative analysis of high-throughput copy number, DNA methylation and gene expression data. To demonstrate the utility of CNAmet, we use copy number, DNA methylation and gene expression data from 50 glioblastoma multiforme and 188 ovarian cancer primary tumor samples. Our results reveal a synergistic effect of DNA methylation and copy number alterations on gene expression for several known oncogenes as well as novel candidate oncogenes. AVAILABILITY: CNAmet R-package and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/CNAmet.     

Mutagenesis of apyrase conserved region 1 alters the nucleotide substrate specificity

Two apyrases having different substrate specificity, MP67 and MpAPY2, are present in Mimosa pudica. The substrate specificity of MP67 is quite high against ADP, and is distinct from any other apyrase. This might be attributed to the nucleotide binding motif (DXG) in apyrase conserved region 1. We performed a single amino acid substitution at position X in the motif. The ratio of the velocity of ATP/ADP hydrolysis was higher (approximately 1) for the S63A-MP67 mutant than for wild type-MP67 (0.19). Binding affinity for ADP of A75S-MpAPY2 mutant was increased to a level higher than that of the wild type MpAPY2. Thus, the residue at position X in the DXG motif plays an important role in determining nucleotide preference.     

Proteinuria during Follow-Up Period and Long-Term Renal Survival of Childhood IgA Nephropathy

Background

Proteinuria is the most important risk factor for IgA nephropathy progression. The purpose of this study is to evaluate the long-term outcome and risk factors for poor prognosis in childhood IgA nephropathy.

Methods

Patients who were diagnosed with IgA nephropathy between 1972 and 1992 at the Tokyo Metropolitan Kiyose Children’s Hospital were included. We analyzed risk factors for progression to end-stage kidney disease (ESKD) and chronic renal insufficiency (CRI) using Kaplan-Meier method and multivariate analyses of Cox proportional hazard model.

Results

One hundred patients were included and the median observation period was 11.8 years. Twelve and 17 patients progressed to ESKD and CRI, respectively. The survival probabilities were 90.0% at 10 years and 79.8% at 20 years for ESKD, and 86.1% at 10 years and 72.3% at 20 years for CRI. Notably, patients with heavy proteinuria with hypoalbuminemia during follow-up period showed extremely poor prognosis. In this group, the survival rate at 10 years from ESKD and CRI was 40.6% and 20.8%, respectively. By multivariate analysis, proteinuria at diagnosis and proteinuria during follow-up period were risk factors for ESKD, whereas glomeruli showing mesangial proliferation ≥50% and proteinuria during follow-up period were risk factors for CRI. Patients without heavy proteinuria during follow-up period did not develop CRI and 63% of patients with mild proteinuria during follow-up period showed no proteinuria at the last observation.

Conclusions

The degree of proteinuria during follow-up period is the strongest risk factor for ESKD and CRI.     

Mutation design of a thermophilic Rubisco based on three‐dimensional structure enhances its activity at ambient temperature

Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) plays a central role in carbon dioxide fixation on our planet. Rubisco from a hyperthermophilic archaeon Thermococcus kodakarensis (Tk‐Rubisco) shows approximately twenty times the activity of spinach Rubisco at high temperature, but only one‐eighth the activity at ambient temperature. We have tried to improve the activity of Tk‐Rubisco at ambient temperature, and have successfully constructed several mutants which showed higher activities than the wild‐type enzyme both in vitro and in vivo. Here, we designed new Tk‐Rubisco mutants based on its three‐dimensional structure and a sequence comparison of thermophilic and mesophilic plant Rubiscos. Four mutations were introduced to generate new mutants based on this strategy, and one of the four mutants, T289D, showed significantly improved activity compared to that of the wild‐type enzyme. The crystal structure of the Tk‐Rubisco T289D mutant suggested that the increase in activity was due to mechanisms distinct from those involved in the improvement in activity of Tk‐Rubisco SP8, a mutant protein previously reported to show the highest activity at ambient temperature. Combining the mutations of T289D and SP8 successfully generated a mutant protein (SP8‐T289D) with the highest activity to date both in vitro and in vivo. The improvement was particularly pronounced for the in vivo activity of SP8‐T289D when introduced into the mesophilic, photosynthetic bacterium Rhodopseudomonas palustris, which resulted in a strain with nearly two‐fold higher specific growth rates compared to that of a strain harboring the wild‐type enzyme at ambient temperature. Proteins 2016; 84:1339–1346. © 2016 Wiley Periodicals, Inc.     

Quantification of Estrogen Receptor-Alpha Expression in Human Breast Carcinomas With a Miniaturized,Low-Cost Digital Microscope: A Comparison with a High-End Whole Slide-Scanner

Introduction

A significant barrier to medical diagnostics in low-resource environments is the lack of medical care and equipment. Here we present a low-cost, cloud-connected digital microscope for applications at the point-of-care. We evaluate the performance of the device in the digital assessment of estrogen receptor-alpha (ER) expression in breast cancer samples. Studies suggest computer-assisted analysis of tumor samples digitized with whole slide-scanners may be comparable to manual scoring, here we study whether similar results can be obtained with the device presented.

Materials and Methods

A total of 170 samples of human breast carcinoma, immunostained for ER expression, were digitized with a high-end slide-scanner and the point-of-care microscope. Corresponding regions from the samples were extracted, and ER status was determined visually and digitally. Samples were classified as ER negative (<1% ER positivity) or positive, and further into weakly (1–10% positivity) and strongly positive. Interobserver agreement (Cohen’s kappa) was measured and correlation coefficients (Pearson’s product-momentum) were calculated for comparison of the methods.

Results

Correlation and interobserver agreement (r = 0.98, p < 0.001, kappa = 0.84, CI95% = 0.75–0.94) were strong in the results from both devices. Concordance of the point-of-care microscope and the manual scoring was good (r = 0.94, p < 0.001, kappa = 0.71, CI95% = 0.61–0.80), and comparable to the concordance between the slide scanner and manual scoring (r = 0.93, p < 0.001, kappa = 0.69, CI95% = 0.60–0.78). Fourteen (8%) discrepant cases between manual and device-based scoring were present with the slide scanner, and 16 (9%) with the point-of-care microscope, all representing samples of low ER expression.

Conclusions

Tumor ER status can be accurately quantified with a low-cost imaging device and digital image-analysis, with results comparable to conventional computer-assisted or manual scoring. This technology could potentially be expanded for other histopathological applications at the point-of-care.     

Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage

The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy—termed the "R-clamp”—that favors the formation of this salt bridge via buttressing Arg77. Comparison of evolutionarily diverse Nef proteins revealed that several distinct R-clamps have evolved that are functionally equivalent but differ in the side chain compositions of Nef residues 83 and 120. Whereas a similar R-clamp design is shared by Nef proteins of HIV-1 groups M, O, and P, as well as SIVgor, the Nef proteins of SIV from the Eastern chimpanzee subspecies (SIVcpz^P.t.s.) exclusively utilize another type of R-clamp. By contrast, SIV of Central chimpanzees (SIVcpz^P.t.t.) and HIV-1 group N strains show more heterogenous R-clamp design principles, including a non-functional evolutionary intermediate of the aforementioned two classes. These data add to our understanding of the structural basis of SH3 binding and kinase deregulation by Nef, and provide an interesting example of primate lentiviral protein evolution.     

Temperature-sensitive plant mutants isolated in vitro

Summary Conditional-lethal, temperature-sensitive plant mutants have been isolated using a simple protoplast cloning method. The leaf protoplasts used were obtained from sterile, haploid shoot cultures of Nicotiana plumbaginifolia. Recessive mutations are described at three loci: ts1, ts2 and ts3. The mutations are lethal when either tissue cultures or plants are incubated at 33°C but not at 26°C.     

Physiological, stomatal and ultrastructural ozone responses in birch (Betula pendula Roth.) are modified by water stress

The physiological, stomatal and ultrastructural responses to ozone and drought of ozone-sensitive and more ozone-tolerant birch ( Betula pendula Roth.) clones were studied singly and in combination, in a high-stress chamber experiment and in a low-stress open-field experiment. In the chamber experiment, well watered (WW), moderately watered (MW) or drought-stressed (DS) saplings were exposed for 36 d to 0 or 130 nmol mol^∠1 ozone. In the open-field experiment, well watered or drought-stressed saplings were grown for one growing season in ambient air or exposed to 1·8 × ambient ozone. Drought stress reduced growth rate, stomatal conductance, stomatal density and the proportion of starch and thylakoids in chloroplasts, but stimulated net photosynthesis, Rubisco and chlorophyll quantity at the end of the growing season, and increased the size and density of plastoglobuli. Ozone fumigations caused more variable, clone- and exposure-dependent responses in growth, decreased stomatal conductance and net photosynthesis, an increased number of stomata, visible and ultrastructural chloroplast injuries, and enhanced autumn yellowing of the leaves. Ozone-induced changes in plastoglobuli, starch and thylakoids resembled drought responses. The two experiments revealed that, depending on the experimental conditions and the variable, the response to drought and ozone stress can be independent, additive or interactive. Drought protected the plants from ozone injuries under high-stress conditions in the chamber experiment. In the low-stress, open-field experiment, however, enhanced ozone damage was observed in birch saplings grown under restricted water supply.