Current practice of diabetes education in children and adolescents with type 1 diabetes in Germany and Austria: analysis based on the German/Austrian DPV database

BACKGROUND

Diabetes education of patients and/or parents is an essential part of diabetes care with effects on diabetes outcome. The objective of our study was to describe the current practice of diabetes education in Germany and Austria with regard to training frequency, patient age, migration background and diabetes therapy in a large cohort of pediatric patients with diabetes mellitus type 1 (T1DM).

METHODS

We analyzed data from pediatric T1DM patients with diabetes training in 2013 and complete data available for treatment year in the multicenter Diabetes Patienten Verlaufsdokumentation (DPV) registry using sas 9.4.

RESULTS

In 2013 21 871 pediatric patients with T1DM were documented [52.4% male, age: 12.70 (9.35-15.30) yr (median (interquartile range)], diabetes duration: 3.80 (1.45-7.00) yr, migration background: 21.4%, twice daily injections: 5.5%, multiple daily injections: 52.5%, insulin-pump therapy: 42%. Of these 32.31% were trained in 2013. Younger patients and their parents were trained more intensely and more frequently as inpatients compared with older patients (0-6 vs. 6-12 and 12-18 yr: teaching units: 13.07 vs. 12.05 and 9.79; inpatient: 79% vs. 72% and 70%). There was also a difference in training frequency with regard to migration background. Severe hypoglycemia or ketoacidosis resulted in intensification of training (4.0 vs. 2.0%; 7.8 vs. 3.1%). Centre-specific education tools were used frequently alone or in combination with published, standardized education programs.

CONCLUSION

Training frequency was highest in younger patients and during the first year of diabetes. Acute complications resulted in more frequent diabetes training, indicating that currently many education sessions take place in consequence to these complications.

Quantifying gene expression: the importance of being subtle

Gene expression is regulated at both the mRNA and protein level through on‐off switches and fine‐tuned control. In their recent study, Edfors et al (2016) use highly accurate, targeted proteomics methods and examine to what extent the amount of protein produced per mRNA transcript varies across different tissues. They find that the bulk part of protein concentrations is set at a per‐gene level: This relationship, the protein/mRNA ratio, is constant across cell types and tissues, but varies by several orders of magnitude across genes.

The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health

Plants are colonized by a variety of bacteria, most of which are not pathogenic. Currently, the plant responses to phyllosphere commensals or to pathogen infection in the presence of commensals are not well understood. Here, we examined the transcriptional response of Arabidopsis thaliana leaves to colonization by common commensal bacteria in a gnotobiotic system using RNA sequencing and conducted plant mutant assays. Arabidopsis responded differently to the model bacteria Sphingomonas melonis Fr1 (S.Fr1) and Methylobacterium extorquens PA1 (M.PA1). Whereas M.PA1 only marginally affected the expression of plant genes (< 10), S.Fr1 colonization changed the expression of almost 400 genes. For the latter, genes related to defense responses were activated and partly overlapped with those elicited by the pathogen Pseudomonas syringae DC3000 (Pst). As S.Fr1 is able to mediate plant protective activity against Pst, we tested plant immunity mutants and found that the pattern-recognition co-receptor mutant bak1/bkk1 showed attenuated S.Fr1-dependent plant protection. The experiments demonstrate that the plant responds differently to members of its natural phyllosphere microbiota. A subset of commensals trigger expression of defense-related genes and thereby may contribute to plant health upon pathogen encounter.

Time-course proteomics dataset monitoring HeLa cells subjected to DTT induced endoplasmic reticulum stress

The data described here provide an analysis of the dynamic response of HeLa cell proteome to dithiothreitol (DTT) inducing stress of the endoplasmic reticulum (ER). During ER stress, accumulation of misfolded and unfolded proteins in the lumen of the ER initiates the Unfolded Protein Response (UPR), resulting in a large-scale redistribution of proteins. We used label-free mass spectrometry to monitor the proteomic changes of HeLa cells during a 30-h time course, monitoring eight time points (0, 0.5, 1, 2, 8, 16, 24, and 30 h). The data are associated with the research article “Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress” [1], which discusses a core dataset of 1237 proteins. Here, we present the extended dataset of 2131 proteins. The raw mass spectrometry data and the analysis results have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PRIDE: PXD002039.

A synopsis on aging-Theories, mechanisms and future prospects

Answering the question as to why we age is tantamount to answering the question of what is life itself. There are countless theories as to why and how we age, but, until recently, the very definition of aging - senescence - was still uncertain. Here, we summarize the main views of the different models of senescence, with a special emphasis on the biochemical processes that accompany aging. Though inherently complex, aging is characterized by numerous changes that take place at different levels of the biological hierarchy. We therefore explore some of the most relevant changes that take place during aging and, finally, we overview the current status of emergent aging therapies and what the future holds for this field of research. From this multi-dimensional approach, it becomes clear that an integrative approach that couples aging research with systems biology, capable of providing novel insights into how and why we age, is necessary.

Preconception and pregnancy: opportunities to intervene to improve women's diets and lifestyles

Recently, large-scale trials of behavioural interventions have failed to show improvements in pregnancy outcomes. They have, however, shown that lifestyle support improves maternal diet and physical activity during pregnancy, and can reduce weight gain. This suggests that pregnancy, and possibly the whole periconceptional period, represents a 'teachable moment' for changes in diet and lifestyle, an idea that was made much of in the recent report of the Chief Medical Officer for England. The greatest challenge with all trials of diet and lifestyle interventions is to engage people and to sustain this engagement. With this in mind, we propose a design of intervention that aims simultaneously to engage women through motivational conversations and to offer access to a digital platform that provides structured support for diet and lifestyle change. This intervention design therefore makes best use of learning from the trials described above and from recent advances in digital intervention design.

Progression-free survival as surrogate end point for overall survival in clinical trials of HER2-targeted agents in HER2-positive metastatic breast cancer

BACKGROUND

The gold standard end point in randomized clinical trials in metastatic breast cancer (MBC) is overall survival (OS). Although therapeutics have been approved based on progression-free survival (PFS), its use as a primary end point is controversial. We aimed to assess to what extent PFS may be used as a surrogate for OS in randomized trials of anti-HER2 agents in HER2+ MBC.

METHODS

Eligible trials accrued HER2+ MBC patients in 1992-2008. A correlation approach was used: at the individual level, to estimate the association between investigator-assessed PFS and OS using a bivariate model and at the trial level, to estimate the association between treatment effects on PFS and OS. Correlation values close to 1.0 would indicate strong surrogacy.

RESULTS

We identified 2545 eligible patients in 13 randomized trials testing trastuzumab or lapatinib. We collected individual patient data from 1963 patients and retained 1839 patients from 9 trials for analysis (7 first-line trials). During follow-up, 1072 deaths and 1462 progression or deaths occurred. The median survival time was 22 months [95% confidence interval (CI) 21-23 months] and the median PFS was 5.7 months (95% CI 5.5-6.1 months). At the individual level, the Spearman correlation was equal to ρ = 0.67 (95% CI 0.66-0.67) corresponding to a squared correlation value of 0.45. At the trial level, the squared correlation between treatment effects (log hazard ratios) on PFS and OS was provided by R(2) = 0.51 (95% CI 0.22-0.81).

CONCLUSIONS

In trials of HER2-targeted agents in HER2+ MBC, PFS moderately correlates with OS at the individual level and treatment effects on PFS correlate moderately with those on overall mortality, providing only modest support for considering PFS as a surrogate. PFS does not completely substitute for OS in this setting.

Greater access to fast-food outlets is associated with poorer bone health in young children

SUMMARY

A healthy diet positively influences childhood bone health, but how the food environment relates to bone development is unknown. Greater neighbourhood access to fast-food outlets was associated with lower bone mass among infants, while greater access to healthy speciality stores was associated with higher bone mass at 4 years.

INTRODUCTION

Identifying factors that contribute to optimal childhood bone development could help pinpoint strategies to improve long-term bone health. A healthy diet positively influences bone health from before birth and during childhood. This study addressed a gap in the literature by examining the relationship between residential neighbourhood food environment and bone mass in infants and children.

METHODS

One thousand one hundred and seven children participating in the Southampton Women's Survey, UK, underwent measurement of bone mineral density (BMD) and bone mineral content (BMC) at birth and 4 and/or 6 years by dual-energy X-ray absorptiometry (DXA). Cross-sectional observational data describing food outlets within the boundary of each participant's neighbourhood were used to derive three measures of the food environment: the counts of fast-food outlets, healthy speciality stores and supermarkets.

RESULTS

Neighbourhood exposure to fast-food outlets was associated with lower BMD in infancy (β = -0.23 (z-score): 95% CI -0.38, -0.08) and lower BMC after adjustment for bone area and confounding variables (β = -0.17 (z-score): 95% CI -0.32, -0.02). Increasing neighbourhood exposure to healthy speciality stores was associated with higher BMD at 4 and 6 years (β = 0.16(z-score): 95% CI 0.00, 0.32 and β = 0.13(z-score): 95% CI -0.01, 0.26 respectively). The relationship with BMC after adjustment for bone area and confounding variables was statistically significant at 4 years, but not at 6 years.

CONCLUSIONS

The neighbourhood food environment that pregnant mothers and young children are exposed may affect bone development during early childhood. If confirmed in future studies, action to reduce access to fast-food outlets could have benefits for childhood development and long-term bone health.

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress

The relative importance of regulation at the mRNA versus protein level is subject to ongoing debate. To address this question in a dynamic system, we mapped proteomic and transcriptomic changes in mammalian cells responding to stress induced by dithiothreitol over 30 h. Specifically, we estimated the kinetic parameters for the synthesis and degradation of RNA and proteins, and deconvoluted the response patterns into common and unique to each regulatory level using a new statistical tool. Overall, the two regulatory levels were equally important, but differed in their impact on molecule concentrations. Both mRNA and protein changes peaked between two and eight hours, but mRNA expression fold changes were much smaller than those of the proteins. mRNA concentrations shifted in a transient, pulse‐like pattern and returned to values close to pre‐treatment levels by the end of the experiment. In contrast, protein concentrations switched only once and established a new steady state, consistent with the dominant role of protein regulation during misfolding stress. Finally, we generated hypotheses on specific regulatory modes for some genes.

High-throughput analyses of hnRNP H1 dissects its multi-functional aspect

hnRNPs are polyvalent RNA binding proteins that have been implicated in a range of regulatory roles including splicing, mRNA decay, translation, and miRNA metabolism. A variety of genome wide studies have taken advantage of methods like CLIP and RIP to identify the targets and binding sites of RNA binding proteins. However, due to the complex nature of RNA-binding proteins, these studies are incomplete without assays that characterize the impact of RBP binding on mRNA target expression. Here we used a suite of high-throughput approaches (RIP-Seq, iCLIP, RNA-Seq and shotgun proteomics) to provide a comprehensive view of hnRNP H1s ensemble of targets and its role in splicing, mRNA decay, and translation. The combination of RIP-Seq and iCLIP allowed us to identify a set of 1,086 high confidence target transcripts. Binding site motif analysis of these targets suggests the TGGG tetramer as a prevalent component of hnRNP H1 binding motif, with particular enrichment around intronic hnRNP H1 sites. Our analysis of the target transcripts and binding sites indicates that hnRNP H1s involvement in splicing is 2-fold: it directly affects a substantial number of splicing events, but also regulates the expression of major components of the splicing machinery and other RBPs with known roles in splicing regulation. The identified mRNA targets displayed function enrichment in MAPK signaling and ubiquitin mediated proteolysis, which might be main routes by which hnRNP H1 promotes tumorigenesis.

Next-generation analysis of gene expression regulation--comparing the roles of synthesis and degradation

Technological advances now enable routine measurement of mRNA and protein abundances, and estimates of their rates of synthesis and degradation that inform on their values and the degree of change in response to stimuli. Importantly, more and more data on time-series experiments are emerging, e.g. of cells responding to stress, enabling first insights into a new dimension of gene expression regulation - its dynamics and how it allows for very different response signals across genes. This review discusses recently published methods and datasets, their impact on what we now know about the relationships between concentrations and synthesis rates of mRNAs and proteins in yeast and mammalian cells, their evolution, and new hypotheses on translation regulatory mechanisms generated by approaches that involve ribosome footprinting.

Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6's multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6's interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions-many of which are likely conserved across eukaryotes.

One third of dynamic protein expression profiles can be predicted by a simple rate equation

Cells respond to environmental stimuli with expression changes at both the mRNA and protein level, and a plethora of known and unknown regulators affect synthesis and degradation rates of the resulting proteins. To investigate the major principles of gene expression regulation in dynamic systems, we estimated protein synthesis and degradation rates from parallel time series data of mRNA and protein expression and tested the degree to which expression changes can be modeled by a simple linear differential equation. Examining three published datasets for yeast responding to diamide, rapamycin, and sodium chloride treatment, we find that almost one-third of genes can be well-modeled, and the estimated rates assume realistic values. Prediction quality is linked to low measurement noise and the shape of the expression profile. Synthesis and degradation rates do not correlate within one treatment, consistent with their independent regulation. When performing robustness analyses of the rate estimates, we observed that most genes adhere to one of two major modes of regulation, which we term synthesis- and degradation-independent regulation. These two modes, in which only one of the rates has to be tightly set, while the other one can assume various values, offer an efficient way for the cell to respond to stimuli and re-establish proteostasis. We experimentally validate degradation-independent regulation under oxidative stress for the heatshock protein Ssa4.

Mass spectrometry analysis of K63-ubiquitinated targets in response to oxidative stress

The data described here provide the first large-scale analysis of lysine 63 (K63)-linked polyubiquitin targets. Protein ubiquitination is a prominent post-translational modification, and a variety of ubiquitin chains exists, serving a multitude of functions [1]. The chains differ by the lysine residue by which the ubiquitin monomers are linked. We used yeast Saccharomyces cerevisiae subjected to oxidative stress as a model to study K63 ubiquitination. K63 ubiquitinated targets were pulled-down by the K63-TUBE system (Tandem Ubiquitin Binding Entities) and analyzed by SILAC-based mass spectrometry [2]. The data are associated to the research article ‘K63 polyubiquitination is a new modulator of the oxidative stress response’ [3]. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000960.