Genetic analysis in European ancestry individuals identifies 517 loci associated with liver enzymes

Plasma levels of liver enzymes provide insights into hepatic function and related diseases. Here, the authors perform a genome-wide association study on three liver enzymes, identifying genetic variants associated with their plasma concentration as well as links to metabolic and cardiovascular diseases. Serum concentration of hepatic enzymes are linked to liver dysfunction, metabolic and cardiovascular diseases. We perform genetic analysis on serum levels of alanine transaminase (ALT), alkaline phosphatase (ALP) and gamma-glutamyl transferase (GGT) using data on 437,438 UK Biobank participants. Replication in 315,572 individuals from European descent from the Million Veteran Program, Rotterdam Study and Lifeline study confirms 517 liver enzyme SNPs. Genetic risk score analysis using the identified SNPs is strongly associated with serum activity of liver enzymes in two independent European descent studies (The Airwave Health Monitoring study and the Northern Finland Birth Cohort 1966). Gene-set enrichment analysis using the identified SNPs highlights involvement in liver development and function, lipid metabolism, insulin resistance, and vascular formation. Mendelian randomization analysis shows association of liver enzyme variants with coronary heart disease and ischemic stroke. Genetic risk score for elevated serum activity of liver enzymes is associated with higher fat percentage of body, trunk, and liver and body mass index. Our study highlights the role of molecular pathways regulated by the liver in metabolic disorders and cardiovascular disease

Développement de nouvelles méthodes chimiométriques d'analyse - application à la caractérisation de la qualité des aliments

The compression properties of PCT allow one to perform or just accelerate the calculations of multivariate methods in the case of very wide matrices, where the number of variables is much greater than the number of objects. The results can be back-transformed into the original vectors base giving exactly the same results as those obtained when using the standard method, without transformation. The ANOVA-PCA method facilitates the comparison of variance attributed to the Factors responsible for the differences between samples and the residual variance. It was used to study, by means of near infrared spectroscopy, the stability of reference materials stored under different conditions. The method was modified to allow the prediction of new samples, as well as to improve its ability to find significant Factors and understand sources of variability. Using one of the main concepts of the ANOVA-PCA method, the calculation of factor levels, a method used for multi-table analysis - CCSWA - was modified for the analysis of the Factor level matrices resulting from an experimental design. Mid-infrared spectroscopy was used for the analysis of food samples with the help of the heated ATR accessory. It allowed the study of the modifications of different edible oils after accelerated heating at different temperatures and simultaneous acquisition of spectra. The same ATR apparatus was used in the analysis of wine to study the effects of different technological treatments, namely Micro-oxygenation and Oak addition. After the evaporation of the main constituents, water and ethanol, directly on the ATR crystal, the peaks corresponding to minor components could be uncovered.Les propriétés de compression de la transformation PCT permettent de réaliser et d'accélérer le calcul des méthodes multivariées même avec des matrices très larges où le nombre de variables est beaucoup plus grand que le nombre d'objets. Les résultats peuvent être retransformés vers le domaine des variables d'origine pour donner exactement les mêmes résultats qu'avec la méthode standard, sans transformation. Nous avons utilisé la PCT pour accélérer la régression PLS et dans le cadre de l'analyse du produit externe avec des très grandes matrices. La méthode ANOVA-PCA facilite la comparaison de la variance des Facteurs responsables des différences entre les échantillons avec la variance résiduelle. Elle a été utilisée pour étudier par spectroscopie d'infrarouge proche la stabilité des matériaux de référence stockés dans différentes conditions. Nous l'avons aussi modifiée de façon à permettre la prédiction de nouveaux échantillons et pour améliorer ses capacités de trouver des facteurs signifiants et pour mieux comprendre les différentes sources de variabilité résiduelle. En profitant d'une des idées de base de la méthode ANOVA-PCA, le calcul des niveaux, nous avons modifié une méthode d'analyse de tableaux multiples, la CCSWA, pour l'adapter à l'analyse des tableaux de niveaux de Facteurs provenant d'un plan d'expériences. La spectroscopie MIR a été utilisée pour l'analyse d'aliments à l'aide d'ATR chauffante. Nous avons étudié des altérations de différentes huiles alimentaires par chauffage accélérée à différentes températures avec acquisition simultanée des spectres. Le même accessoire a été utilisé dans l'analyse de vin pour étudier les effets de différents traitements technologiques, tels que la micro-oxygénation et l'ajout de copeaux de bois. Après évaporation, sur le crystal, de l'eau et de l'éthanol, les constituants majoritaires, des pics correspondants aux autres composantes du vin, normalement cachées, ont pu donc se révéler

Preliminary studies on the mid-infrared analysis of edible oils by direct heating on an ATR diamond crystal

In this work a new, easy and rapid MIR-ATR technique to monitor the thermal stability of oils is presented. The method uses a heated ATR apparatus set at selected temperatures to thermally modify the oils and simultaneously acquire spectra. Because of the larger sample surface to volume ratio, degradation reactions are faster compared to other heating methods. Three different edible oils (sunflower, olive and canola), are subjected to the method. Sunflower oil with or without tocopherol and at three different temperatures (130, 150 and 170 degrees C) was also analysed. Wavenumbers; known to be relevant to oil degradation processes are selected to show the modifications in the spectra over time

Evidence for involvement of the alcohol consumption WDPCP gene in lipid metabolism, and liver cirrhosis.

Acknowledgements: R.P. was supported by Rutherford Fund fellowship from the Medical Research Council (MR/R026505/1 and MR/R026505/2). B.A., X.J., and F.O. were supported by Rutherford Fund from Medical Research Council MR/R026505/2. R.M. was funded by the President’s PhD Scholarship from Imperial College London. PE is Director of the MRC Centre for Environment and Health and acknowledges support from the Medical Research Council (MR/S019669/1). PE also acknowledges support from the UK Dementia Research Institute, Imperial College London (UKDRI-5001), Health Data Research UK London (HDRUK-1004231) and the British Heart Foundation Imperial College London Centre for Research Excellence (BHF-RE/18/4/34215). The Airwave Health Monitoring Study was funded by the UK Home Office (780- TETRA, 2003-2018) and is currently funded by the MRC and ESRC (MR/R023484/1) with additional support from the NIHR Imperial College Biomedical Research Centre in collaboration with Imperial College NHS Healthcare Trust. R.C.P is supported by the UK Dementia Research Institute (UKDRI-5001), which receives its funding from UK DRI Ltd, funded by the UK Medical Research Council, Alzheimer’s Society and Alzheimer’s Research UK. Work in LMM’s laboratory is supported by the UK Medical Research Council, intramural project MC_UU_00025/3 (RG94521). The views expressed are those of the authors and not necessarily those of the sponsors. We thank Prof. Ulrike Heberlein, (Janelia Research Campus, Virginia, USA) for generously providing us the hppy17-51 fly lines. This research was funded, in whole or in part, by the Medical Research Council (MR/R026505/1 and MR/R026505/2). A CC BY or equivalent licence is applied to the Author Accepted Manuscript (AAM) arising from this submission, in accordance with the grant’s open access conditions.Biological pathways between alcohol consumption and alcohol liver disease (ALD) are not fully understood. We selected genes with known effect on (1) alcohol consumption, (2) liver function, and (3) gene expression. Expression of the orthologs of these genes in Caenorhabditis elegans and Drosophila melanogaster was suppressed using mutations and/or RNA interference (RNAi). In humans, association analysis, pathway analysis, and Mendelian randomization analysis were performed to identify metabolic changes due to alcohol consumption. In C. elegans, we found a reduction in locomotion rate after exposure to ethanol for RNAi knockdown of ACTR1B and MAPT. In Drosophila, we observed (1) a change in sedative effect of ethanol for RNAi knockdown of WDPCP, TENM2, GPN1, ARPC1B, and SCN8A, (2) a reduction in ethanol consumption for RNAi knockdown of TENM2, (3) a reduction in triradylglycerols (TAG) levels for RNAi knockdown of WDPCP, TENM2, and GPN1. In human, we observed (1) a link between alcohol consumption and several metabolites including TAG, (2) an enrichment of the candidate (alcohol-associated) metabolites within the linoleic acid (LNA) and alpha-linolenic acid (ALA) metabolism pathways, (3) a causal link between gene expression of WDPCP to liver fibrosis and liver cirrhosis. Our results imply that WDPCP might be involved in ALD

Finding Correspondence between Metabolomic Features in Untargeted Liquid Chromatography-Mass Spectrometry Metabolomics Datasets

Integration of multiple datasets can greatly enhance bioanalytical studies, for example, by increasing power to discover and validate biomarkers. In liquid chromatography-mass spectrometry (LC-MS) metabolomics, it is especially hard to combine untargeted datasets since the majority of metabolomic features are not annotated and thus cannot be matched by chemical identity. Typically, the information available for each feature is retention time (RT), mass-to-charge ratio (m/z), and feature intensity (FI). Pairs of features from the same metabolite in separate datasets can exhibit small but significant differences, making matching very challenging. Current methods to address this issue are too simple or rely on assumptions that cannot be met in all cases. We present a method to find feature correspondence between two similar LC-MS metabolomics experiments or batches using only the features' RT, m/z, and FI. We demonstrate the method on both real and synthetic datasets, using six orthogonal validation strategies to gauge the matching quality. In our main example, 4953 features were uniquely matched, of which 585 (96.8%) of 604 manually annotated features were correct. In a second example, 2324 features could be uniquely matched, with 79 (90.8%) out of 87 annotated features correctly matched. Most of the missed annotated matches are between features that behave very differently from modeled inter-dataset shifts of RT, MZ, and FI. In a third example with simulated data with 4755 features per dataset, 99.6% of the matches were correct. Finally, the results of matching three other dataset pairs using our method are compared with a published alternative method, metabCombiner, showing the advantages of our approach. The method can be applied using M2S (Match 2 Sets), a free, open-source MATLAB toolbox, available at https://github.com/rjdossan/M2S

Determinants of accelerated metabolomic and epigenetic aging in a UK cohort

Abstract Markers of biological aging have potential utility in primary care and public health. We developed a model of age based on untargeted metabolic profiling across multiple platforms, including nuclear magnetic resonance spectroscopy and liquid chromatography–mass spectrometry in urine and serum, within a large sample (N = 2,239) from the UK Airwave cohort. We validated a subset of model predictors in a Finnish cohort including repeat measurements from 2,144 individuals. We investigated the determinants of accelerated aging, including lifestyle and psychological risk factors for premature mortality. The metabolomic age model was well correlated with chronological age (mean r = 0.86 across independent test sets). Increased metabolomic age acceleration (mAA) was associated after false discovery rate (FDR) correction with overweight/obesity, diabetes, heavy alcohol use and depression. DNA methylation age acceleration measures were uncorrelated with mAA. Increased DNA methylation phenotypic age acceleration (N = 1,110) was associated after FDR correction with heavy alcohol use, hypertension and low income. In conclusion, metabolomics is a promising approach for the assessment of biological age and appears complementary to established epigenetic clocks

Metabolome-wide association study on ABCA7 indicates a role of ceramide metabolism in Alzheimer's disease

Genome-wide association studies (GWASs) have identified genetic loci associated with the risk of Alzheimer's disease (AD), but the molecular mechanisms by which they confer risk are largely unknown. We conducted a metabolome-wide association study (MWAS) of AD-associated loci from GWASs using untargeted metabolic profiling (metabolomics) by ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). We identified an association of lactosylceramides (LacCer) with AD-related single-nucleotide polymorphisms (SNPs) in ABCA7 (P = 5.0 × 10-5 to 1.3 × 10-44). We showed that plasma LacCer concentrations are associated with cognitive performance and genetically modified levels of LacCer are associated with AD risk. We then showed that concentrations of sphingomyelins, ceramides, and hexosylceramides were altered in brain tissue from Abca7 knockout mice, compared with wild type (WT) (P = 0.049-1.4 × 10-5), but not in a mouse model of amyloidosis. Furthermore, activation of microglia increases intracellular concentrations of hexosylceramides in part through induction in the expression of sphingosine kinase, an enzyme with a high control coefficient for sphingolipid and ceramide synthesis. Our work suggests that the risk for AD arising from functional variations in ABCA7 is mediated at least in part through ceramides. Modulation of their metabolism or downstream signaling may offer new therapeutic opportunities for AD