Comparative analysis of perturbed molecular pathways identified in in vitro and in vivo toxicology studies.

The development of in vitro toxicological testing strategies are hampered by the difficulty in extrapolation to the intact organism. Academic toxicological literature contains a wealth of mechanistically rich information, especially arising from omic studies, which could potentially be utilized to uncover commonalities between in vitro and in vivo observations on the cellular level. Using a literature mining strategy, we identified 1221 unique human genes as being associated to nephrotoxicity, hepatotoxicity, or CNS toxicity, either linked to in vitro, in vivo, or both experimental conditions. Among this large set of relevant molecular features four genes were found in common to all tissues and experimental conditions analyzed, namely heme oxygenase-1, nitric oxide synthetase 2, NFκB1 and p53. Pathway enrichment revealed 17 relevant pathways for kidney, 26 for liver, and 30 for CNS bridging in vitro and in vivo toxicity effects. Such joint markers and pathways may serve as indicators for extrapolating from in vitro results to in vivo.

Hemocompatibility of Inorganic Physical Vapor Deposition (PVD) Coatings on Thermoplastic Polyurethane Polymers.

Biocompatibility improvements for blood contacting materials are of increasing interest for implanted devices and interventional tools. The current study focuses on inorganic (titanium, titanium nitride, titanium oxide) as well as diamond-like carbon (DLC) coating materials on polymer surfaces (thermoplastic polyurethane), deposited by magnetron sputtering und pulsed laser deposition at room temperature. DLC was used pure (a-C:H) as well as doped with silicon, titanium, and nitrogen + titanium (a-C:H:Si, a-C:H:Ti, a-C:H:N:Ti). In-vitro testing of the hemocompatibility requires mandatory dynamic test conditions to simulate in-vivo conditions, e.g., realized by a cone-and-plate analyzer. In such tests, titanium- and nitrogen-doped DLC and titanium nitride were found to be optimally anti-thrombotic and better than state-of-the-art polyurethane polymers. This is mainly due to the low tendency to platelet microparticle formation, a high content of remaining platelets in the whole blood after testing and low concentration of platelet activation and aggregation markers. Comparing this result to shear-flow induced cell motility tests with e.g., Dictostelium discoideum cell model organism reveals similar tendencies for the investigated materials.

Data and knowledge management in cross-Omics research projects.

Cross-Omics studies aimed at characterizing a specific phenotype on multiple levels are entering the -scientific literature, and merging e.g. transcriptomics and proteomics data clearly promises to improve Omics data interpretation. Also for Systems Biology the integration of multi-level Omics profiles (also across species) is considered as central element. Due to the complexity of each specific Omics technique, specialization of experimental and bioinformatics research groups have become necessary, in turn demanding collaborative efforts for effectively implementing cross-Omics. This setting imposes specific emphasis on data sharing platforms for Omics data integration and cross-Omics data analysis and interpretation. Here we describe a software concept and methodology fostering Omics data sharing in a distributed team setting which next to the data management component also provides hypothesis generation via inference, semantic search, and community functions. Investigators are supported in data workflow management and interpretation, supporting the transition from a collection of heterogeneous Omics profiles into an integrated body of knowledge.

Hypoxia response and VEGF-A expression in human proximal tubular epithelial cells in stable and progressive renal disease.

Proteinuria, inflammation, chronic hypoxia, and rarefaction of peritubular capillaries contribute to the progression of renal disease by affecting proximal tubular epithelial cells (PTECs). To study the transcriptional response that separates patients with a stable course from those with a progressive course of disease, we isolated PTECs by laser capture microdissection from cryocut tissue sections of patients with proteinuric glomerulopathies (stable n=20, progressive n=11) with a median clinical follow-up of 26 months. Gene-expression profiling and a systems biology analysis identified activation of intracellular vascular endothelial growth factor (VEGF) signaling and hypoxia response pathways in progressive patients, which was associated with upregulation of hypoxia-inducible-factor (HIF)-1alpha and several HIF target genes, such as transferrin, transferrin-receptor, p21, and VEGF-receptor 1, but downregulation of VEGF-A. The inverse expression levels of HIF-1alpha and VEGF-A were significantly superior in predicting clinical outcome as compared with proteinuria, renal function, and degree of tubular atrophy and interstitial fibrosis at the time of biopsy. Interactome analysis showed the association of attenuated VEGF-A expression with the downregulation of genes that usually stimulate VEGF-A expression, such as epidermal growth factor (EGF), insulin-like growth factor-1 (IGF-1), and HIF-2alpha. In vitro experiments confirmed the positive regulatory effect of EGF and IGF-1 on VEGF-A transcription in human proximal tubular cells. Thus, in progressive but not in stable proteinuric kidney disease, human PTECs show an attenuated VEGF-A expression despite an activation of intracellular hypoxia response and VEGF signaling pathways, which might be due to a reduced expression of positive coregulators, such as EGF and IGF-1.

Bortezomib-induced survival signals and genes in human proximal tubular cells.

Bortezomib has been introduced recently in the therapy of multiple myeloma (MM), a disease that is frequently associated with progressive renal failure. Because bortezomib-based therapy has been reported to lead to a rapid recovery of kidney function in patients with MM, we decided to study its direct effects in proximal tubular epithelial cells (PTCs) compared with glomerular mesangial cells (GMCs). After 24 h of stimulation, 50 nM bortezomib led to a 6.37-fold induction of apoptosis and markedly activated caspase-9 and -3 in GMCs but not in PTCs. In PTCs but not in GMCs, bortezomib led to a strong time-dependent degradation of IkappaB-alpha and to a long-lasting phosphorylation of both NF-kappaBp65 and extracellular signal-regulated kinase 1/2. Microarray analysis in bortezomib-treated PTCs revealed a time-dependent predominance of antiapoptotic genes compared with proapoptotic genes. Bortezomib (50 nM) induced heat shock protein (Hsp) 70 mRNA and protein levels in PTCs, whereas basal and bortezomib-stimulated Hsp70 protein expression was much weaker in GMCs. Moreover, bortezomib induced Bcl-2-associated athanogene (BAG) 3 mRNA and protein expression but inhibited BAG5 mRNA levels in PTCs. These data suggest that the reduced susceptibility of PTCs to bortezomib-induced cell apoptosis is because of cell type-specific effects of this compound on apoptosis/survival genes and pathways. The concept of bortezomib representing a blocker of both NF-kappaB activation and cell survival should be carefully examined in particular renal cell types.

Biomarker candidates for cardiovascular disease and bone metabolism disorders in chronic kidney disease: a systems biology perspective.

Patients with chronic kidney disease (CKD) show a panel of partially de-regulated serum markers indicative for bone metabolism disorders and cardiovascular diseases (CVDs). This review provides an overview of currently reported biomarker candidates at the interface of kidney disease, bone metabolism disorders and CVDs, and gives details on their functional interplay on the level of protein-protein interaction data. We retrieved 13 publications from 1999 to 2006 reporting 31 genes associated with CVDs, and 46 genes associated with bone metabolism disorders in patients with CKD. We identified these genes to be functionally involved in signal transduction processes, cell communication, immunity and defence, as well as skeletal development. On the basis of the given set of 77 genes further 276 interacting proteins were identified using reference data on known protein interactions. Their functional interplay was estimated by linking properties reflected by gene expression data characterizing CKD, gene ontology terms as provided by the gene ontology consortium and transcription factor binding site profiles. Highly connected sub-networks of proteins associated with CKD, CVDs or bone metabolism disorders were detected involving proteins like collagens (COL1A1, COL1A2), fibronectin, transforming growth factor-?1, or components of fibrinogen (FG-alpha, FG-beta, FG-gamma). A systems biology approach provides a methodological framework for linking singular biomarker candidates towards deriving functional dependencies among clinically interlinked diseases.