Papers by Johan Westerhuis
Lc Gc North America, Jun 2, 2020
Food Quality and Preference
Clinical and Translational Medicine
BackgroundThe risk of esophageal adenocarcinoma (EAC) is associated with gastro‐esophageal reflux... more BackgroundThe risk of esophageal adenocarcinoma (EAC) is associated with gastro‐esophageal reflux disease (GERD) and obesity. Lipid metabolism‐targeted therapies decrease the risk of progressing from Barrett's esophagus (BE) to EAC, but the precise lipid metabolic changes and their roles in genotoxicity during EAC development are yet to be established.MethodsEsophageal biopsies from the normal epithelium (NE), BE, and EAC, were analyzed using concurrent lipidomics and proteomics (n = 30) followed by orthogonal validation on independent samples using RNAseq transcriptomics (n = 22) and immunohistochemistry (IHC, n = 80). The EAC cell line FLO‐1 was treated with FADS2 selective inhibitor SC26196, and/or bile acid cocktail, followed by immunofluorescence staining for γH2AX.ResultsMetabolism‐focused Reactome analysis of the proteomics data revealed enrichment of fatty acid metabolism, ketone body metabolism, and biosynthesis of specialized pro‐resolving mediators in EAC pathogenesis...
FEMS Microbiology Ecology, 2022
Strigolactones are endogenous plant hormones regulating plant development and are exuded into the... more Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish—through the exudation of strigolactones—mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that s...
Trends in Analytical Chemistry, 2001
Current Opinion in Biotechnology, 2021
The plant microbiome plays an essential role in supporting plant growth and health, but plant mol... more The plant microbiome plays an essential role in supporting plant growth and health, but plant molecular mechanisms underlying its recruitment are still unclear. Multi-omics data integration methods can be used to unravel new signalling relationships. Here, we review the effects of plant genetics and root exudates on root microbiome recruitment, and discuss methodological advances in data integration approaches that can help us to better understand and optimise the crop-microbiome interaction for a more sustainable agriculture.
European Journal of Nutrition, 2019
Purpose Coffee is widely consumed and implicated in numerous health outcomes but the mechanisms b... more Purpose Coffee is widely consumed and implicated in numerous health outcomes but the mechanisms by which coffee contributes to health is unclear. The purpose of this study was to test the effect of coffee drinking on candidate proteins involved in cardiovascular, immuno-oncological and neurological pathways. Methods We examined fasting serum samples collected from a previously reported single blinded, three-stage clinical trial. Forty-seven habitual coffee consumers refrained from drinking coffee for 1 month, consumed 4 cups of coffee/day in the second month and 8 cups/day in the third month. Samples collected after each coffee stage were analyzed using three multiplex proximity extension assays that, after quality control, measured a total of 247 proteins implicated in cardiovascular, immuno-oncological and neurological pathways and of which 59 were previously linked to coffee exposure. Repeated measures ANOVA was used to test the relationship between coffee treatment and each protein. Results Two neurology-related proteins including carboxypeptidase M (CPM) and neutral ceramidase (N-CDase or ASAH2), significantly increased after coffee intake (P < 0.05 and Q < 0.05). An additional 46 proteins were nominally associated with coffee intake (P < 0.05 and Q > 0.05); 9, 8 and 29 of these proteins related to cardiovascular, immuno-oncological and neurological pathways, respectively, and the levels of 41 increased with coffee intake. Conclusions CPM and N-CDase levels increased in response to coffee intake. These proteins have not previously been linked to coffee and are thus novel markers of coffee response worthy of further study. Clinical trial registry http://www.isrct n.com/ISRCT N1254 7806.
Journal of Internal Medicine, 2018
BackgroundCoffee is widely consumed and contains many bioactive compounds, any of which may impac... more BackgroundCoffee is widely consumed and contains many bioactive compounds, any of which may impact pathways related to disease development.ObjectiveTo identify individual metabolite changes in response to coffee.MethodsWe profiled the metabolome of fasting serum samples collected from a previously reported single‐blinded, three‐stage clinical trial. Forty‐seven habitual coffee consumers refrained from drinking coffee for 1 month, consumed four cups of coffee/day in the second month and eight cups/day in the third month. Samples collected after each coffee stage were subject to nontargeted metabolomic profiling using UPLC‐ESI‐MS/MS. A total of 733 metabolites were included for univariate and multivariate analyses.ResultsA total of 115 metabolites were significantly associated with coffee intake (P < 0.05 and Q < 0.05). Eighty‐two were of known identity and mapped to one of 33 predefined biological pathways. We observed a significant enrichment of metabolite members of five path...
Scientific Reports, 2018
Metabolomics studies of diseases associated with chronic alcohol consumption provide compelling e... more Metabolomics studies of diseases associated with chronic alcohol consumption provide compelling evidence of several perturbed metabolic pathways. Moreover, the holistic approach of such studies gives insights into the pathophysiological risk factors associated with chronic alcohol-induced disability, morbidity and mortality. Here, we report on a GC–MS-based organic acid profiling study on acute alcohol consumption. Our investigation — involving 12 healthy, moderate-drinking young men — simulated a single binge drinking event, and indicated its metabolic consequences. We generated time-dependent data that predicted the metabolic pathophysiology of the alcohol intervention. Multivariate statistical modelling was applied to the longitudinal data of 120 biologically relevant organic acids, of which 13 provided statistical evidence of the alcohol effect. The known alcohol-induced increased NADH:NAD+ ratio in the cytosol of hepatocytes contributed to the global dysregulation of several me...
Journal of Chemometrics, 2017
Multi-omics approaches use a diversity of high-throughput technologies to profile the different m... more Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multiomics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemen...
PloS one, 2016
Benzoic acid is widely used as a preservative in food products and is detoxified in humans throug... more Benzoic acid is widely used as a preservative in food products and is detoxified in humans through glycine conjugation. Different viewpoints prevail on the physiological significance of the glycine conjugation reaction and concerns have been raised on potential public health consequences following uncontrolled benzoic acid ingestion. We performed a metabolomics study which used commercial benzoic acid containing flavored water as vehicle for designed interventions, and report here on the controlled consumption of the benzoic acid by 21 cases across 6 time points for a total of 126 time points. Metabolomics data from urinary samples analyzed by nuclear magnetic resonance spectroscopy were generated in a time-dependent cross-over study. We used ANOVA-simultaneous component analysis (ASCA), repeated measures analysis of variance (RM-ANOVA) and unfolded principal component analysis (unfolded PCA) to supplement conventional statistical methods to uncover fully the metabolic perturbations...
<p>The shaded area around the white lines marks the 95% confidence interval of the mean, th... more <p>The shaded area around the white lines marks the 95% confidence interval of the mean, the thin lines show the individual results. The four metrics unanimously point to lag 1, but the different metrics center on different aspects of the relation between ACTH and cortisol.</p
Chemometrics and Intelligent Laboratory Systems, 2014
ABSTRACT Challenge tests are used to reveal the adaptability and resilience of humans to get insi... more ABSTRACT Challenge tests are used to reveal the adaptability and resilience of humans to get insight in their health. When contrasting challenge tests are used, various forms of adaptability can be tested and this gives a multidimensional view on the health of these individuals. Here we introduce methodology to describe the similarities and differences on how individuals are positioned in the health space based on the responses to different challenge tests. Results show that anabolic and catabolic challenges differentiate healthy subjects in rather different ways. Considering these results we hypothesize that combining challenge tests can improve the understanding of the underlying multidimensional phenotype.
Metabolomics, 2008
Metabolomics and other omics tools are generally characterized by large data sets with many varia... more Metabolomics and other omics tools are generally characterized by large data sets with many variables obtained under different environmental conditions. Clustering methods and more specifically two-mode clustering methods are excellent tools for analyzing this type of data. Two-mode clustering methods allow for analysis of the behavior of subsets of metabolites under different experimental conditions. In addition, the results are easily visualized. In this paper we introduce a two-mode clustering method based on a genetic algorithm that uses a criterion that searches for homogeneous clusters. Furthermore we introduce a cluster stability criterion to validate the clusters and we provide an extended knee plot to select the optimal number of clusters in both experimental and metabolite modes. The genetic algorithm-based two-mode clustering gave biological relevant results when it was applied to two real life metabolomics data sets. It was, for instance, able to identify a catabolic pathway for growth on several of the carbon sources.
Langmuir, 2005
Near-infrared (NIR) spectroscopy is used to monitor online a large variety of processes. Hydrocar... more Near-infrared (NIR) spectroscopy is used to monitor online a large variety of processes. Hydrocarbons with their strong NIR spectral signature are good candidate analytes. For this work, the sorption data are measured in a manometric setup coupled with online NIR spectroscopy, to monitor the bulk composition. The assessment of time based results faces a baseline stability problem. The goal of this article is to study the robustness of different spectral preprocessing methods when dealing with time based data. In this study, it was found that for time based experiments it is necessary to perform drift correction on the spectra combined with a water band correction. For the calibration experiments, which only last few seconds, offset correction and drift correction performed equally well.
Food Quality and Preference, 2003
Generalized Procrustes Analysis (GPA), SUM Principal Component Analysis (SUM-PCA) and Multi-block... more Generalized Procrustes Analysis (GPA), SUM Principal Component Analysis (SUM-PCA) and Multi-block Component Analysis (MBCA) were applied to a cross-continental flavor language study from industrial practice. One aspect that these explorative methods have in common is that data from different tables (blocks) are jointly decomposed into a low dimensional sub-representation by pursuing a consensus between the blocks. For GPA and SUM-PCA the blocks are considered to be of equal rank. However, the data from this flavor language study consisted of three blocks (panels) of different rank due to different profiling methods and different descriptive performances of the panels. It is demonstrated that, when adequately scaled, SUM-PCA and GPA yield similar results but fail to describe consensus in higher flavor dimensions when the blocks are of different rank. MBCA allows blocks of different rank and provides flexible means to study the data structures within and between the blocks.
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Papers by Johan Westerhuis