Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways

Background

Cellular activities are governed by the physical and the functional interactions among several proteins involved in various biological pathways. With the availability of sequenced genomes and high-throughput experimental data one can identify genome-wide protein-protein interactions using various computational techniques. Comparative assessments of these techniques in predicting protein interactions have been frequently reported in the literature but not their ability to elucidate a particular biological pathway.

Methods

Towards the goal of understanding the prediction capabilities of interactions among the specific biological pathway proteins, we report the analyses of 14 biological pathways of Escherichia coli catalogued in KEGG database using five protein-protein functional linkage prediction methods. These methods are phylogenetic profiling, gene neighborhood, co-presence of orthologous genes in the same gene clusters, a mirrortree variant, and expression similarity.

Conclusions

Our results reveal that the prediction of metabolic pathway protein interactions continues to be a challenging task for all methods which possibly reflect flexible/independent evolutionary histories of these proteins. These methods have predicted functional associations of proteins involved in amino acids, nucleotide, glycans and vitamins & co-factors pathways slightly better than the random performance on carbohydrate, lipid and energy metabolism. We also make similar observations for interactions involved among the environmental information processing proteins. On the contrary, genetic information processing or specialized processes such as motility related protein-protein linkages that occur in the subset of organisms are predicted with comparable accuracy. Metabolic pathways are best predicted by using neighborhood of orthologous genes whereas phyletic pattern is good enough to reconstruct central dogma pathway protein interactions. We have also shown that the effective use of a particular prediction method depends on the pathway under investigation. In case one is not focused on specific pathway, gene expression similarity method is the best option.     

Alterations in certain lysosomal glycohydrolases and cathepsins in rats on dexamethasone administration

Glucocorticoids have been used in the treatment of a number of diseases where immunological intolerance plays a predominant role. Since immunological intolerance points to the involvement of lysosomal enzymes and glucocorticoids are known to affect their activities, we have attempted to study the effect of these steroids on cardiac and renal enzymes. Dexamethasone, a glucocorticoid, is administered subcutaneously to male Wistar rats at a dosage of 2.5 mg/kg/week on alternate days for two weeks. After withdrawing the steroid, the animals are monitored for one week to oversee the recovery process. Total and free activities of glycohydrolases and cathepsins in serum, heart and kidney are assayed on the days 4, 8, 12, 16 of dexamethasone administration and also on days 4 and 8 following discontinuation of the steroid. During dexamethasone administration, a significant decrease in both the free and total activities of -glucuronidase, -N-acetyl glucosaminidase, -galactosidase, -galactosidase, -mannosidase, cathepsin B and cathepsin D are observed in heart and kidney, but the enzyme levels are shown to increase in serum. On withdrawal of the steroid, the activities of -glucuronidase, -N-acetyl glucosaminidase, -galactosidase are found to be increased in heart and kidney, whereas, the activity of -mannosidase remains within normal values. Thus, it could be seen that dexamethasone alters the pattern of glycohydrolases and cathepsins, which are involved in protein degradation.     

Development and Validation of a Risk Score for Predicting Death after Pneumonectomy

Pneumonectomy is associated with significant postoperative mortality. This study was undertaken to develop and validate a risk model of mortality following pneumonectomy. We reviewed our prospective database and identified 774 pneumonectomies from a total of 7792 consecutive anatomical lung resections in the years 2003 to 2010 (rate of pneumonectomy: 9.9%). Based on data from 542 pneumonectomies between 2003 and 2007 (i.e., the "discovery set"), a penalized multivariable logistic regression analysis was performed to identify preoperative risk factors. A risk model was developed and validated in an independent data set of 232 pneumonectomies that were performed between 2008 and 2010 (i.e., the "validation set"). Of the 542 patients in the discovery set (DS), 35 patients (6.5%) died after pneumonectomy during the same admission. We developed a risk prediction model for in-hospital mortality following pneumonectomy; that model included age, current alcohol use, coronary artery disease, preoperative leukocyte count and palliative indication as possible risk factors. The risk model was subsequently successfully validated in an independent data set (n = 232) in which 18 patients (7.8%) died following pneumonectomy. For the validation set, the sensitivity of the model was 53.3% (DS: 54.3%), the specificity was 88.0% (DS: 87.4%), the positive predictive value was 26.7% (DS: 22.9%) and the negative predictive value was 95.8% (DS: 96.5%). The Brier score was 0.062 (DS: 0.054). The prediction model is statistically valid and clinically relevant.     

Studies on the breeding habits and development of the brood-pouch of a viviparous prosobranch; Melania scabra

Studie son the breeding habits and development of the brood-pouch of a freshwater prosobranch, Melania scabra, have revealed that the snail is ovoviviparous, showing parthenogenetic reproduction. The embryos complete their development in a special incubatory pouch called the brood-pouch or brood chamber, and hatch out in a form completely resembling that of the adult. The snail was found to be a continuous breeder, showing gravid condition throughout the year. General structure, development and functions of the brood-pouch were studied in detail. The brood-pouch was found to contain a slightly alkaline albuminous fluid with a pH 7.2, Qualitative and histochemical studies of the brood-pouch revealed the presence of glycogen, fat and protein as the major constituents. These probably play an important role in the nutrition of embryos.     

Influence of alkali-treated cornsteep liquor containing medium on protein A production byStaphylococcus aureus

Staphylococcus aureus cultivated in liquid media containing untreated cornsteep liquor (CSL) and alkali-treated CSL produced similar biomass yields (6.5–6.9 g/L). However, contents of protein A in the biomass was 0.5% and 1.56% for untreated CSL and treated CSL, respectively. Addition of treated CSL at 20 g/L achieved optimal enhancement of protein A production (0.11 g/L). Probable factors associated in treated CSL for the enhanced protein A production are discussed.     

Cadmium reduces nitric oxide production by impairing phosphorylation of endothelial nitric oxide synthase.

Cadmium (Cd) perturbs vascular health and interferes with endothelial function. However, the effects of exposing endothelial cells to low doses of Cd on the production of nitric oxide (NO) are largely unknown. The objective of the present study was to evaluate these effects by using low levels of CdCl2 concentrations, ranging from 10 to 1000 nmol/L. Cd perturbations in endothelial function were studied by employing wound-healing and MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays. The results suggest that a CdCl2 concentration of 100 nmol/L maximally attenuated NO production, cellular migration, and energy metabolism in endothelial cells. An egg yolk angiogenesis model was employed to study the effect of Cd exposure on angiogenesis. The results demonstrate that NO supplementation restored Cd-attenuated angiogenesis. Immunofluorescence, Western blot, and immuno-detection studies showed that low levels of Cd inhibit NO production in endothelial cells by blocking eNOS phosphorylation, which is possibly linked to processes involving endothelial function and dysfunction, including angiogenesis.     

Exposing cardiomyocytes to subclinical concentrations of doxorubicin rapidly reduces their creatine transport

Doxorubicin is commonly used to treat leukemia, lymphomas, and solid tumors, such as soft tissue sarcomas or breast cancer. A major side effect of doxorubicin therapy is dose-dependent cardiotoxicity. Doxorubicin's effects on cardiac energy metabolism are emerging as key elements mediating its toxicity. We evaluated the effect of doxorubicin on [(14)C]creatine uptake in rat neonatal cardiac myocytes and HL-1 murine cardiac cells expressing the human creatine transporter protein. A significant and irreversible decrease in creatine transport was detected after an incubation with 50-100 nmol/l doxorubicin. These concentrations are well below peak plasma levels (5 μmol/l) and within the ranges (25-250 nmol/l) for steady-state plasma concentrations reported after the administration of 15-90 mg/m(2) doxorubicin for chemotherapy. The decrease in creatine transport was not solely because of increased cell death due to doxorubicin's cytotoxic effects. Kinetic analysis showed that doxorubicin decreased V(max), K(m), and creatine transporter protein content. Cell surface biotinylation experiments confirmed that the amount of creatine transporter protein present at the cell surface was reduced. Cardiomyocytes rely on uptake by a dedicated creatine transporter to meet their intracellular creatine needs. Our findings show that the cardiomyocellular transport capacity for creatine is substantially decreased by doxorubicin administration and suggest that this effect may be an important early event in the pathogenesis of doxorubicin-mediated cardiotoxicity.     

Validation of a blood protein signature for non-small cell lung cancer

Background

CT screening for lung cancer is effective in reducing mortality, but there are areas of concern, including a positive predictive value of 4% and development of interval cancers. A blood test that could manage these limitations would be useful, but development of such tests has been impaired by variations in blood collection that may lead to poor reproducibility across populations.

Results

Blood-based proteomic profiles were generated with SOMAscan technology, which measured 1033 proteins. First, preanalytic variability was evaluated with Sample Mapping Vectors (SMV), which are panels of proteins that detect confounders in protein levels related to sample collection. A subset of well collected serum samples not influenced by preanalytic variability was selected for discovery of lung cancer biomarkers. The impact of sample collection variation on these candidate markers was tested in the subset of samples with higher SMV scores so that the most robust markers could be used to create disease classifiers. The discovery sample set (n = 363) was from a multi-center study of 94 non-small cell lung cancer (NSCLC) cases and 269 long-term smokers and benign pulmonary nodule controls. The analysis resulted in a 7-marker panel with an AUC of 0.85 for all cases (68% adenocarcinoma, 32% squamous) and an AUC of 0.93 for squamous cell carcinoma in particular. This panel was validated by making blinded predictions in two independent cohorts (n = 138 in the first validation and n = 135 in the second). The model was recalibrated for a panel format prior to unblinding the second cohort. The AUCs overall were 0.81 and 0.77, and for squamous cell tumors alone were 0.89 and 0.87. The estimated negative predictive value for a 15% disease prevalence was 93% overall and 99% for squamous lung tumors. The proteins in the classifier function in destruction of the extracellular matrix, metabolic homeostasis and inflammation.

Conclusions

Selecting biomarkers resistant to sample processing variation led to robust lung cancer biomarkers that performed consistently in independent validations. They form a sensitive signature for detection of lung cancer, especially squamous cell histology. This non-invasive test could be used to improve the positive predictive value of CT screening, with the potential to avoid invasive evaluation of nonmalignant pulmonary nodules.