Network-based identification of key proteins involved in apoptosis and cell cycle regulation

OBJECTIVES

Cancer cells differ from normal body cells in their ability to divide indefinitely and to evade programmed cell death. Crosstalk between apoptosis and cell cycle processes promotes balance between proliferation and death, and limits population growth and survival of cells. However, intricate relationships between them and how they are able to manipulate the fate of cancer cells still remain to be clarified. Identification of key factors involved in both apoptosis and cell cycle regulation may help to address this problem.

MATERIALS AND METHODS

Identification of such key proteins was carried out, using a series of bioinformatics methods, such as network construction and key protein identification.

RESULTS

In this study, we computationally constructed human apoptotic/cell cycle-related protein-protein interactions (PPIs) networks from five experimentally supported protein interaction databases, and further integrated these high-throughput data sets into a Naïve Bayesian model to predict protein functional connections. On the basis of modified apoptotic/cell cycle related PPI networks, we calculated and ranked all protein members involved in apoptosis and cell cycle regulation. Our results not only identified some already known key proteins such as p53, Rb, Myc and Src but also found that the proteasome, Cullin family members, kinases and transcriptional repressors play important roles in regulating apoptosis and the cell cycle. Furthermore, we found that the top 100 proteins ranked by PeC were enriched in some pathways such as those of cancer, the proteasome, the cell cycle and Wnt signalling.

CONCLUSIONS

We constructed the global human apoptotic/cell cycle related PPI network based on five online databases, and a Naïve Bayesian model. In addition, we systematically identified apoptotic/cell cycle related key proteins in cancer cells. These findings may uncover intricate relationships between apoptosis and cell cycle processes and thus provide further new clues towards future anticancer drug discovery.

Bioinformatics analysis of gene expression in peripheral blood mononuclear cells from children with type 1 diabetes in 3 periods

To explore the expression changes of potential key genes and relevant biological processes in peripheral blood mononuclear cells of children with newly diagnosis of type 1 diabetes (T1D).Microarray data GSE9006 were downloaded from Gene Expression Omnibus (GEO) database, including peripheral blood mononuclear cells samples from 43 children with newly diagnosed T1D (NEW), 19 one-month (1-MO) follow-up samples, 19 4-month (4-MO) follow-up samples and 24 healthy controls. The differentially expressed genes (DEGs) were identified using Affy package in R, and cluster analysis of DEGs were performed following functional enrichment analysis with Database for Annotation, Visualization and Integrated Discovery (DAVID) and construction of protein-protein interaction (PPI) network with STRING database.We identified 73, 73, 96 DEGs in NEW group, 1-MO group and 4-MO group, respectively by comparing with healthy controls with |logFC|>0.58 and P-value<0.05. The cluster analysis of these DEGs showed that 4 genes, including human leukocyte antigen (HLA-DQA1), HLA-DRB4, integrin 3 (ITGB3) and killer cell lectin-like receptor subfamily F member 1 (KLRF1) were all significantly expressed in 3 groups, which were significantly enriched in asthma, T1D and intestinal immune network for IgA production pathway. And 57 genes enriched in cluster 5, which were only differentially expressed in NEW group, were involved in response to wounding, inflammatory response and blood coagulation as well as chemokine signaling pathway. Besides, the hub genes in PPI network of cluster 5 were identified, containing FOS, pro-platelet basic protein (PPBP), interleukin 8 (IL8), formyl peptide receptor-like 2 (FPR2) and platelet factor 4 (PF4).HLA-DQA1, HLA-DRB4, ITGB3 and KLRF1 might be targets for treatment of T1D, and 5 hub proteins, FOS, PPBP, IL8, FPR2 and PF4, were likely to be new markers for diagnosis of T1D.

Low intensity conduction states in FeS2: implications for absorption, open-circuit voltage and surface recombination

Pyrite (FeS2), being a promising material for future solar technologies, has so far exhibited in experiments an open-circuit voltage (OCV) of around 0.2 V, which is much lower than the frequently quoted 'accepted' value for the fundamental bandgap of ∼0.95 eV. Absorption experiments show large subgap absorption, commonly attributed to defects or structural disorder. However, computations using density functional theory with a semi-local functional predict that the bottom of the conduction band consists of a very low intensity sulfur p-band that may be easily overlooked in experiments because of the high intensity onset that appears 0.5 eV higher in energy. The intensity of absorption into the sulfur p-band is found to be of the same magnitude as contributions from defects and disorder. Our findings suggest the need to re-examine the value of the fundamental bandgap of pyrite presently in use in the literature. If the contribution from the p-band has so far been overlooked, the substantially lowered bandgap would partly explain the discrepancy with the OCV. Furthermore, we show that more states appear on the surface within the low energy sulfur p-band, which suggests a mechanism of thermalization into those states that would further prevent extracting electrons at higher energy levels through the surface. Finally, we speculate on whether misidentified states at the conduction band onset may be present in other materials.

Spontaneous intramural small-bowel hematoma secondary to anticoagulant therapy: a case series

Spontaneous small-bowel hematomas most commonly involve the jejunum, followed by the ileum and duodenum, and occur in patients who receive excessive anticoagulation with phenprocoumon/warfarin or who have additional risk factors for bleeding. We report three cases of intramural small-bowel hematoma, all complications of treatment with phenprocoumon, which nowadays is used extensively for therapeutic and prophylactic purposes. Diagnosis can be readily attained by sonography and confirmed using computed tomography. Early diagnosis is crucial because most patients can be treated successfully without surgery. Based on this experience and data from the literature, conservative treatment is recommended for intramural intestinal hematomas, when other complications needing laparotomy have been excluded.

A neural network model of causality

This paper proposes a model for commonsense causal reasoning, based on the basic idea of neural networks. After an analysis of the advantages and limitations of existing accounts of causality, a fuzzy logic based formalism FEL is proposed that takes into account the inexactness and the cumulative evidentiality of commonsense causal reasoning, overcoming the limitations of existing accounts. Analyses concerning how FEL handles various aspects of commonsense causal reasoning are performed, in an abstract way. FEL can be implemented (naturally) in a neural (connectionist) network. This work also serves to link rule-based reasoning with neural network models, in that a rule-encoding scheme (FEL) is equated directly to a neural network model.

Mechanisms of smooth muscle responses to inflammation

BACKGROUND

Inflammation-induced changes in smooth muscle may be the consequence of changes in the properties of smooth muscle itself, in the control by nerves and hormones, in the microenvironment, or in the balance of constitutive or induced mediators. A general concept is that the specific characteristics and effects of inflammation can be linked to the nature of the infiltrate and the associated mediators, which are dictated predominantly by the immune environment. Inflammatory mediators may regulate smooth muscle function by directly acting on smooth muscle cells or, indirectly, through stimulation of the release of mediators from other cells. In addition, smooth muscle is not a passive bystander during inflammation and our knowledge of molecular signaling pathways that control smooth muscle function, and the contribution of the immune mechanisms to smooth muscle homeostasis, has expanded greatly in the last decade. Recent studies also demonstrated the relevance of extracellular proteases, of endogenous or exogenous origin, redox imbalance, or epigenetic mechanisms, to gastrointestinal dismotility and inflammation in the context of functional and organic disorders.

PURPOSE

In this review we discuss the various types of inflammation and the established and emerging mechansims of inflammation-induced changes in smooth muscle morphology and function.

Comparison of micafungin and voriconazole in the treatment of invasive fungal infections in kidney transplant recipients

WHAT IS KNOWN AND OBJECTIVE

Invasive fungal infections are a major threat to renal transplant recipients. Micafungin and voriconazole are two useful antifungal agents for treating such infections. Our objective is to evaluate the comparative efficacy and safety of micafungin and voriconazole in the initial treatment of such infections.

METHODS

In this prospective, multicentre, open-labelled, randomized, controlled trial, renal transplant recipients with invasive fungal infections were assigned to receive either micafungin or voriconazole. The enrolled subjects received a kidney transplant between March 2008 and March 2010 at one of the two transplant centres in Henan Province, China. The efficacy and adverse effects of the two treatments were compared.

RESULTS AND DISCUSSION

The clinical trial enrolled 65 patients, of whom 31 were treated with micafungin, and 34 with voriconazole. The rates of microbiological evidence of infection in the micafungin and voriconazole groups were 64.5% and 70.5%, respectively, whereas the rates of Candida as the major cultured fungus were 80.0% and 75.0%, respectively. Complicated bacterial infection rates in the two treatment groups were 38.7% and 32.4%, respectively, whereas complicated CMV viral infection occurred at a rate of 19.2% and 23.5%, respectively. Fungal infection within one to 3 months after transplant was 83.6% (26/31) and 85.3% (29/34) in the micafungin and voriconazole groups, respectively. There was no significant difference between the two groups in terms of efficacy, survival beyond 10 days and discontinuation of treatment because of lack of efficacy (P > 0.05). Mortality rates in the micafungin and voriconazole groups were 9.7% (3/31) and 12.1% (4/33), respectively. Rates of adverse effects in the two groups were 41.9% and 51.6% (P > 0.05), respectively.

WHAT IS NEW AND CONCLUSIONS

This is the first comparison of micafungin and voriconazole in renal transplant patients. Our study shows that the effectiveness of micafungin was similar to that of voriconazole in such patients.

[Partial thrombosis of the inferior vena cava in a patient with non-Hodgkin lymphoma and history of lumbar spine surgery]

Complete or partial thrombosis of the inferior vena cava is usually due to pre-existing malformation of the vessel, malignant tumors, ascending thrombosis, or thrombophilic disorders. We report the case of an 81-year-old woman, in whom a partial thrombosis of the vena cava was observed in the CT scan when re-staging was performed after six cycles of R-CHOP because of high-grade malignant non-Hodgkin lymphoma. Before chemotherapy was started, the patient had undergone an operation of the lumbar spine using cement augmentation. Retrospective analysis showed that cement had penetrated a segmental vein and spilled into the vena cava leading to formation of an adhering blood thrombus. The patient was free of symptoms and anticoagulation was started. Spillage of cement frequently occurs in the process of vertebroplasty and kyphoplasty and may result in serious sequelae. As these procedures are increasingly being used, physicians should be aware of these complications if a patient presents with thrombosis of the caval vein or signs of pulmonary embolism.

P2-08-03: Quantitative MRI for Noninvasive Prediction of Prognostic Markers in Breast Cancer

Background: Magnetic resonance imaging (MRI) is a valuable tool for assessing extent of breast cancer and monitoring treatment response. Quantitative measures by diffusion-weighted MRI (DWI) and dynamic contrast-enhanced (DCE) MRI reflect tumor cellularity and vascularity. Tumor grade and some histopathological markers, such as ER, PR, HER-2, Ki67 and P53, are prognostic factors that can also be associated with tumor cellularity and vascularity. DWI and DCE measures may therefore provide a noninvasive means for predicting disease prognosis and stratifying patients to appropriate therapies. The purpose of this study was to investigate the correlation between quantitative MRI features and prognostic pathological factors in patients with invasive breast cancer.

Methods: This IRB-approved retrospective study included patients with biopsy-proven invasive cancer who underwent 1.5T breast MRI (including DCE and DWI) from October 2005 to May 2006 prior to treatment. Pathology data was obtained from pre-treatment biopsy and intrinsic subtype classification was approximated by standard immunohistochemistry characteristics. After excluding cases with missing MRI or pathology data, the final study cohort included 41 invasive cancers (36 ductal and 5 lobular carcinomas) in 36 patients. MRI measures included lesion DCE kinetic features: peak initial enhancement (PE), percent rapid enhancement (RE), and percent washout (WO), and DWI normalized apparent diffusion coefficient values (nADC). Associations between imaging features and pathology markers, cancer grades and intrinsic subtypes were evaluated by Mann-Whitney U test and multivariate logistic regression.

Results: Results of univariate comparisons are summarized in Table 1. One or more DCE-MRI kinetic parameters were significantly predictive (p&lt;0.05) of each of the histopathological markers with the exception of ER, which was marginally associated with WO (p=0.05). Each of the DCE kinetics parameters significantly discriminated grade III tumors from grades I and II and luminal A from luminal B and basal-like intrinsic subtypes. In multivariate regression, both PE and WO were significant independent predictors of tumor grade (p=0.0094, p=0.0005, respectively). WO and nADC were significant independent predictors of PR status (p=0.0054, p=0.0027), while PE was the only significant independent predictor of both Ki67 (p=0.014) and intrinsic subtype (p=0.015).

Conclusion: This preliminary study suggests that quantitative MRI measures are associated with prognostic tumor markers and may provide valuable noninvasive characterization of tumor biology. Larger prospective studies are needed to validate our findings.

A novel lift-off method for fabricating patterned and vertically-aligned W18O49 nanowire arrays with good field emission performance

A novel lift-off method has been developed for fabricating patterned W(18)O(49) nanowires in vertical arrays and on a large scale. These W(18)O(49) nanowire arrays have an average diameter of about 30 nm, and their lengths range from 2-3 μm. In every pattern of a 2 inch sample, the nanowires exhibit the same morphology and growth density. They are single crystals with monoclinic structure and grow along the [010] direction. Field emission (FE) measurements show that they have a turn-on field of 6.2 V μm(-1) and their emission current density can reach 500 μA cm(-2) at an electric field of 10.9 V μm(-1). Because the W(18)O(49) nanowire patterns synthesized by this simple method still have good FE performance, comparable to many cathode nanostructures with excellent FE properties, it suggests that it may provide an effective and simple preparation technique for patterned growth of nanowire arrays in future FE applications.

Identification and characterization of mitochondrial factors modulating thymidine kinase 2 activity

Thymidine kinase 2 (TK2) is one of four deoxynucleoside kinases (dNKs) in humans and plays a crucial role in the initial phosphorylation of pyrimidine nucleosides in the salvage pathway in mitochondria. Nucleoside analogues, like AZT, are substrates of TK2 and induced mitochondrial toxicity in long-term therapy. We found that AZT and FLT inhibited dThd phosphorylation but stimulated dCyd phosphorylation catalyzed by TK2. However, mitochondrial phosphorylation of both dThd and dCyd was inhibited by AZT and FLT. Here a preliminary identification and characterization of mitochondrial factors is reported.

Lymphocytic HLA-A mRNA is a reliable indicator of acute rejection in renal transplantation

BACKGROUND

Rejection in renal transplantation is the most frequent event causing transplant failure. It is important to identify parameters to predict rejection, which are helpful in a timely fashion.

METHODS

Fifty-nine renal transplant recipients were divided into two groups: group 1 (stable renal function) and group 2 (acute rejection episodes). The levels of HLA-A mRNA in peripheral blood lymphocytes (both pre- and posttransplantation) were measured by reverse transcriptase-polymerase chain reaction (RT-PCR) with glucose-6-phosphate dehydrogenase (G6PDH) as an internal reference. The TEST software was used to analyze the relative expressions of HLA-A mRNA.

RESULTS

There was no statistical significance between features of the two groups pretransplant versus normal controls. Posttransplant, the HLA-A mRNA levels decreased significantly compared to those of pretransplant and normal control individuals. The levels of HLA-A mRNA among the 10 patients with acute rejection episodes were significantly increased. There was no significant change in the lymphocyte populations in the early stage of an acute rejection episode compared with the prerejection value.

CONCLUSION

HLA-A mRNA expression was strongly correlated with immune status. The HLA-A mRNA levels may provide an effective and reliable indicator to predict acute rejection episodes in renal transplantation.

Coordination-dependent surface atomic contraction in nanocrystals revealed by coherent diffraction

Surface atoms have fewer interatomic bonds than those in the bulk that they often relax and reconstruct on extended two-dimensional surfaces. Far less is known about the surface structures of nanocrystals. Here, we show that coherent diffraction patterns recorded from individual nanocrystals are very sensitive to the atomic structure of nanocrystal surfaces. Nanocrystals of Au of 3-5 nm in diameter were studied by examining diffraction intensity oscillations around the Bragg peaks. Both results obtained from modelling the experimental data and molecular dynamics simulations strongly suggest inhomogeneous relaxations, involving large out-of-plane bond length contractions for the edge atoms (approximately 0.2 A); a significant contraction (approximately 0.13 A) for {100} surface atoms; and a much smaller contraction (approximately 0.05 A) for atoms in the middle of the {111} facets. These results denote a coordination/facet dependence that markedly differentiates the structural dynamics of nanocrystals from bulk crystalline surfaces.