Systematic comparison of approaches to analyze clustered competing risks data.

BACKGROUND: In many clinical trials the study interest lies in the comparison of a treatment to a control group regarding a time to event endpoint like time to myocardial infarction, time to relapse, or time to a specific cause of death. Thereby, an event can occur before the primary event of interest that alters the risk for or prohibits observing the latter, i.e. a competing event. Furthermore, multi-center studies are often conducted. Hence, a cluster structure might be observed. However, commonly only the aspect of competing events or the aspect of the cluster structure is modelled within primary analysis, although both are given within the study design. Methods to adequately analyze data in such a design were recently described but were not systematically compared yet. METHODS: Within this work we provide a systematic comparison of four approaches for the analysis of competing events where a cluster structure is present based on a real life data set and a simulation study. The considered methods are the commonly applied cause-specific Cox proportional hazards model with a frailty, the Fine and Gray model for considering competing risks, and extensions of the latter model by Katsahian et al. and Zhou et al. RESULTS: Based on our simulation results, the model by Katsahian et al. showed the best performance in bias, square root of mean squared error, and power in nearly all scenarios. In contrast to the other three models this approach allows both unbiased effect estimation and prognosis. CONCLUSION: The provided comparison and simulations help to guide applied researchers to choose an adequate method for the analysis of competing events where a cluster structure is present. Based on our simulation results the approach by Katsahian et al. can be recommended.

Deficiency in Retinal TGFß Signaling Aggravates Neurodegeneration by Modulating Pro-Apoptotic and MAP Kinase Pathways.

Transforming growth factor ß (TGFß) signaling has manifold functions such as regulation of cell growth, differentiation, migration, and apoptosis. Moreover, there is increasing evidence that it also acts in a neuroprotective manner. We recently showed that TGFß receptor type 2 (Tgfbr2) is upregulated in retinal neurons and Müller cells during retinal degeneration. In this study we investigated if this upregulation of TGFß signaling would have functional consequences in protecting retinal neurons. To this end, we analyzed the impact of TGFß signaling on photoreceptor viability using mice with cell type-specific deletion of Tgfbr2 in retinal neurons and Müller cells (Tgfbr2ΔOC) in combination with a genetic model of photoreceptor degeneration (VPP). We examined retinal morphology and the degree of photoreceptor degeneration, as well as alterations of the retinal transcriptome. In summary, retinal morphology was not altered due to TGFß signaling deficiency. In contrast, VPP-induced photoreceptor degeneration was drastically exacerbated in double mutant mice (Tgfbr2ΔOC; VPP) by induction of pro-apoptotic genes and dysregulation of the MAP kinase pathway. Therefore, TGFß signaling in retinal neurons and Müller cells exhibits a neuroprotective effect and might pose promising therapeutic options to attenuate photoreceptor degeneration in humans.

Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa.

Hereditary retinal degenerations like retinitis pigmentosa (RP) are among the leading causes of blindness in younger patients. To enable in vivo investigation of cellular and molecular mechanisms responsible for photoreceptor cell death and to allow testing of therapeutic strategies that could prevent retinal degeneration, animal models have been created. In this study, we deeply characterized the transcriptional profile of mice carrying the transgene rhodopsin V20G/P23H/P27L (VPP), which is a model for autosomal dominant RP. We examined the degree of photoreceptor degeneration and studied the impact of the VPP transgene-induced retinal degeneration on the transcriptome level of the retina using next generation RNA sequencing (RNASeq) analyses followed by weighted correlation network analysis (WGCNA). We furthermore identified cellular subpopulations responsible for some of the observed dysregulations using in situ hybridizations, immunofluorescence staining, and 3D reconstruction. Using RNASeq analysis, we identified 9256 dysregulated genes and six significantly associated gene modules in the subsequently performed WGCNA. Gene ontology enrichment showed, among others, dysregulation of genes involved in TGF-ß regulated extracellular matrix organization, the (ocular) immune system/response, and cellular homeostasis. Moreover, heatmaps confirmed clustering of significantly dysregulated genes coding for components of the TGF-ß, G-protein activated, and VEGF signaling pathway. 3D reconstructions of immunostained/in situ hybridized sections revealed retinal neurons and Müller cells as the major cellular population expressing representative components of these signaling pathways. The predominant effect of VPP-induced photoreceptor degeneration pointed towards induction of neuroinflammation and the upregulation of neuroprotective pathways like TGF-ß, G-protein activated, and VEGF signaling. Thus, modulation of these processes and signaling pathways might represent new therapeutic options to delay the degeneration of photoreceptors in diseases like RP.

Light Intensity-Dependent Dysregulation of Retinal Reference Genes.

The degeneration of photoreceptors is a common hallmark of ocular diseases like retinitis pigmentosa (RP) or age-related macular degeneration (AMD). To experimentally induce photoreceptor degeneration, the light damage paradigm is frequently used. In this study we show that the exposure to high amounts of cool white light (10,000 lux, 1 h) resulted in a more than 11-fold higher apoptotic rate in the retina compared to light exposure with 5000 lux for 30 min. Consequently, exposure to intense light resulted in a significant downregulation of retinal mRNA expression levels of the reference genes Gapdh, Gnb2l, Rpl32, Rps9, Actb, Ubc or Tbp compared to untreated controls. Investigators performing light-induced photoreceptor degeneration should be aware of the fact that higher light intensities will result in a dysregulation of reference genes.

New Insights into Endothelin Signaling and Its Diverse Roles in the Retina.

The vasoactive peptide endothelin is an effective regulator of blood pressure and vascular homeostasis. In addition, the dysregulation of the endothelin signaling pathway is discussed to contribute to ocular diseases like glaucoma or diabetic retinopathy. Furthermore, our workgroup and others showed a protective effect of endothelin 2 for the survival of photoreceptors. In this study, we analyzed mRNA expression levels of the endothelin signaling family in wild-type mice after a puncture of the eye, intravitreal PBS injections, or light-induced photoreceptor degeneration. We observed elevated endothelin receptor a (Eta), endothelin receptor b (Etb), endothelin 1(Et1), and endothelin 2 (Et2) levels, while endothelin 3 (Et3) mRNA levels were not significantly altered. Our findings indicate an important role of the endothelin signaling pathway in response to ocular trauma or disease. These findings make endothelin signaling a promising target to attenuate retinal degeneration.

SMAD7 deficiency stimulates Müller progenitor cell proliferation during the development of the mammalian retina.

The transforming growth factor-ß (TGF-ß) pathway contributes to maintain the quiescence of adult neural stem and progenitor cells in the brain. In the retina, Müller cells are discussed to represent a glial cell population with progenitor-like characteristics. Here, we aimed to investigate if elevated TGF-ß signaling modulates the proliferation of Müller cells during retinal development. We generated mutant mice with a systemic, heterozygous up-regulation of TGF-ß signaling by deleting its inhibitor SMAD7. We investigated apoptosis, proliferation, and differentiation of Müller cells in the developing retina. We show that a heterozygous deletion of SMAD7 results in an increased proliferation of Müller cell progenitors in the central retina at postnatal day 4, the time window when Müller cells differentiate in the mouse retina. This in turn results in a thickened retina and inner nuclear layer and a higher number of differentiated Müller cells in the more developed retina. Müller cells in mutant mice contain higher amounts of nestin than those of control animals which indicates that the increase in TGF-ß signaling activity during retinal development contribute to maintain some progenitor-like characteristics in Müller cells even after their differentiation period. We conclude that TGF-ß signaling influences Müller cell proliferation and differentiation during retinal development.

[Quality of biomaterials in liquid- and tissue-biobanking]. / Qualität von Biomaterialien im Biobanking von Flüssig- und Gewebeproben.

During the last years, many biobanks that collect and provide biomaterials as well as associated phenotypical data have been established on national and international levels. However, due to the heterogeneity in structure and process landscape between biobanks, quality issues arise, which might affect equivalence of sample quality and thus usability of biomaterials for scientific research projects as well as interoperability of biobanks.Here, we will give an overview on the influence of biobanking procedures on sample quality and on potential quality control measures for research biobanks, mainly focusing on tissue and liquid biomaterials. General infrastructural requirements as well as the influence of preanalytical variables affecting sample quality and usability are described and opportunities and drawbacks of different quality assurance procedures are discussed. As there is increasing consensus on national and international levels that evidence-based standardization and harmonization of biobank structures and workflows are urgently needed for quality-assured biobanking, recent activities in the development and implementation of an ISO Standard for biobanks will be illustrated in the last section of this article.

Nuclear accumulation of seven in absentia homologue-2 supports motility and proliferation of liver cancer cells.

Stability of many tumor-relevant proteins is partly mediated by E3 ligases, which determine substrate specificity within the ubiquitin system. Recent data demonstrated that increased nuclear expression of the E3 ligase seven in absentia homologue (SIAH)-1 in human hepatocarcinogenesis supports tumor cell proliferation and migration. To define whether closely related SIAH-2 synergizes with protumorigenic SIAH-1, we systematically analyzed expression, localization and functional relevance of SIAH-2 in human hepatocellular carcinoma (HCC). Nuclear accumulation of SIAH-2 is detectable in more than 60% of all HCCs and correlates with tumor progression, cell proliferation and distant metastasis. An inverse correlation between nuclear SIAH-1 and SIAH-2 was detected, suggesting independent mechanisms for nuclear enrichment. Inhibition of nuclear SIAH-2 by RNAi in HCC cell lines reduced proliferation as well as lateral tumor cell motility and transmigration; however, combined knock down of both SIAH-1 and SIAH-2 did not further amplify biological effects compared to single gene inhibition. Reduction of SIAH-2 expression sensitizes HCC cells to the treatment with different cytostatic drugs, demonstrating that SIAH-2-targeting approaches may increase the response of HCC cells to conventional chemotherapy. Together, these data show that SIAH-2--as described for SIAH-1--accumulates in nuclei of HCC cells where it supports tumor growth and tumor cell dissemination. Because the nuclear pattern of SIAH-2 differs in HCC tissues from the SIAH-1 pattern and because the inactivation of SIAH-2 is not compensated by SIAH-1, the specific inhibition of SIAH-2 (especially in combination with other drugs) represents a promising therapeutic strategy for HCC.

[Quality assurance in tissue biobanking-an overview]. / Qualitätssicherung im Gewebebiobanking ­ Ein Überblick.

Tissue biobanks are important resource and technology platforms for biomedical research, which deals with molecular pathogenesis and the prevention, diagnosis and treatment of diseases.Due to this central role in the standardised collection, storage and distribution of human tissue and its derivatives, a practised quality management is one of the most important measures to achieve and maintain a comprehensive quality assurance of all biobanking processes. At the same time, this promotes acceptance and credibility. External quality assurance of biobanks can be achieved through accreditation. Within the German biobanking community, increasing harmonisation of biobanking processes has also been achieved through the provision of various quality assurance measures by the German Biobank Node (GBN).In the following, challenges and opportunities in the implementation of a comprehensive quality assurance in biobanking will be discussed and solutions for tissue biobanking will be presented using the example of the tissue bank of the National Centre for Tumour Diseases (NCT).

Complement Components Showed a Time-Dependent Local Expression Pattern in Constant and Acute White Light-Induced Photoreceptor Damage.

Background: Photoreceptor cell death due to extensive light exposure and induced oxidative-stress are associated with retinal degeneration. A correlated dysregulation of the complement system amplifies the damaging effects, but the local and time-dependent progression of this mechanism is not thoroughly understood. Methods: Light-induced photoreceptor damage (LD) was induced in Balb/c mice with white light illumination either for 24 h with 1000 lux (constant model) or 0.5 h with 5000 lux (acute model). Complement protein and mRNA expression levels were compared at 1 and 3 days post-LD for C1s, complement factor B (CFB), mannose binding lectin A, mannose-binding protein-associated serine protease 1 (MASP-1), C3, C4, C9, and complement factor P in retina and RPE/choroid. Histological analyses visualized apoptosis, microglia/macrophage migration, gliosis and deposition of the complement activation marker C3d. Systemic anaphylatoxin serum concentrations were determined using an ELISA. Results: Apoptosis, gliosis and microglia/macrophage migration into the outer nuclear layer showed similar patterns in both models. Local complement factor expression revealed an early upregulation of complement factor mRNA in the acute and constant light regimen at 1 day post-treatment for c1s, cfb, masp-1, c3, c4 and c9 in the RPE/choroid. However, intraretinal complement mRNA expression for c1s, cfb, c3 and c4 was increased at 1 day in the constant and at 3 days in the acute model. A corresponding regulation on protein level in the retina following both LD models was observed for C3, which was upregulated at 1 day and correlated with increased C3d staining in the ganglion cell layer and at the RPE. In the RPE/choroid C1s-complex protein detection was increased at 3 days after LD irrespectively of the light intensities used. Conclusion: LD in mouse eyes is correlated with local complement activity. The time-dependent local progression of complement regulation on mRNA and protein levels were equivalent in the acute and constant LD model, except for the intraretinal, time-dependent mRNA expression. Knowing the relative time courses of local complement expression and cellular activity can help to elucidate novel therapeutic options in retinal degeneration indicating at which time point of disease complement has to be rebalanced.

Directed random walks and constraint programming reveal active pathways in hepatocyte growth factor signaling.

An effective means to analyze mRNA expression data is to take advantage of established knowledge from pathway databases, using methods such as pathway-enrichment analyses. However, pathway databases are not case-specific and expression data could be used to infer gene-regulation patterns in the context of specific pathways. In addition, canonical pathways may not always describe the signaling mechanisms properly, because interactions can frequently occur between genes in different pathways. Relatively few methods have been proposed to date for generating and analyzing such networks, preserving the causality between gene interactions and reasoning over the qualitative logic of regulatory effects. We present an algorithm (MCWalk) integrated with a logic programming approach, to discover subgraphs in large-scale signaling networks by random walks in a fully automated pipeline. As an exemplary application, we uncover the signal transduction mechanisms in a gene interaction network describing hepatocyte growth factor-stimulated cell migration and proliferation from gene-expression measured with microarray and RT-qPCR using in-house perturbation experiments in a keratinocyte-fibroblast co-culture. The resulting subgraphs illustrate possible associations of hepatocyte growth factor receptor c-Met nodes, differentially expressed genes and cellular states. Using perturbation experiments and Answer Set programming, we are able to select those which are more consistent with the experimental data. We discover key regulator nodes by measuring the frequency with which they are traversed when connecting signaling between receptors and significantly regulated genes and predict their expression-shift consistently with the measured data. The Java implementation of MCWalk is publicly available under the MIT license at: https://bitbucket.org/akittas/biosubg.

Stathmin regulates keratinocyte proliferation and migration during cutaneous regeneration.

Cutaneous regeneration utilizes paracrine feedback mechanisms to fine-tune the regulation of epidermal keratinocyte proliferation and migration. However, it is unknown how fibroblast-derived hepatocyte growth factor (HGF) affects these mutually exclusive processes in distinct cell populations. We here show that HGF stimulates the expression and phosphorylation of the microtubule-destabilizing factor stathmin in primary human keratinocytes. Quantitative single cell- and cell population-based analyses revealed that basal stathmin levels are important for the migratory ability of keratinocytes in vitro; however, its expression is moderately induced in the migration tongue of mouse skin or organotypic multi-layered keratinocyte 3D cultures after full-thickness wounding. In contrast, clearly elevated stathmin expression is detectable in hyperproliferative epidermal areas. In vitro, stathmin silencing significantly reduced keratinocyte proliferation. Automated quantitative and time-resolved analyses in organotypic cocultures demonstrated a high correlation between Stathmin/phospho-Stathmin and Ki67 positivity in epidermal regions with proliferative activity. Thus, activation of stathmin may stimulate keratinocyte proliferation, while basal stathmin levels are sufficient for keratinocyte migration during cutaneous regeneration.

A new application of lipid nanoemulsions as coating agent, providing zero-order hydrophilic drug release from tablets.

The objective of the present investigation was to evaluate potential of nanoemulsions as a coating material for the tablets. The nanoemulsion of size less than 100 nm was prepared using a simple and low-energy spontaneous emulsification method. Conventional tablets containing theophylline as a model hydrophilic drug were prepared. The theophylline tablets were coated with the nanoemulsion using a fluid bed coater. The effect of different levels of the nanoemulsion coating on the theophylline release was evaluated. The theophylline tablets containing different levels of the nanoemulsion coating could be successfully prepared. Interestingly, the coating of tablet with the nanoemulsion resulted in zero-order release of theophylline from the tablets. The noncoated theophylline tablets release the entire drug in less than 2 minutes, whereas nanoemulsion coating delayed the release of theophylline from tablets. This investigation establishes the proof of concept for the potential of nanoemulsions as a coating material for tablets.

Extracorporeal photophoresis augments function of CD4+CD25+FoxP3+ regulatory T cells by triggering adenosine production.

BACKGROUND: During extracorporeal photophoresis (ECP), peripheral blood mononuclear cells are treated with DNA-intercalating agents and irradiated with ultraviolet light. This procedure exerts immunosuppressive effects, most likely mediated by regulatory T cells (Treg). However, the underlying mechanisms are not clear yet. In our study, we investigated the effect of ECP on frequency and function of Treg in the peripheral blood of patients suffering from graft-versus-host disease. METHODS: Whole blood samples from graft-versus-host disease patients were taken before and after the ECP treatment on 2 consecutive days. Phenotypical analysis of changes in distinct leukocyte subsets within the peripheral blood of patients and healthy controls was performed by means of flow cytometry. Functional analysis of the Treg population after magnetic bead isolation was performed using conventional suppression assays, and adenosine was detected by means of high pressure liquid chromatography and Lanzetta assays. RESULTS: We show that the frequency of CD4/CD25/FoxP3 Treg in the peripheral blood increases after each cycle of ECP and also in the course of treatment. The suppressive capacity of Treg after ECP was increased compared with that of Treg before ECP, although not reaching the suppression levels obtained with Treg from healthy controls. Furthermore, we show that ECP stimulates the CD39-mediated production of adenosine by Treg, which substantially reduces the T-cell proliferation in in vitro suppression assays. CONCLUSION: Our data indicate that ECP stimulates the conversion of ATP to adenosine by the ectonucleotiodase CD39, which acts as a novel soluble immunosuppressive reagent mediating immunosuppression of Treg.

Murine serum deoxyribonuclease 1 (Dnase1) activity partly originates from the liver.

Reduction of serum DNASE1 (DNase I) activity is supposed to aggravate anti-nuclear autoimmunity, i.e. Systemic Lupus Erythematosus (SLE) in man and mice. To evaluate the etiology of this reduction, more information is needed about the source(s) and regulation of serum DNASE1. In this work we used male C57BL/6 wild-type (WT) mice to verify that serum Dnase1 activity partly depends on hepatic Dnase1 gene expression. Thus serum and liver Dnase1 activity showed a parallel oscillatory course during 24h, which was accompanied by a phase-shifted fluctuation of the hepatic Dnase1 mRNA content. Performing native PAGE zymography (NPZ) we detected a presumably premature non-sialylated and a mature sialylated hepatic Dnase1 isoform, which both show a parallel circadian fluctuation, indicating continuous secretion of Dnase1. The sialylated form was also detectable in serum. By immunostaining the hepatocytes were identified as the source of hepatic Dnase1 gene expression. After 70% hepatectomy, the serum Dnase1 activity increased markedly due to the occurrence of ischemic hepatocellular necrosis in the vicinity of the surgical suture. Similarly, hepatocellular necrosis induced by injection of streptolysin-O (SLO) into the liver led to a rapid parallel increase of Dnase1 and of aspartate- and alanine aminotransferase (AST/ALT) in serum. Subsequent to hepatectomy, Dnase1 gene expression was up-regulated in the regenerating liver most likely leading to an enhanced serum Dnase1 level until complete regeneration. These data demonstrate that serum Dnase1 at least partly originates from the liver and hint to the possibility that natural as well as pathological hepatic conditions influence its activity.

Análise da satisfação dos usuários em um hospital universitário / Analysis of satisfaction of users in a university hospital

Este é um estudo exploratório descritivo de abordagem quantitativa cujo objetivo foi o de analisar o grau de satisfação dos usuários internados no pronto socorro de um hospital universitário da região central do Rio Grande do Sul. A amostra constituiu-se de 167 pacientes e a coleta de dados foi realizada no período de abril a outubro de 2011 por meio de questionário adaptado de Pena (2010). Os resultados permitem concluir que os usuários estão satisfeitos com os serviços prestados pelas equipes de enfermagem, médica e de nutrição, e insatisfeitos com algumas variáveis relativas à insfraestrutura e ao ambiente do pronto socorro.

This is a descriptive exploratory study of quantitative approach whose objective was to analyze the degree of satisfaction of users admitted to the emergency room of a university hospital in the central region of Rio Grande do Sul State, Brazil. The sample consisted of 167 patients and data collection was carried out during the period April-October 2011 by means of a questionnaire adapted from Pena (2010). The results allow concluding that users are satisfied with the services provided by nursing, medical and nutrition teams, but dissatisfied with variables concerning the infrastructure and the environment.