Diagnostic markers based on a computational model of lipoprotein metabolism

Abstract Background: Dyslipidemia is an important risk factor for cardiovascular disease and type II diabetes. Lipoprotein diagnostics, such as LDL cholesterol and HDL cholesterol, help to diagnose these diseases. Lipoprotein profile measurements could improve lipoprotein diagnostics, but interpretational complexity has limited their clinical application to date. We have previously developed a computational model called Particle Profiler to interpret lipoprotein profiles. In the current study we further developed and calibrated Particle Profiler using subjects with specific genetic conditions. We subsequently performed technical validation and worked at an initial indication of clinical usefulness starting from available data on lipoprotein concentrations and metabolic fluxes. Since the model outcomes cannot be measured directly, the only available technical validation was corroboration. For an initial indication of clinical usefulness, pooled lipoprotein metabolic flux data was available from subjects with various types of dyslipidemia. Therefore we investigated how well lipoprotein metabolic ratios derived from Particle Profiler distinguished reported dyslipidemic from normolipidemic subjects. Results: We found that the model could fit a range of normolipidemic and dyslipidemic subjects from fifteen out of sixteen studies equally well, with an average 8.8% ± 5.0% fit error; only one study showed a larger fit error. As initial indication of clinical usefulness, we showed that one diagnostic marker based on VLDL metabolic ratios better distinguished dyslipidemic from normolipidemic subjects than triglycerides, HDL cholesterol, or LDL cholesterol. The VLDL metabolic ratios outperformed each of the classical diagnostics separately; they also added power of distinction when included in a multivariate logistic regression model on top of the classical diagnostics. Conclusions: In this study we further developed, calibrated, and corroborated the Particle Profiler computational model using pooled lipoprotein metabolic flux data. From pooled lipoprotein metabolic flux data on dyslipidemic patients, we derived VLDL metabolic ratios that better distinguished normolipidemic from dyslipidemic subjects than standard diagnostics, including HDL cholesterol, triglycerides and LDL cholesterol. Since dyslipidemias are closely linked to cardiovascular disease and diabetes type II development, lipoprotein metabolic ratios are candidate risk markers for these diseases. These ratios can in principle be obtained by applying Particle Profiler to a single lipoprotein profile measurement, which makes clinical application feasible

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis

<p>Abstract</p> <p>Background</p> <p>The application of high-throughput genomic tools in nutrition research is a widespread practice. However, it is becoming increasingly clear that the outcome of individual expression studies is insufficient for the comprehensive understanding of such a complex field. Currently, the availability of the large amounts of expression data in public repositories has opened up new challenges on microarray data analyses. We have focused on PPARα, a ligand-activated transcription factor functioning as fatty acid sensor controlling the gene expression regulation of a large set of genes in various metabolic organs such as liver, small intestine or heart. The function of PPARα is strictly connected to the function of its target genes and, although many of these have already been identified, major elements of its physiological function remain to be uncovered. To further investigate the function of PPARα, we have applied a cross-species meta-analysis approach to integrate sixteen microarray datasets studying high fat diet and PPARα signal perturbations in different organisms.</p> <p>Results</p> <p>We identified 164 genes (MDEGs) that were differentially expressed in a constant way in response to a high fat diet or to perturbations in PPARs signalling. In particular, we found five genes in yeast which were highly conserved and homologous of PPARα targets in mammals, potential candidates to be used as models for the equivalent mammalian genes. Moreover, a screening of the MDEGs for all known transcription factor binding sites and the comparison with a human genome-wide screening of Peroxisome Proliferating Response Elements (PPRE), enabled us to identify, 20 new potential candidate genes that show, both binding site, both change in expression in the condition studied. Lastly, we found a non random localization of the differentially expressed genes in the genome.</p> <p>Conclusion</p> <p>The results presented are potentially of great interest to resume the currently available expression data, exploiting the power of <it>in silico </it>analysis filtered by evolutionary conservation. The analysis enabled us to indicate potential gene candidates that could fill in the gaps with regards to the signalling of PPARα and, moreover, the non-random localization of the differentially expressed genes in the genome, suggest that epigenetic mechanisms are of importance in the regulation of the transcription operated by PPARα.</p

A Dietary Mixture Containing Fish Oil, Resveratrol, Lycopene, Catechins, and Vitamins E and C Reduces Atherosclerosis in Transgenic Mice123

Chronic inflammation and proatherogenic lipids are important risk factors of cardiovascular disease (CVD). Specific dietary constituents such as polyphenols and fish oils may improve cardiovascular risk factors and may have a beneficial effect on disease outcomes. We hypothesized that the intake of an antiinflammatory dietary mixture (AIDM) containing resveratrol, lycopene, catechin, vitamins E and C, and fish oil would reduce inflammatory risk factors, proatherogenic lipids, and endpoint atherosclerosis. AIDM was evaluated in an inflammation model, male human C-reactive protein (CRP) transgenic mice, and an atherosclerosis model, female ApoE*3Leiden transgenic mice. Two groups of male human-CRP transgenic mice were fed AIDM [0.567% (wt:wt) powder and 0.933% (wt:wt oil)] or placebo for 6 wk. The effects of AIDM on basal and IL-1β–stimulated CRP expression were investigated. AIDM reduced cytokine-induced human CRP and fibrinogen expression in human-CRP transgenic mice. In the atherosclerosis study, 2 groups of female ApoE*3Leiden transgenic mice were fed an atherogenic diet supplemented with AIDM [0.567% (wt:wt) powder and 0.933% (wt:wt oil)] or placebo for 16 wk. AIDM strongly reduced plasma cholesterol, TG, and serum amyloid A concentrations compared with placebo. Importantly, long-term treatment of ApoE*3Leiden mice with AIDM markedly reduced the development of atherosclerosis by 96% compared with placebo. The effect on atherosclerosis was paralleled by a reduced expression of the vascular inflammation markers and adhesion molecules inter-cellular adhesion molecule-1 and E-selectin. Dietary supplementation of AIDM improves lipid and inflammatory risk factors of CVD and strongly reduces atherosclerotic lesion development in female transgenic mice

Time- and dose-dependent effects of curcumin on gene expression in human colon cancer cells

BACKGROUND: Curcumin is a spice and a coloring food compound with a promising role in colon cancer prevention. Curcumin protects against development of colon tumors in rats treated with a colon carcinogen, in colon cancer cells curcumin can inhibit cell proliferation and induce apoptosis, it is an anti-oxidant and it can act as an anti-inflammatory agent. The aim of this study was to elucidate mechanisms and effect of curcumin in colon cancer cells using gene expression profiling. METHODS: Gene expression changes in response to curcumin exposure were studied in two human colon cancer cell lines, using cDNA microarrays with four thousand human genes. HT29 cells were exposed to two different concentrations of curcumin and gene expression changes were followed in time (3, 6, 12, 24 and 48 hours). Gene expression changes after short-term exposure (3 or 6 hours) to curcumin were also studied in a second cell type, Caco-2 cells. RESULTS: Gene expression changes (>1.5-fold) were found at all time points. HT29 cells were more sensitive to curcumin than Caco-2 cells. Early response genes were involved in cell cycle, signal transduction, DNA repair, gene transcription, cell adhesion and xenobiotic metabolism. In HT29 cells curcumin modulated a number of cell cycle genes of which several have a role in transition through the G2/M phase. This corresponded to a cell cycle arrest in the G2/M phase as was observed by flow cytometry. Functional groups with a similar expression profile included genes involved in phase-II metabolism that were induced by curcumin after 12 and 24 hours. Expression of some cytochrome P450 genes was downregulated by curcumin in HT29 and Caco-2 cells. In addition, curcumin affected expression of metallothionein genes, tubulin genes, p53 and other genes involved in colon carcinogenesis. CONCLUSIONS: This study has extended knowledge on pathways or processes already reported to be affected by curcumin (cell cycle arrest, phase-II genes). Moreover, potential new leads to genes and pathways that could play a role in colon cancer prevention by curcumin were identified

Intensive Lifestyle (e)Support to Reverse Diabetes-2

Advanced diabetes-type-2 patients often have high insulin resistance. Over the years their insulin medication rises, which further increases their insulin resistance and glucose management problems. A HINTc (High Intensity Nutrition, Training & coaching) pilot study was conducted with 11 insulin-dependent patients. Hybrid eHealth support was given, with electronic support plus a multi-disciplinary health support team. Based on preliminary 12 week results, attractiveness and feasibility of the intervention were high: recommendation 9,0 out of 10 and satisfaction 9,1 out of 10. TAM (Technology Acceptance Model) surveys showed high usefulness, feasibility and intentions for future use. Acceptance and health behaviours were also reinforced by the rapid results (average 9% weight loss, 20% lower fasting glucose and 71% lower insulin medication, plus a 46% increase on the Quality of Life Physical Health dimension). Our analysis supports three types of conclusions. First, patients’ health literacy and quality of life improved strongly, both supporting healthier behaviours. Second, a virtuous cycle was started, helping patients reverse diabetes-2 progression. Third, a design analysis was conducted regarding service mix efficacy in relation to key requirements for designing ICT-enabled lifestyle interventions

Diabetes Lifestyle (e)Coaching 50 Weeks Follow Up; Technology Acceptance & e-Relationships

We report on the 50 weeks follow up results from a healthy lifestyle pilot (High Intensity Nutrition, Training & coaching), conducted with 11 insulin-dependent Type 2 Diabetes Mellites (DM2) patients. Hybrid eHealth support was given, with electronic support plus a multi-disciplinary health support team. Regarding the pilot goal of long term healthy lifestyle adoption in senior DM2 patients, challenges were: low ICT- and health literacy. This exploratory design analysis formulates design lessons based on 50 weeks follow up. The first 12 weeks contained intensive face-to-face and eSupported coaching. After that, patient self- management and eTools were key. After 50 weeks, attractiveness and feasibility of the intervention were perceived as high: recommendation 9,5 out of 10 and satisfaction 9,6 out of 10. TAM (Technology Acceptance Model) surveys showed high usefulness and feasibility. Acceptance and health behaviours were reinforced by the prolonged health results: Aerobic and strength capacity levels were improved at 50 weeks, plus Health Related Quality of Life (and biometric benefits and medication reductions, reported elsewhere). We draw three types of conclusions. First, patients’ health literacy and quality of life improved strongly, which both supported healthy behaviours, even after 50 weeks. Second, regarding eHealth theory, iterative growth cycles are beneficial for long term adoption and e-relationships. Third, a design analysis was conducted regarding long term service mix efficacy in relation to key requirements for designing ICT-enabled lifestyle interventions. Several suggestions for long term lifestyle eSupport are given

Greenhouse gas emissions from the grassy outdoor run of organic broilers

Nitrous oxide (N&lt;sub&gt;2&lt;/sub&gt;O), methane (CH&lt;sub&gt;4&lt;/sub&gt;) and carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;) fluxes over the grassy outdoor run of organically grown broilers were monitored using static chambers over two production batches in contrasted seasons. Measured N&lt;sub&gt;2&lt;/sub&gt;O and CH&lt;sub&gt;4&lt;/sub&gt; fluxes were extremely variable in time and space for both batches, with fluxes ranging from a small uptake by soil to large emissions peaks, the latter of which always occurred in the chambers located closest to the broiler house. In general, fluxes decreased with increasing distance to the broiler house, demonstrating that the foraging of broilers and the amount of excreted nutrients (carbon, nitrogen) largely control the spatial variability of emissions. Spatial integration by kriging methods was carried out to provide representative fluxes on the outdoor run for each measurement day. Mechanistic relationships between plot-scale estimates and environmental conditions (soil temperature and water content) were calibrated in order to fill gaps between measurement days. Flux integration over the year 2010 showed that around 3 ± 1 kg N&lt;sub&gt;2&lt;/sub&gt;O-N ha&lt;sup&gt;−1&lt;/sup&gt; were emitted on the outdoor run, equivalent to 0.9% of outdoor N excretion and substantially lower than the IPCC default emission factor of 2%. By contrast, the outdoor run was found to be a net CH&lt;sub&gt;4&lt;/sub&gt; sink of about −0.56 kg CH&lt;sub&gt;4&lt;/sub&gt;-C ha&lt;sup&gt;−1&lt;/sup&gt;, though this sink compensated less than 1.5% (in CO&lt;sub&gt;2&lt;/sub&gt; equivalents) of N&lt;sub&gt;2&lt;/sub&gt;O emissions. The net greenhouse gas (GHG) budget of the outdoor run is explored, based on measured GHG fluxes and short-term (1.5 yr) variations in soil organic carbon

Exploring the benefits and challenges of establishing a DRI-like process for bioactives

Bioactives can be defined as: "Constituents in foods or dietary supplements, other than those needed to meet basic human nutritional needs, which are responsible for changes in health status" (Office of Disease Prevention and Health Promotion, Office of Public Health and Science, Department of Health and Human Services in Fed Reg 69:55821-55822, 2004). Although traditional nutrients, such as vitamins, minerals, protein, essential fatty acids and essential amino acids, have dietary reference intake (DRI) values, there is no such evaluative process for bioactives. For certain classes of bioactives, substantial scientific evidence exists to validate a relationship between their intake and enhanced health conditions or reduced risk of disease. In addition, the study of bioactives and their relationship to disease risk is a growing area of research supported by government, academic institutions, and food and supplement manufacturers. Importantly, consumers are purchasing foods containing bioactives, yet there is no evaluative process in place to let the public know how strong the science is behind the benefits or the quantitative amounts needed to achieve these beneficial health effects. This conference, Bioactives: Qualitative Nutrient Reference Values for Life-stage Groups?, explored why it is important to have a DRI-like process for bioactives and challenges for establishing such a process.Fil: J. R. Lupton.Fil: S. A. Atkinson.Fil: N. Chang.Fil: Fraga, César Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Bioquímica y Medicina Molecular. Universidad de Buenos Aires. Facultad Medicina. Instituto de Bioquímica y Medicina Molecular; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Química Analitica y Fisicoquímica. Cátedra de Fisicoquímica; ArgentinaFil: J. Levy.Fil: M. Messina.Fil: D. P. Richardson.Fil: B. van Ommen.Fil: Y. Yang.Fil: J. C. Griffiths.Fil: J. Hathcock

Time-Resolved and Tissue-Specific Systems Analysis of the Pathogenesis of Insulin Resistance

BACKGROUND: The sequence of events leading to the development of insulin resistance (IR) as well as the underlying pathophysiological mechanisms are incompletely understood. As reductionist approaches have been largely unsuccessful in providing an understanding of the pathogenesis of IR, there is a need for an integrative, time-resolved approach to elucidate the development of the disease. METHODOLOGY/PRINCIPAL FINDINGS: Male ApoE3Leiden transgenic mice exhibiting a humanized lipid metabolism were fed a high-fat diet (HFD) for 0, 1, 6, 9, or 12 weeks. Development of IR was monitored in individual mice over time by performing glucose tolerance tests and measuring specific biomarkers in plasma, and hyperinsulinemic-euglycemic clamp analysis to assess IR in a tissue-specific manner. To elucidate the dynamics and tissue-specificity of metabolic and inflammatory processes key to IR development, a time-resolved systems analysis of gene expression and metabolite levels in liver, white adipose tissue (WAT), and muscle was performed. During HFD feeding, the mice became increasingly obese and showed a gradual increase in glucose intolerance. IR became first manifest in liver (week 6) and then in WAT (week 12), while skeletal muscle remained insulin-sensitive. Microarray analysis showed rapid upregulation of carbohydrate (only liver) and lipid metabolism genes (liver, WAT). Metabolomics revealed significant changes in the ratio of saturated to polyunsaturated fatty acids (liver, WAT, plasma) and in the concentrations of glucose, gluconeogenesis and Krebs cycle metabolites, and branched amino acids (liver). HFD evoked an early hepatic inflammatory response which then gradually declined to near baseline. By contrast, inflammation in WAT increased over time, reaching highest values in week 12. In skeletal muscle, carbohydrate metabolism, lipid metabolism, and inflammation was gradually suppressed with HFD. CONCLUSIONS/SIGNIFICANCE: HFD-induced IR is a time- and tissue-dependent process that starts in liver and proceeds in WAT. IR development is paralleled by tissue-specific gene expression changes, metabolic adjustments, changes in lipid composition, and inflammatory responses in liver and WAT involving p65-NFkB and SOCS3. The alterations in skeletal muscle are largely opposite to those in liver and WAT