Validation of the Mobile App Version of the EQ-5D-5L Quality of Life Questionnaire Against the Gold Standard Paper-Based Version: Randomized Crossover Study.

BACKGROUND: Study participants and patients often perceive (long) questionnaires as burdensome. In addition, paper-based questionnaires are prone to errors such as (unintentionally) skipping questions or filling in a wrong type of answer. Such errors can be prevented with the emergence of mobile questionnaire apps. OBJECTIVE: This study aimed to validate an innovative way to measure the quality of life using a mobile app based on the EQ-5D-5L questionnaire. This validation study compared the EQ-5D-5L questionnaire requested by a mobile app with the gold standard paper-based version of the EQ-5D-5L. METHODS: This was a randomized, crossover, and open study. The main criteria for participation were participants should be aged ≥18 years, healthy at their own discretion, in possession of a smartphone with at least Android version 4.1 or higher or iOS version 9 or higher, digitally skilled in downloading the mobile app, and able to read and answer questionnaires in Dutch. Participants were recruited by a market research company that divided them into 2 groups balanced for age, gender, and education. Each participant received a digital version of the EQ-5D-5L questionnaire via a mobile app and the EQ-5D-5L paper-based questionnaire by postal mail. In the mobile app, participants received, for 5 consecutive days, 1 question in the morning and 1 question in the afternoon; as such, all questions were asked twice (at time point 1 [App T1] and time point 2 [App T2]). The primary outcomes were the correlations between the answers (scores) of each EQ-5D-5L question answered via the mobile app compared with the paper-based questionnaire to assess convergent validity. RESULTS: A total of 255 participants (healthy at their own discretion), 117 (45.9%) men and 138 (54.1%) women in the age range of 18 to 64 years, completed the study. To ensure randomization, the measured demographics were checked and compared between groups. To compare the results of the electronic and paper-based questionnaires, polychoric correlation analysis was performed. All questions showed a high correlation (0.64-0.92; P<.001) between the paper-based and the mobile app-based questions at App T1 and App T2. The scores and their variance remained similar over the questionnaires, indicating no clear difference in the answer tendency. In addition, the correlation between the 2 app-based questionnaires was high (>0.73; P<.001), illustrating a high test-retest reliability, indicating it to be a reliable replacement for the paper-based questionnaire. CONCLUSIONS: This study indicates that the mobile app is a valid tool for measuring the quality of life and is as reliable as the paper-based version of the EQ-5D-5L, while reducing the response burden.

Effects of a 13-Week Personalized Lifestyle Intervention Based on the Diabetes Subtype for People with Newly Diagnosed Type 2 Diabetes.

A type 2 diabetes mellitus (T2DM) subtyping method that determines the T2DM phenotype based on an extended oral glucose tolerance test is proposed. It assigns participants to one of seven subtypes according to their ß-cell function and the presence of hepatic and/or muscle insulin resistance. The effectiveness of this subtyping approach and subsequent personalized lifestyle treatment in ameliorating T2DM was assessed in a primary care setting. Sixty participants, newly diagnosed with (pre)diabetes type 2 and not taking diabetes medication, completed the intervention. Retrospectively collected data of 60 people with T2DM from usual care were used as controls. Bodyweight (p < 0.01) and HbA1c (p < 0.01) were significantly reduced after 13 weeks in the intervention group, but not in the usual care group. The intervention group achieved 75.0% diabetes remission after 13 weeks (fasting glucose ≤ 6.9 mmol/L and HbA1c < 6.5% (48 mmol/mol)); for the usual care group, this was 22.0%. Lasting (two years) remission was especially achieved in subgroups with isolated hepatic insulin resistance. Our study shows that a personalized diagnosis and lifestyle intervention for T2DM in a primary care setting may be more effective in improving T2DM-related parameters than usual care, with long-term effects seen especially in subgroups with hepatic insulin resistance.

Stakeholder Perspectives on Barriers and Facilitators for the Adoption of Virtual Clinical Trials: Qualitative Study.

BACKGROUND: Conventional clinical trials are essential for generating high-quality evidence by measuring the efficacy of interventions in rigorously controlled clinical environments. However, their execution can be expensive and time-consuming. In addition, clinical trials face several logistical challenges regarding the identification, recruitment, and retention of participants; consistent data collection during trials; and adequate patient follow-up. This might lead to inefficient resource utilization. In order to partially address the current problems with conventional clinical trials, there exists the need for innovations. One such innovation is the virtual clinical trial (VCT). VCTs allow for the collection and integration of diverse data from multiple information sources, such as electronic health records, clinical and demographic data, patient-reported outcomes, anthropometric and activity measurements, and data collected by digital biomarkers or (small) samples that participants can collect themselves. Although VCTs have the potential to provide substantial value to clinical research and patients because they can lower clinical trial costs, increase the volume of data collected from patients' daily environment, and reduce the burden of patient participation, so far VCT adoption is not commonplace. OBJECTIVE: This paper aims to better understand the barriers and facilitators to VCT adoption by determining the factors that influence individuals' considerations regarding VCTs from the perspective of various stakeholders. METHODS: Based on online semistructured interviews, a qualitative study was conducted with pharmaceutical companies, food and health organizations, and an applied research organization in Europe. Data were thematically analyzed using Rogers' diffusion of innovation theory. RESULTS: A total of 16 individuals with interest and experience in VCTs were interviewed, including persons from pharmaceutical companies (n=6), food and health organizations (n=4), and a research organization (n=6). Key barriers included a potentially low degree of acceptance by regulatory authorities, technical issues (standardization, validation, and data storage), compliance and adherence, and lack of knowledge or comprehension regarding the opportunities VCTs have to offer. Involvement of regulators in development processes, stakeholder exposure to the results of pilot studies, and clear and simple instructions and assistance for patients were considered key facilitators. CONCLUSIONS: Collaboration among all stakeholders in VCT development is crucial to increase knowledge and awareness. Organizations should invest in accurate data collection technologies, and compliance of patients in VCTs needs to be ensured. Multicriteria decision analysis can help determine if a VCT is a preferred option by stakeholders. The findings of this study can be a good starting point to accelerate the development and widespread implementation of VCTs.

Exploring the Potential of Personalized Dietary Advice for Health Improvement in Motivated Individuals With Premetabolic Syndrome: Pretest-Posttest Study.

BACKGROUND: Dietary quality plays an essential role in the prevention and management of metabolic syndrome (MetS). OBJECTIVE: The aim of this pilot study is to organize personalized dietary advice in a real-life setting and to explore the effects on dietary intake, metabolic health, and perceived health. METHODS: We followed a one-group pretest-posttest design and included 37 individuals at risk of MetS, who indicated motivation to change dietary behavior. For a period of 16 weeks, participants received personalized advice (t=0 and t=8) and feedback (t=0, t=4, t=8, t=12 and t=16) on dietary quality and metabolic health (ie, waist circumference, BMI, blood pressure, lipid profile, fasting glucose levels, and C-peptide). Personalized advice was generated in a two-stage process. In stage 1, an automated algorithm generated advice per food group, integrating data on individual dietary quality (Dutch Healthy Diet Index; total score 8-80) and metabolic health parameters. Stage 2 included a telephone consultation with a trained dietitian to define a personal dietary behavior change strategy and to discuss individual preferences. Dietary quality and metabolic health markers were assessed at t=0, t=8, and t=16. Self-perceived health was evaluated on 7-point Likert scales at t=0 and t=16. RESULTS: At the end of the study period, dietary quality was significantly improved compared with the baseline (Dutch Healthy Diet Index +4.3; P<.001). In addition, lipid profile (triglycerides, P=.02; total cholesterol, P=.01; high-density lipoprotein, P<.001; and low-density lipoprotein, P<.001), BMI (P<.001), waist circumference (P=.01), and C-peptide (P=.01) were all significantly improved, whereas plasma glucose increased by 0.23 nmol/L (P=.04). In line with these results, self-perceived health scores were higher at t=16 weeks than at baseline (+0.67; P=.005). CONCLUSIONS: This exploratory study showed that personalized dietary advice resulted in positive effects on dietary behavior, metabolic health, and self-perceived health in motivated pre-MetS adults. The study was performed in a do-it-yourself setting, highlighting the potential of at-home health improvement through dietary changes. TRIAL REGISTRATION: ClinicalTrials.gov NCT04595669; https://clinicaltrials.gov/ct2/show/NCT04595669.

Digital Resilience Biomarkers for Personalized Health Maintenance and Disease Prevention.

Health maintenance and disease prevention strategies become increasingly prioritized with increasing health and economic burden of chronic, lifestyle-related diseases. A key element in these strategies is the empowerment of individuals to control their health. Self-measurement plays an essential role in achieving such empowerment. Digital measurements have the advantage of being measured non-invasively, passively, continuously, and in a real-world context. An important question is whether such measurement can sensitively measure subtle disbalances in the progression toward disease, as well as the subtle effects of, for example, nutritional improvement. The concept of resilience biomarkers, defined as the dynamic evaluation of the biological response to an external challenge, has been identified as a viable strategy to measure these subtle effects. In this review, we explore the potential of integrating this concept with digital physiological measurements to come to digital resilience biomarkers. Additionally, we discuss the potential of wearable, non-invasive, and continuous measurement of molecular biomarkers. These types of innovative measurements may, in the future, also serve as a digital resilience biomarker to provide even more insight into the personal biological dynamics of an individual. Altogether, digital resilience biomarkers are envisioned to allow for the measurement of subtle effects of health maintenance and disease prevention strategies in a real-world context and thereby give personalized feedback to improve health.

Beneficial effect of personalized lifestyle advice compared to generic advice on wellbeing among Dutch seniors - An explorative study.

The aim of this explorative study is to evaluate whether personalized compared to generic lifestyle advice improves wellbeing in a senior population. We conducted a nine-week single-blind randomized controlled trial including 59 participants (age 67.7 ±â€¯4.8 years) from Wageningen and its surrounding areas in the Netherlands. Three times during the intervention period, participants received either personalized advice (PA), or generic advice (GA) to improve lifestyle behavior. Personalization was based on metabolic health measures and dietary intake resulting in an advice that highlighted food groups and physical activity types for which behavior change was most urgent. Before and after the intervention period self-perceived health was evaluated as parameter of wellbeing using a self-perceived health score (single-item) and two questionnaires (Vita-16 and Short Form-12). Additionally, anthropometry and physical functioning (short physical performance battery, SPPB) were assessed. Overall scores for self-perceived health did not change over time in any group. Resilience and motivation (Vita-16) slightly improved only in the PA group, whilst mental health (SF-12) and energy (Vita-16) showed slight improvement only in the GA group. SPPB scores improved over time in both the PA and GA group. PA participants also showed a reduction in body fat percentage and hip circumference, whereas these parameters increased in the GA group Our findings suggest that although no clear effects on wellbeing were found, still, at least on the short term, personalized advice may evoke health benefits in a population of seniors as compared to generic advice.

Systems biology of personalized nutrition.

Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the basis of a person's health status and goals. The biology underpinning these recommendations is complex, and thus any recommendations must account for multiple biological processes and subprocesses occurring in various tissues and must be formed with an appreciation for how these processes interact with dietary nutrients and environmental factors. Therefore, a systems biology-based approach that considers the most relevant interacting biological mechanisms is necessary to formulate the best recommendations to help people meet their wellness goals. Here, the concept of "systems flexibility" is introduced to personalized nutrition biology. Systems flexibility allows the real-time evaluation of metabolism and other processes that maintain homeostasis following an environmental challenge, thereby enabling the formulation of personalized recommendations. Examples in the area of macro- and micronutrients are reviewed. Genetic variations and performance goals are integrated into this systems approach to provide a strategy for a balanced evaluation and an introduction to personalized nutrition. Finally, modeling approaches that combine personalized diagnosis and nutritional intervention into practice are reviewed.

Effect of Caffeine on Attention and Alertness Measured in a Home-Setting, Using Web-Based Cognition Tests.

BACKGROUND: There is an increasing interest among nutritional researchers to perform lifestyle and nutritional intervention studies in a home setting instead of testing subjects in a clinical unit. The term used in other disciplines is 'ecological validity' stressing a realistic situation. This becomes more and more feasible because devices and self-tests that enable such studies are more commonly available. Here, we present such a study in which we reproduced the effect of caffeine on attention and alertness in an at-home setting. OBJECTIVE: The study was aimed to reproduce the effect of caffeine on attention and alertness using a Web-based study environment of subjects, at home, performing different Web-based cognition tests. METHODS: The study was designed as a randomized, placebo-controlled, double-blind, crossover study. Subjects were provided with coffee sachets (2 with and 2 without caffeine). They were also provided with a written instruction of the test days. Healthy volunteers consumed a cup of coffee after an overnight fast. Each intervention was repeated once. Before and 1 hour after coffee consumption subjects performed Web-based cognitive performance tests at home, which measured alertness and attention, established by 3 computerized tests provided by QuantifiedMind. Each test was performed for 5 minutes. RESULTS: Web-based recruitment was fast and efficient. Within 2 weeks, 102 subjects applied, of whom 70 were eligible. Of the 66 subjects who started the study, 53 completed all 4 test sessions (80%), indicating that they were able to perform the do it yourself tests, at home, correctly. The Go-No Go cognition test performed at home showed the same significant improvement in reaction time with caffeine as found in controlled studies in a metabolic ward (P=.02). For coding and N-back the second block was performed approximately 10% faster. No effect was seen on correctness. CONCLUSIONS: The study showed that the effects of caffeine consumption on a cognition test in an at-home setting revealed similar results as in a controlled setting. The Go-No Go test applied showed improved results after caffeine intake, similar as seen in clinical trials. This type of study is a fast, reliable, economical, and easy way to demonstrate effectiveness of a supplement and is rapidly becoming a viable alternative for the classical randomized control trial to evaluate life style and nutritional interventions. TRIAL REGISTRATION: Clinicaltrials.gov NCT02061982; https://clinicaltrials.gov/ct2/show/NCT02061982 (Archived by WebCite at https://clinicaltrials.gov/ct2/show/NCT02061982).

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data.

BACKGROUND: Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment identification, for pharmacological mechanism elucidation, and for comparing compound toxicity profiles. METHODS: We created 30,211 chemical response-specific gene sets for human and mouse by next-gen TM, and derived 1,189 (human) and 588 (mouse) gene sets from the Comparative Toxicogenomics Database (CTD). We tested for significant differential expression (SDE) (false discovery rate -corrected p-values < 0.05) of the next-gen TM-derived gene sets and the CTD-derived gene sets in gene expression (GE) data sets of five chemicals (from experimental models). We tested for SDE of gene sets for six fibrates in a peroxisome proliferator-activated receptor alpha (PPARA) knock-out GE dataset and compared to results from the Connectivity Map. We tested for SDE of 319 next-gen TM-derived gene sets for environmental toxicants in three GE data sets of triazoles, and tested for SDE of 442 gene sets associated with embryonic structures. We compared the gene sets to triazole effects seen in the Whole Embryo Culture (WEC), and used principal component analysis (PCA) to discriminate triazoles from other chemicals. RESULTS: Next-gen TM-derived gene sets matching the chemical treatment were significantly altered in three GE data sets, and the corresponding CTD-derived gene sets were significantly altered in five GE data sets. Six next-gen TM-derived and four CTD-derived fibrate gene sets were significantly altered in the PPARA knock-out GE dataset. None of the fibrate signatures in cMap scored significant against the PPARA GE signature. 33 environmental toxicant gene sets were significantly altered in the triazole GE data sets. 21 of these toxicants had a similar toxicity pattern as the triazoles. We confirmed embryotoxic effects, and discriminated triazoles from other chemicals. CONCLUSIONS: Gene set analysis with next-gen TM-derived chemical response-specific gene sets is a scalable method for identifying similarities in gene responses to other chemicals, from which one may infer potential mode of action and/or toxic effect.

Comparative analysis of transcriptome and fitness profiles reveals general and condition-specific cellular functions involved in adaptation to environmental change in Saccharomyces cerevisiae.

The transcriptional responses of yeast cells to a wide variety of stress conditions have been studied extensively. In addition, deletion mutant collections have been widely used to measure the combined effect of gene loss and stress on growth (fitness). Here we present a comparative analysis of 1,095 publicly available transcription and genome-wide fitness profiles in yeast, from different laboratories and experimental platforms. We analyzed these data, using T-profiler, to describe the correlation in behavior of a priori defined functional groups. Two-mode clustering analysis of the fitness T-profiles revealed that functional groups involved in regulating ribosome biogenesis and translation offer general stress resistance. These groups are closely related to growth rate and nutrient availability. General stress sensitivity was found in deletion mutant groups functioning in intracellular vesicular transport, actin cytoskeleton organization, and cell polarity, indicating that they play an key role in maintaining yeast adaptability. Analysis of the phenotypic and transcriptional variability of our a priori defined functional groups showed that the quantitative effect on fitness of both resistant and sensitive groups is highly condition-dependent. Finally, we discuss the implications of our results for combinatorial drug design.

Time series analysis of benzo[A]pyrene-induced transcriptome changes suggests that a network of transcription factors regulates the effects on functional gene sets.

Chemical carcinogens may cause a multitude of effects inside cells, thereby affecting transcript levels of genes by direct activation of transcription factors (TF) or indirectly through the formation of DNA damage. As the temporal profiles of these responses may be profoundly different, examining time-dependent changes may provide new insights in TF networks related to cellular responses to chemical carcinogens. Therefore, we investigated in human hepatoma cells gene expression changes caused by benzo[a]pyrene at 12 time points after exposure, in relation to DNA adduct and cell cycle. Temporal profiles for functional gene sets demonstrate both early and late effects in up- and downregulation of relevant gene sets involved in cell cycle, apoptosis, DNA repair, and metabolism of amino acids and lipids. Many significant transcription regulation networks appeared to be around TF that are proto-oncogenes or tumor suppressor genes. The time series analysis tool Short Time-series Expression Miner (STEM) was used to identify time-dependent correlation of pathways, gene sets, TF networks, and biological parameters. Most correlations are with DNA adduct levels, which is an early response, and less with the later responses on G1 and S phase cells. The majority of the modulated genes in the Reactome pathways can be regulated by several of these TF, e.g., 73% by nuclear factor-kappa B and 34-42% by c-MYC, SRF, AP1, and E2F1. All these TF can also regulate one or more of the others. Our data indicate that a complex network of a few TF is responsible for the majority of the transcriptional changes induced by BaP. This network hardly changes over time, despite that the transcriptional profiles clearly alter, suggesting that also other regulatory mechanisms are involved.

Keratinocyte gene expression profiles discriminate sensitizing and irritating compounds.

Many chemicals can induce allergic contact dermatitis. Because evaluation of skin sensitizing potential by animal testing is prohibited for cosmetics, and screening of many chemicals is required within Registration, Evaluation, Authorisation and Restriction of Chemicals, urgent need exists for predictive in vitro assays to identify contact allergens. Keratinocytes (KC) are the first cells encountered when chemicals land on the skin. Therefore, KC form an important site of haptenization and their metabolism is likely to be important. Moreover, KC secrete mediators that affect processing and presentation of haptenized proteins by dendritic cells. To develop a KC-based in vitro assay to predict sensitizing potential of chemicals, in vitro exposure effects of eight contact sensitizers and six irritants on the KC cell line HaCaT were examined by gene profiling. Classifiers predictive of the class sensitizers or irritants were calculated, based on support vector machine (SVM) and random forest (RF) algorithms. Classifiers using high-ranking genes were 70% (SVM) and 62% (RF) accurate, based on three (SVM) and two to five (RF) features. Classifiers using oxidative stress pathway gene sets were 68-73% (SVM) and 69-71% (RF) accurate. Cross-validation showed that the top-3 of most discriminating genes added up to 13 genes and included oxidative stress gene HMOX1 irrespective of the chemical left out. Moreover, HMOX1 was the most significantly regulated gene. Gene Set Enrichment Analysis showed upregulation of "Keap1 dependent" and "oxidative stress" gene lists. In conclusion, KC expression profiling can identify contact sensitizers, providing opportunities for nonanimal testing for sensitizing potential. Moreover, our data suggest that contact sensitizers induce the oxidative stress pathway in KC.

Discrimination for genotoxic and nongenotoxic carcinogens by gene expression profiling in primary mouse hepatocytes improves with exposure time.

Assessing the potential carcinogenicity of chemicals for humans represents an ongoing challenge. Chronic rodent bioassays predict human cancer risk at only limited reliability and are simultaneously expensive and long lasting. In order to seek for alternatives, the ability of a transcriptomics-based primary mouse hepatocyte model to classify carcinogens by their modes of action was evaluated. As it is obvious that exposure will induce a cascade of gene expression modifications, in particular, the influence of exposure time in vitro on discriminating genotoxic (GTX) carcinogens from nongenotoxic (NGTX) carcinogens class discrimination was investigated. Primary mouse hepatocytes from male C57Bl6 mice were treated for 12, 24, 36, and 48 h with two GTX and two NGTX carcinogens. For validation, two additional GTX compounds were studied at 24 and 48 h. Immunostaining of gammaH2AX foci was applied in order to phenotypically verify DNA damage. It confirmed significant induction of DNA damage after treatment with GTX compounds but not with NGTX compounds. Whole-genome gene expression modifications were analyzed by means of Affymetrix microarrays. When using differentially expressed genes from data sets normalized by Robust Multi-array Average, the two classes and various compounds were better separated from each other by hierarchical clustering when increasing the treatment period. Discrimination of GTX and NGTX carcinogens by Prediction Analysis of Microarray improved with time and resulted in correct classification of the validation compounds. The present study shows that gene expression profiling in primary mouse hepatocytes is promising for discriminating GTX from NGTX compounds and that this discrimination improves with increasing treatment period.

A toxicogenomics-based parallelogram approach to evaluate the relevance of coumarin-induced responses in primary human hepatocytes in vitro for humans in vivo.

A compound for which marked species differences have been reported in laboratory animals and humans is coumarin. In rats, metabolites of coumarin are highly toxic, whereas in humans, the compound is mainly metabolized to non-toxic metabolites. In the present study, a toxicogenomics-based parallelogram approach was used to compare effects of coumarin on gene expression in human hepatocytes relevant for the situation in vivo. To this purpose, gene expression profiling was performed on human hepatocytes treated with coumarin in a pharmacological relevant and proposed toxic concentration and results were compared to a previously performed coumarin in vivo and in vitro rat toxicogenomics study. No cytotoxicity was observed in human hepatocytes at both concentrations, whereas rats showed clear toxic effects in vitro as well as in vivo. In all three systems, coumarin affected genes involved in the blood coagulation pathway; this indicates relevant responses in cases of human exposure. However, no pathways and processes related to hepatotoxicity in rats were observed in human hepatocytes. Still, repression of energy-consuming biochemical pathways and impairment of mitochondrial function were observed in human hepatocytes treated with the highest concentration of coumarin, possibly indicating toxicity. In conclusion, although species differences in response to coumarin are evident in the present results, the toxicogenomics-based parallelogram approach enables clear discrimination between pharmacological responses at pharmacological doses and proposed toxic responses at high (toxic) doses relevant for humans in vivo.

Parallelogram approach using rat-human in vitro and rat in vivo toxicogenomics predicts acetaminophen-induced hepatotoxicity in humans.

The frequent use of rodent hepatic in vitro systems in pharmacological and toxicological investigations challenges extrapolation of in vitro results to the situation in vivo and interspecies extrapolation from rodents to humans. The toxicogenomics approach may aid in evaluating relevance of these model systems for human risk assessment by direct comparison of toxicant-induced gene expression profiles and infers mechanisms between several systems. In the present study, acetaminophen (APAP) was used as a model compound to compare gene expression responses between rat and human using in vitro cellular models, hepatocytes, and between rat in vitro and in vivo. Comparison at the level of modulated biochemical pathways and biological processes rather than at that of individual genes appears preferable as it increases the overlap between various systems. Pathway analysis by T-profiler revealed similar biochemical pathways and biological processes repressed in rat and human hepatocytes in vitro, as well as in rat liver in vitro and in vivo. Repressed pathways comprised energy-consuming biochemical pathways, mitochondrial function, and oxidoreductase activity. The present study is the first that used a toxicogenomics-based parallelogram approach, extrapolating in vitro to in vivo and interspecies, to reveal relevant mechanisms indicative of APAP-induced liver toxicity in humans in vivo.

Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

BACKGROUND: A key goal of systems biology is to understand how genomewide mRNA expression levels are controlled by transcription factors (TFs) in a condition-specific fashion. TF activity is frequently modulated at the post-translational level through ligand binding, covalent modification, or changes in sub-cellular localization. In this paper, we demonstrate how prior information about regulatory network connectivity can be exploited to infer condition-specific TF activity as a hidden variable from the genomewide mRNA expression pattern in the yeast Saccharomyces cerevisiae. METHODOLOGY/PRINCIPAL FINDINGS: We first validate experimentally that by scoring differential expression at the level of gene sets or "regulons" comprised of the putative targets of a TF, we can accurately predict modulation of TF activity at the post-translational level. Next, we create an interactive database of inferred activities for a large number of TFs across a large number of experimental conditions in S. cerevisiae. This allows us to perform TF-centric analysis of the yeast regulatory network. CONCLUSIONS/SIGNIFICANCE: We analyze the degree to which the mRNA expression level of each TF is predictive of its regulatory activity. We also organize TFs into "co-modulation networks" based on their inferred activity profile across conditions, and find that this reveals functional and mechanistic relationships. Finally, we present evidence that the PAC and rRPE motifs antagonize TBP-dependent regulation, and function as core promoter elements governed by the transcription regulator NC2. Regulon-based monitoring of TF activity modulation is a powerful tool for analyzing regulatory network function that should be applicable in other organisms. Tools and results are available online at http://bussemakerlab.org/RegulonProfiler/.

Genomic analysis suggests higher susceptibility of children to air pollution.

Differences in biological responses to exposure to hazardous airborne substances between children and adults have been reported, suggesting children to be more susceptible. Aim of this study was to improve our understanding of differences in susceptibility in cancer risk associated with air pollution by comparing genome-wide gene expression profiles in peripheral blood of children and their parents. Gene expression analysis was performed in blood from children and parents living in two different regions in the Czech Republic with different levels of air pollution. Data were analyzed by two different approaches: one method first selected significantly differentially expressed genes and analyzed these gene lists for overrepresented biological processes, whereas the other applied the T-profiler tool to directly perform pathway analyses on the total gene set without preselection of significantly modulated gene expressions. In addition, gene expressions in both children and adults were investigated for associations with micronuclei frequencies. Both analysis approaches returned considerably more genes or gene groups and pathways that significantly differed between children from both regions than between parents. Very little overlap was observed between children and adults. The two most important biological processes or molecular functions significantly modulated in children, but not in adults, are nucleosome and immune response related. Our study suggests differences between children and adults in relation to air pollution exposure at the transcriptome level. The findings underline the necessity of implementing environmental health policy measures specifically for protecting children's health.

The contact allergen dinitrochlorobenzene (DNCB) and respiratory allergy in the Th2-prone Brown Norway rat.

All LMW respiratory allergens known to date can also induce skin allergy in test animals. The question here was if in turn skin allergens can induce allergy in the respiratory tract. Respiratory allergy was tested in Th2-prone Brown Norway (BN) rats by dermal sensitization with the contact allergen dinitrochlorobenzene (DNCB; 1%, day 0; 0.5%, day 7) and a head/nose-only inhalation challenge of 27mg/m3 of DNCB (15 min, day 21), using a protocol that successfully identified chemical respiratory allergens. Skin allergy to DNCB was examined in BN rats and Th1-prone Wistar rats in a local lymph node assay followed by a topical patch challenge of 0.1% DNCB. Sensitization of BN rats via the skin induced DNCB-specific IgG in serum, but not in all animals, and an increased number of CD4+ cells in the lung parenchyma. Subsequent inhalation challenge with DNCB did not provoke apneas or allergic inflammation (signs of respiratory allergy) in the BN rats. However, microarray analysis of mRNA isolated from the lung revealed upregulation of the genes for Ccl2 (MCP-1), Ccl4 (MIP-1beta), Ccl7 and Ccl17. Skin challenge induced considerably less skin irritation and allergic dermatitis in the BN rat than in the Wistar rat. In conclusion, the Th2-prone BN rat appeared less sensitive to DNCB than the Wistar rat; nevertheless, DNCB induced allergic inflammation in the skin of BN rats but even a relatively high challenge concentration did not induce allergy in the respiratory tract, although genes associated with allergy were upregulated in lung tissue.

Transcriptome analysis of sorbic acid-stressed Bacillus subtilis reveals a nutrient limitation response and indicates plasma membrane remodeling.

The weak organic acid sorbic acid is a commonly used food preservative, as it inhibits the growth of bacteria, yeasts, and molds. We have used genome-wide transcriptional profiling of Bacillus subtilis cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance mechanisms. Our analysis demonstrated that sorbic acid-stressed cells induce responses normally seen upon nutrient limitation. This is indicated by the strong derepression of the CcpA, CodY, and Fur regulon and the induction of tricarboxylic acid cycle genes, SigL- and SigH-mediated genes, and the stringent response. Intriguingly, these conditions did not lead to the activation of sporulation, competence, or the general stress response. The fatty acid biosynthesis (fab) genes and BkdR-regulated genes are upregulated, which may indicate plasma membrane remodeling. This was further supported by the reduced sensitivity toward the fab inhibitor cerulenin upon sorbic acid stress. We are the first to present a comprehensive analysis of the transcriptional response of B. subtilis to sorbic acid stress.

Physiological and transcriptional characterization of Saccharomyces cerevisiae strains with modified expression of catabolic regulators.

A comparative physiological and transcriptional study is presented on wild-type Saccharomyces cerevisiae and mutants with altered levels of catabolic regulators: hxk2Delta lacking hexokinase2, HAP4 / overproducing hap4p and hxk2 Delta HAP4 upward arrow. Relative to the wild-type, HAP4 / showed the same growth rate with some increased yield on glucose, and hxk2Delta grew 28% slower but with a dramatically improved yield. Hxk2 Delta HAP4 / grew 14% slower but showed fully oxidative growth. A higher yield correlated with increased respiration. For both hxk2 Delta strains, glucose repression was suppressed (upregulation of high-affinity sugar transporters, invertase and oxidative phosphorylation). T-profiler analysis showed that genes under control of the hap2/3/4/5-binding motif were significantly altered in expression in all strains. HAP4 overexpression, directly or in hxk2 knockouts, led to repression of the genes containing the Zap1p motif including ZAP1 itself, indicating altered zinc metabolism. Whereas HAP4 overexpression resulted in a shift towards oxidative metabolism only, deletion of HXK2 resulted in a strain that, in addition to being oxidative, almost completely lacked the ability to sense glucose. As the double mutant had an energy efficiency close to the maximum even with excess glucose and was derepressed to a larger extent and over a broader range, the functioning of the two regulators is in general considered to be additive.