Showing papers by "Matej Orešič published in 2009"

Integration of microRNA miR-122 in hepatic circadian gene expression.

Abstract: In liver, most metabolic pathways are under circadian control, and hundreds of protein-encoding genes are thus transcribed in a cyclic fashion. Here we show that rhythmic transcription extends to the locus specifying miR-122, a highly abundant, hepatocyte-specific microRNA. Genetic loss-of-function and gain-of-function experiments have identified the orphan nuclear receptor REV-ERBalpha as the major circadian regulator of mir-122 transcription. Although due to its long half-life mature miR-122 accumulates at nearly constant rates throughout the day, this miRNA is tightly associated with control mechanisms governing circadian gene expression. Thus, the knockdown of miR-122 expression via an antisense oligonucleotide (ASO) strategy resulted in the up- and down-regulation of hundreds of mRNAs, of which a disproportionately high fraction accumulates in a circadian fashion. miR-122 has previously been linked to the regulation of cholesterol and lipid metabolism. The transcripts associated with these pathways indeed show the strongest time point-specific changes upon miR-122 depletion. The identification of Pparbeta/delta and the peroxisome proliferator-activated receptor alpha (PPARalpha) coactivator Smarcd1/Baf60a as novel miR-122 targets suggests an involvement of the circadian metabolic regulators of the PPAR family in miR-122-mediated metabolic control.

Hepatic Stearoyl-CoA Desaturase (SCD)-1 Activity and Diacylglycerol but Not Ceramide Concentrations Are Increased in the Nonalcoholic Human Fatty Liver

Abstract: OBJECTIVE—To determine whether 1) hepatic ceramide and diacylglycerol concentrations, 2) SCD1 activity, and 3) hepatic lipogenic index are increased in the human nonalcoholic fatty liver. RESEARCH DESIGN AND METHODS—We studied 16 subjects with (n = 8) and without (n = 8) histologically determined nonalcoholic fatty liver (NAFL+ and NAFL−) matched for age, sex, and BMI. Hepatic concentrations of lipids and fatty acids were quantitated using ultra-performance liquid chromatography coupled to mass spectrometry and gas chromatography. RESULTS—The absolute (nmol/mg) hepatic concentrations of diacylglycerols but not ceramides were increased in the NAFL+ group compared with the NAFL− group. The livers of the NAFL+ group contained proportionally less long-chain polyunsaturated fatty acids as compared with the NAFL− group. Liver fat percent was positively related to hepatic stearoyl-CoA desaturase 1 (SCD1) activity index (r = 0.70, P = 0.003) and the hepatic lipogenic index (r = 0.54, P = 0.030). Hepatic SCD1 activity index was positively related to the concentrations of diacylglycerols (r = 0.71, P = 0.002) but not ceramides (r = 0.07, NS). CONCLUSIONS—We conclude that diacylglycerols but not ceramides are increased in NAFL. The human fatty liver is also characterized by depletion of long polyunsaturated fatty acids in the liver and increases in hepatic SCD1 and lipogenic activities.

Serum saturated fatty acids containing triacylglycerols are better markers of insulin resistance than total serum triacylglycerol concentrations

Abstract: Aims/hypothesis The weak relationship between insulin resistance and total serum triacylglycerols (TGs) could be in part due to heterogeneity of TG molecules and their distribution within different lipoproteins. We determined concentrations of individual TGs and the fatty acid composition of serum and major lipoprotein particles and analysed how changes in different TGs and fatty acid composition are related to features of insulin resistance and abdominal obesity.

Metabolomics, a novel tool for studies of nutrition, metabolism and lipid dysfunction

Abstract: Aims In this review metabolomics is introduced in historic perspective, with key platforms and bioinformatics methodologies described. An overview is provided covering recent applications of metabolomics and lipidomics in the context of human physiology, lipid metabolism and nutrition. Data synthesis Global coverage of human metabolome requires application of multiple analytical platforms. The choice of a particular targeted or non-targeted analytical strategy depends on the hypothesis tested, state-of-the-art in the field, as well as on sample availability. Human metabolome has been shown to be sensitive to age, gut microbial composition, and lifestyle. Several studies have shown that, given the appropriate experimental design, subtle effects of interventions such as change of diet or weight loss can be detected by metabolomics and studied in the context of human physiology and health status. Conclusion Metabolome provides a sensitive intermediate phenotype linking the genotype, gut microbial composition and personal health status. Innovative experimental designs combined with novel computational tools for handling metabolomics data offer new opportunities for early disease detection as well as for characterization of dietary and therapeutic interventions in the context of human physiology.

Link between plasma ceramides, inflammation and insulin resistance: association with serum IL-6 concentration in patients with coronary heart disease.

Abstract: Aims/hypothesis Ceramides and IL-6 have a role in immune–inflammatory responses and cardiovascular diseases, and are suggested to be involved in insulin and glucose metabolism. We sought to assess the associations of circulating levels of IL-6, TNF-α and high-sensitivity C reactive protein (hsCRP), which are inflammatory markers related to insulin resistance (IR), with the plasma lipid metabolites ceramides and diacylglycerols (DAG) in patients with CHD.

ApoCIII-Enriched LDL in Type 2 Diabetes Displays Altered Lipid Composition, Increased Susceptibility for Sphingomyelinase and Increased binding to Biglycan

Abstract: OBJECTIVE Apolipoprotein CIII (apoCIII) is an independent risk factor for cardiovascular disease, but the molecular mechanisms involved are poorly understood. We investigated potential proatherogenic properties of apoCIII-containing LDL from hypertriglyceridemic patients with type 2 diabetes. RESEARCH DESIGN AND METHODS LDL was isolated from control subjects, subjects with type 2 diabetes, and apoB transgenic mice. LDL-biglycan binding was analyzed with a solid-phase assay using immunoplates coated with biglycan. Lipid composition was analyzed with mass spectrometry. Hydrolysis of LDL by sphingomyelinase was analyzed after labeling plasma LDL with [ 3 H]sphingomyelin. ApoCIII isoforms were quantified after isoelectric focusing. Human aortic endothelial cells were incubated with desialylated apoCIII or with LDL enriched with specific apoCIII isoforms. RESULTS We showed that enriching LDL with apoCIII only induced a small increase in LDL-proteoglycan binding, and this effect was dependent on a functional site A in apoB100. Our findings indicated that intrinsic characteristics of the diabetic LDL other than apoCIII are responsible for further increased proteoglycan binding of diabetic LDL with high-endogenous apoCIII, and we showed alterations in the lipid composition of diabetic LDL with high apoCIII. We also demonstrated that high apoCIII increased susceptibility of LDL to hydrolysis and aggregation by sphingomyelinases. In addition, we demonstrated that sialylation of apoCIII increased with increasing apoCIII content and that sialylation of apoCIII was essential for its proinflammatory properties. CONCLUSIONS We have demonstrated a number of features of apoCIII-containing LDL from hypertriglyceridemic patients with type 2 diabetes that could explain the proatherogenic role of apoCIII.

Fatty fish intake decreases lipids related to inflammation and insulin signaling--a lipidomics approach.

Abstract: Background The evidence of the multiple beneficial health effects of fish consumption is strong, but physiological mechanisms behind these effects are not completely known. Little information is available on the effects of consumption of different type of fish. The aim of this study was to investigate how fatty fish or lean fish in a diet affect serum lipidomic profiles in subjects with coronary heart disease. Methodology and Principal Findings A pilot study was designed which included altogether 33 subjects with myocardial infarction or unstable ischemic attack in an 8-week parallel controlled intervention. The subjects were randomized to either fatty fish (n = 11), lean fish (n = 12) or control (n = 10) groups. Subjects in the fish groups had 4 fish meals per week and subjects in the control group consumed lean beef, pork and chicken. A fish meal was allowed once a week maximum. Lipidomics analyses were performed using ultra performance liquid chromatography coupled to electrospray ionization mass spectrometry and gas chromatography. Multiple bioactive lipid species, including ceramides, lysophosphatidylcholines and diacylglycerols, decreased significantly in the fatty fish group, whereas in the lean fish group cholesterol esters and specific long-chain triacylglycerols increased significantly (False Discovery Rate q-value <0.05). Conclusions/Significance The 8-week consumption of fatty fish decreased lipids which are potential mediators of lipid-induced insulin resistance and inflammation, and may be related to the protective effects of fatty fish on the progression of atherosclerotic vascular diseases or insulin resistance. Trial Registration ClinicalTrials.gov NCT00720655

Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations.

Abstract: Mitochondrial membranes are unique in many ways. Unlike other cellular membranes, they are comprised of two membranes instead of just one, and cardiolipins, one of the abundant lipid species in mitochondrial membranes, are not found in significant amounts elsewhere in the cell. Among other aspects, the exceptional nature of cardiolipins is characterized by their small charged head group connected to typically four hydrocarbon chains. In this work, we present atomic-scale molecular dynamics simulations of the inner mitochondrial membrane modeled as a mixture of cardiolipins (CLs), phosphatidylcholines (PCs), and phosphatidylethanolamines (PEs). For comparison, we also consider pure one-component bilayers and mixed PC-PE, PC-CL, and PE-CL membranes. We find that the influence of CLs on membrane properties depends strongly on membrane composition. This is highlighted by studies of the stability of CL-containing membranes, which indicate that the interactions of CL in ternary lipid bilayers cannot be deduced from the corresponding ones in binary membranes. Moreover, while the membrane properties in the hydrocarbon region are only weakly affected by CLs, the changes at the membrane-water interface turn out to be prominent. The effects at the interface are most evident in membrane properties related to hydrogen bonding and the binding phenomena associated with electrostatic interactions.

The effect of fatty or lean fish intake on inflammatory gene expression in peripheral blood mononuclear cells of patients with coronary heart disease

Abstract: Background Little is known about the effect of fish consumption on gene expression of inflammation-related genes in immune cells in coronary heart disease (CHD).

Adaptation and failure of pancreatic beta cells in murine models with different degrees of metabolic syndrome.

Abstract: SUMMARY The events that contribute to the expansion of -cell mass and enhanced -cell function in insulin-resistant states have not been elucidated fully. Recently, we showed that -cell adaptation failed dramatically in adult, insulin-resistant POKO mice, which contrasts with the appropriate expansion of  cells in their ob/ob littermates. Thus, we hypothesised that characterisation of the islets in these mouse models at an early age should provide a unique opportunity to: (1) identify mechanisms involved in sensing insulin resistance at the level of the  cells, (2) identify molecular effectors that contribute to increasing -cell mass and function, and (3) distinguish primary events from secondary events that are more likely to be present at more advanced stages of diabetes. Our results define the POKO mouse as a model of early lipotoxicity. At 4 weeks of age, it manifests with inappropriate -cell function and defects in proliferation markers. Other well-recognised pathogenic effectors that were observed previously in 16-week-old mice, such as increased reactive oxygen species (ROS), macrophage infiltration and endoplasmic reticulum (ER) stress, are also present in both young POKO and young ob/ob mice, indicating the lack of predictive power with regards to the severity of -cell failure. Of interest, the relatively preserved lipidomic profile in islets from young POKO mice contrasted with the large changes in lipid composition and the differences in the chain length of triacylglycerols in the serum, liver, muscle and adipose tissue in adult POKO mice. Later lipotoxic insults in adult  cells contribute to the failure of the POKO  cell. Our results indicate that the rapid development of insulin resistance and -cell failure in POKO mice makes this model a useful tool to study early molecular events leading to insulin resistance and -cell failure. Furthermore, comparisons with ob/ob mice might reveal important adaptive mechanisms in  cells with either therapeutic or diagnostic potential.

Proteomic-Based Detection of a Protein Cluster Dysregulated during Cardiovascular Development Identifies Biomarkers of Congenital Heart Defects

Abstract: BACKGROUND: Cardiovascular development is vital for embryonic survival and growth. Early gestation embryo loss or malformation has been linked to yolk sac vasculopathy and congenital heart defects ...

Elevated pro-inflammatory and lipotoxic mucosal lipids characterise irritable bowel syndrome

Abstract: AIM: To investigate the pathophysiology of irritable bowel syndrome (IBS) by comparing the global mucosal metabolic profiles of IBS patients with those of healthy controls. METHODS: Fifteen IBS patients fulfilling the Rome II criteria, and nine healthy volunteers were included in the study. A combined lipidomics (UPLC/MS) and metabolomics (GC × GC-TOF) approach was used to achieve global metabolic profiles of mucosal biopsies from the ascending colon. RESULTS: Overall, lipid levels were elevated in patients with IBS. The most significant upregulation was seen for pro-inflammatory lysophosphatidylcholines. Other lipid groups that were significantly upregulated in IBS patients were lipotoxic ceramides, glycosphingolipids, and di- and triacylglycerols. Among the metabolites, the cyclic ester 2(3H)-furanone was almost 14-fold upregulated in IBS patients compared to healthy subjects (P = 0.03). CONCLUSION: IBS mucosa is characterised by a distinct pro-inflammatory and lipotoxic metabolic profile. Especially, there was an increase in several lipid species such as lysophospholipids and ceramides.

Two-way analysis of high-dimensional collinear data

Abstract: We present a Bayesian model for two-way ANOVA-type analysis of high-dimensional, small sample-size datasets with highly correlated groups of variables. Modern cellular measurement methods are a main application area; typically the task is differential analysis between diseased and healthy samples, complicated by additional covariates requiring a multi-way analysis. The main complication is the combination of high dimensionality and low sample size, which renders classical multivariate techniques useless. We introduce a hierarchical model which does dimensionality reduction by assuming that the input variables come in similarly-behaving groups, and performs an ANOVA-type decomposition for the set of reduced-dimensional latent variables. We apply the methods to study lipidomic profiles of a recent large-cohort human diabetes study.

Bioinformatics Strategies for the Analysis of Lipids

Abstract: Summary Owing to their importance in cellular physiology and pathology as well as to recent technological advances, the study of lipids has reemerged as a major research target. However, the structural diversity of lipids presents a number of analytical and informatics challenges. The field of lipidomics is a new postgenome discipline that aims to develop comprehensive methods for lipid analysis, necessitating concomitant developments in bioinformatics. The evolving research paradigm requires that new bioinformatics approaches accommodate genomic as well as high-level perspectives, integrating genome, protein, chemical and network information. The incorporation of lipidomics information into these data structures will provide mechanistic understanding of lipid functions and interactions in the context of cellular and organismal physiology. Accordingly, it is vital that specific bioinformatics methods be developed to analyze the wealth of lipid data being acquired. Herein, we present an overview of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and application of its tools to the analysis of lipid data. We also describe a series of software tools and databases (KGML-ED, VANTED, MZmine, and LipidDB) that can be used for the processing of lipidomics data and biochemical pathway reconstruction, an important next step in the development of the lipidomics field.

Integrating post-genomic approaches as a strategy to advance our understanding of health and disease.

Abstract: Following the publication of the complete human genomic sequence, the post-genomic era is driven by the need to extract useful information from genomic data. Genomics, transcriptomics, proteomics, metabolomics, epidemiological data and microbial data provide different angles to our understanding of gene-environment interactions and the determinants of disease and health. Our goal and our challenge are to integrate these very different types of data and perspectives of disease into a global model suitable for dissecting the mechanisms of disease and for predicting novel therapeutic strategies. This review aims to highlight the need for and problems with complex data integration, and proposes a framework for data integration. While there are many obstacles to overcome, biological models based upon multiple datasets will probably become the basis that drives future biomedical research.

Bioinformatics and computational approaches applicable to lipidomics

Abstract: Lipidomics owes its emergence to technologies developed over the past decade that empowered us with the ability to detect and quantify hundreds of intact lipid molecular species in parallel. One of the biggest current challenges of lipidomics is the elucidation of important pathobiological phenomena from the integration of large amounts of new data becoming available. In this respect, development of lipidomics as a field bears many similarities to the emergence and progress of genomics. Initial excitement over the ability to measure the expression of large numbers of genes in parallel was soon overshadowed by concerns over the ability to reliably analyze and interpret the expression data. This led to active research in the area of bioinformatics, which led to improved statistical methods as well as to new approaches for the analysis of transcriptome data in the pathway context. This review covers recent bioinformatics developments of relevance to analysis and interpretation of analytical lipidomics data, with the focus primarily on practical aspects of lipid bioinformatics.

Detection of Molecular Paths Associated with Insulitis and Type 1 Diabetes in Non-Obese Diabetic Mouse

Abstract: Recent clinical evidence suggests important role of lipid and amino acid metabolism in early pre-autoimmune stages of type 1 diabetes pathogenesis. We study the molecular paths associated with the incidence of insulitis and type 1 diabetes in the Non-Obese Diabetic (NOD) mouse model using available gene expression data from the pancreatic tissue from young pre-diabetic mice. We apply a graph-theoretic approach by using a modified color coding algorithm to detect optimal molecular paths associated with specific phenotypes in an integrated biological network encompassing heterogeneous interaction data types. In agreement with our recent clinical findings, we identified a path downregulated in early insulitis involving dihydroxyacetone phosphate acyltransferase (DHAPAT), a key regulator of ether phospholipid synthesis. The pathway involving serine/threonine-protein phosphatase (PP2A), an upstream regulator of lipid metabolism and insulin secretion, was found upregulated in early insulitis. Our findings provide further evidence for an important role of lipid metabolism in early stages of type 1 diabetes pathogenesis, as well as suggest that such dysregulation of lipids and related increased oxidative stress can be tracked to beta cells.

Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast

Abstract: In response to environmental challenges, biological systems respond with dynamic adaptive changes in order to maintain the functionality of the system. Such adaptations may lead to cumulative stress over time, possibly leading to global failure of the system. When studying such systems responses, it is therefore important to understand them in system-wide and dynamic context. Here we hypothesize that dynamic changes in the topology of functional modules of integrated biological networks reflect their activity under specific environmental challenges. We introduce topological enrichment analysis of functional subnetworks (TEAFS), a method for the analysis of integrated molecular profile and interactome data, which we validated by comprehensive metabolomic analysis of dynamic yeast response under oxidative stress. TEAFS identified activation of multiple stress response related mechanisms, such as lipid metabolism and phospholipid biosynthesis. We identified, among others, a fatty acid elongase IFA38 as a hub protein which was absent at all time points under oxidative stress conditions. The deletion mutant of the IFA38 encoding gene is known for the accumulation of ceramides. By applying a comprehensive metabolomic analysis, we confirmed the increased concentrations over time of ceramides and palmitic acid, a precursor of de novo ceramide biosynthesis. Our results imply that the connectivity of the system is being dynamically modulated in response to oxidative stress, progressively leading to the accumulation of (lipo)toxic lipids such as ceramides. Studies of local network topology dynamics can be used to investigate as well as predict the activity of biological processes and the system's responses to environmental challenges and interventions.

Two-way analysis of high-dimensional collinear data

Abstract: We present a Bayesian model for two-way ANOVA-type analysis of high-dimensional, small sample-size datasets with highly correlated groups of variables Modern cellular measurement methods are a main application area; typically the task is differential analysis between diseased and healthy samples, complicated by additional covariates requiring a multi-way analysis The main complication is the combination of high dimensionality and low sample size, which renders classical multivariate techniques useless We introduce a hierarchical model which does dimensionality reduction by assuming that the input variables come in similarly-behaving groups, and performs an ANOVA-type decomposition for the set of reduced-dimensional latent variables We apply the methods to study lipidomic profiles of a recent large-cohort human diabetes study

Multi-Way, Multi-View Learning

Abstract: We extend multi-way, multivariate ANOVA-type analysis to cases where one covariate is the view, with features of each view coming from different, high-dimensional domains. The different views are assumed to be connected by having paired samples; this is a common setup in recent bioinformatics experiments, of which we analyze metabolite profiles in different conditions (disease vs. control and treatment vs. untreated) in different tissues (views). We introduce a multi-way latent variable model for this new task, by extending the generative model of Bayesian canonical correlation analysis (CCA) both to take multi-way covariate information into account as population priors, and by reducing the dimensionality by an integrated factor analysis that assumes the metabolites to come in correlated groups.

Systems Biology Strategies in Studies of Energy Homeostasis In Vivo

Abstract: In this chapter the authors report on their experience with the analysis and modeling of data obtained from studies of animal models related to obesity and metabolic syndrome. The complex interactions of genetic and environmental factors contributing to the failure of energy balance that lead to obesity, as well as tight systemic regulation to maintain energy homeostasis, require application of the systems biology strategy at the physiological level. In vivo systems offer the possibility of investigating not only the effects of specific genetic modifications or treatments in selected tissues and organs, but also to elucidate compensatory allostatic mechanisms induced to maintain the homeostasis of the whole system. A key challenge for systems biology is to characterize different systems’ responses in the context of activated pathways. One possible strategy is based on reconstruction of tissue specific pathways using lipidomics, or metabolomics in general, in combination with proteomic and transcriptomic profiles. This approach was applied to obese mouse model and revealed activation of multiple liver pathways that may lead to metabolic products, which may impair insulin sensitivity.