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Di X, Martinez-Tellez B, Krekels EHJ, Jurado-Fasoli L, Osuna-Prieto FJ, Ortiz-Alvarez L, Hankemeier T, Rensen PCN, Ruiz JR, Kohler I. Higher Plasma Levels of Endocannabinoids and Analogues Correlate With a Worse Cardiometabolic Profile in Young Adults. J Clin Endocrinol Metab 2024; 109:1351-1360. [PMID: 37967236 PMCID: PMC11031222 DOI: 10.1210/clinem/dgad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023]
Abstract
CONTEXT The endocannabinoid system (ECS) is a signaling system composed of endocannabinoids (eCBs), their receptors, and the enzymes involved in their synthesis and metabolism. Alterations in the ECS are linked to the development of cardiometabolic diseases. OBJECTIVE Here, we investigated the relationship between plasma levels of eCBs and their analogues with body composition and cardiometabolic risk factors. METHODS The study included 133 young adults (age 22.1 ± 2.2 years, 67% women). Fasting plasma levels of eCBs and their analogues were measured using liquid chromatography-tandem mass spectrometry. Body composition, brown adipose tissue (BAT) volume, glucose uptake, and traditional cardiometabolic risk factors were measured. RESULTS Plasma levels of eCBs and several eCB analogues were positively correlated with adiposity and traditional cardiometabolic risk factors (eg, serum insulin and triacylglyceride levels, all r ≥ 0.17 and P ≤ .045). Plasma levels of 2-arachidonoyl glycerol and N-pentadecenoylethanolamine were negatively correlated with BAT volume and glucose uptake (all r ≤ -0.17 and P ≤ .047). We observed that the plasma levels of eCBs and their analogues were higher in metabolically unhealthy overweight-obese participants than in metabolically healthy overweight-obese participants. CONCLUSION Our findings show that the plasma levels of eCBs and their analogues are related to higher levels of adiposity and worse cardiometabolic profile.
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Affiliation(s)
- Xinyu Di
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Borja Martinez-Tellez
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), Department of Physical Education and Sports, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- SPORT Research Group, CERNEP Research Center, University of Almería, 04120 Almería, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 18100 Granada, Spain
| | - Elke H J Krekels
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Lucas Jurado-Fasoli
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), Department of Physical Education and Sports, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, 18012 Granada, Spain
| | - Francisco J Osuna-Prieto
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), Department of Physical Education and Sports, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, 18012 Granada, Spain
| | - Lourdes Ortiz-Alvarez
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), Department of Physical Education and Sports, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, 18012 Granada, Spain
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jonatan R Ruiz
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH), Sport and Health University Research Institute (iMUDS), Department of Physical Education and Sports, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 18100 Granada, Spain
- Instituto de Investigación Biosanitaria, ibs.Granada, 18012 Granada, Spain
| | - Isabelle Kohler
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Center for Analytical Sciences Amsterdam, 1081 HZ Amsterdam, The Netherlands
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Yang W, Schoeman JC, Di X, Lamont L, Harms AC, Hankemeier T. A comprehensive UHPLC-MS/MS method for metabolomics profiling of signaling lipids: Markers of oxidative stress, immunity and inflammation. Anal Chim Acta 2024; 1297:342348. [PMID: 38438234 DOI: 10.1016/j.aca.2024.342348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 03/06/2024]
Abstract
Signaling lipids (SLs) play a crucial role in various signaling pathways, featuring diverse lipid backbone structures. Emerging evidence showing the biological significance and biomedical values of SLs has strongly spurred the advancement of analytical approaches aimed at profiling SLs. Nevertheless, the dramatic differences in endogenous abundances across lipid classes as well as multiple isomers within the same lipid class makes the development of a generic analytical method challenging. A better analytical method that combines comprehensive coverage and high sensitivity is needed to enable us to gain a deeper understanding of the biochemistry of these molecules in health and disease. In this study, we developed a fast and comprehensive targeted ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for profiling SLs. The platform enables analyses of 260 metabolites covering oxylipins (isoprostanes, prostaglandins and other oxidized lipids), free fatty acids, lysophospholipids, sphingoid bases (C16, C18), platelet activating factors (C16, C18), endocannabinoids and bile acids. Various validation parameters including linearity, limit of detection, limit of quantification, extraction recovery, matrix effect, intra-day and inter-day precision were used to characterize this method. Metabolite quantitation was successfully achieved in both NIST Standard Reference Material for human plasma (NIST SRM 1950) and pooled human plasma, with 109 and 144 metabolites quantitated. The quantitation results in NIST SRM 1950 plasma demonstrated good correlations with certified or previously reported values in published literature. This study introduced quantitative data for 37 SLs for the first time. Metabolite concentrations measured in NIST SRM 1950 will serve as essential reference data for facilitating interlaboratory comparisons. The methodology established here will be the cornerstone for in-depth profiling of signaling lipids across diverse biological samples and contexts.
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Affiliation(s)
- Wei Yang
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC, Leiden, the Netherlands
| | - Johannes C Schoeman
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC, Leiden, the Netherlands
| | - Xinyu Di
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2333 CC, Leiden, the Netherlands
| | - Lieke Lamont
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC, Leiden, the Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC, Leiden, the Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, 2333 CC, Leiden, the Netherlands.
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Nuñez Santiago I, Machushynets NV, Mladic M, van Bergeijk DA, Elsayed SS, Hankemeier T, van Wezel GP. nanoRAPIDS as an analytical pipeline for the discovery of novel bioactive metabolites in complex culture extracts at the nanoscale. Commun Chem 2024; 7:71. [PMID: 38561415 PMCID: PMC10984978 DOI: 10.1038/s42004-024-01153-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Microbial natural products form the basis of most of the antibiotics used in the clinic. The vast majority has not yet been discovered, among others because the hidden chemical space is obscured by previously identified (and typically abundant) antibiotics in culture extracts. Efficient dereplication is therefore key to the discovery of our future medicines. Here we present an analytical platform for the efficient identification and prioritization of low abundance bioactive compounds at nanoliter scale, called nanoRAPIDS. NanoRAPIDS encompasses analytical scale separation and nanofractionation of natural extracts, followed by the bioassay of interest, automated mass spectrometry identification, and Global Natural Products Social molecular networking (GNPS) for dereplication. As little as 10 μL crude extract is fractionated into 384 fractions. First, bioactive congeners of iturins and surfactins were identified in Bacillus, based on their bioactivity. Subsequently, bioactive molecules were identified in an extensive network of angucyclines elicited by catechol in cultures of Streptomyces sp. This allowed the discovery of a highly unusual N-acetylcysteine conjugate of saquayamycin, despite low production levels in an otherwise abundant molecular family. These data underline the utility and broad application of the technology for the prioritization of minor bioactive compounds in complex extracts.
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Affiliation(s)
- Isabel Nuñez Santiago
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Marija Mladic
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- DSM-Firmenich, Delft, The Netherlands
| | - Doris A van Bergeijk
- Department of Microbiology, KU Leuven, Immunology and Transplantation (Laboratory of Molecular Bacteriology), Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
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Bonanini F, Singh M, Yang H, Kurek D, Harms AC, Mardinoglu A, Hankemeier T. A comparison between different human hepatocyte models reveals profound differences in net glucose production, lipid composition and metabolism in vitro. Exp Cell Res 2024; 437:114008. [PMID: 38499143 DOI: 10.1016/j.yexcr.2024.114008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Hepatocytes are responsible for maintaining a stable blood glucose concentration during periods of nutrient scarcity. The breakdown of glycogen and de novo synthesis of glucose are crucial metabolic pathways deeply interlinked with lipid metabolism. Alterations in these pathways are often associated with metabolic diseases with serious clinical implications. Studying energy metabolism in human cells is challenging. Primary hepatocytes are still considered the golden standard for in vitro studies and have been instrumental in elucidating key aspects of energy metabolism found in vivo. As a result of several limitations posed by using primary cells, a multitude of alternative hepatocyte cellular models emerged as potential substitutes. Yet, there remains a lack of clarity regarding the precise applications for which these models accurately reflect the metabolic competence of primary hepatocytes. In this study, we compared primary hepatocytes, stem cell-derived hepatocytes, adult donor-derived liver organoids, immortalized Upcyte-hepatocytes and the hepatoma cell line HepG2s in their response to a glucose production challenge. We observed the highest net glucose production in primary hepatocytes, followed by organoids, stem-cell derived hepatocytes, Upcyte-hepatocytes and HepG2s. Glucogenic gene induction was observed in all tested models, as indicated by an increase in G6PC and PCK1 expression. Lipidomic analysis revealed considerable differences across the models, with organoids showing the closest similarity to primary hepatocytes in the common lipidome, comprising 347 lipid species across 19 classes. Changes in lipid profiles as a result of the glucose production challenge showed a variety of, and in some cases opposite, trends when compared to primary hepatocytes.
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Affiliation(s)
| | - Madhulika Singh
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Netherlands
| | - Hong Yang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Amy C Harms
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Netherlands
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Netherlands.
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van Mever M, He B, van Veen M, Slaats J, Buijs MM, Wieringa JE, Hankemeier T, de Winter P, Ramautar R. Capillary electrophoresis-mass spectrometry for creatinine analysis in residual clinical plasma samples and comparison with gold standard assay. Electrophoresis 2024. [PMID: 38456383 DOI: 10.1002/elps.202300264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024]
Abstract
When hospitalized, infants, particularly preterm, are often subjected to multiple painful needle procedures to collect sufficient blood for metabolic screening or diagnostic purposes using standard clinical tests. For example, at least 100 µL of whole blood is required to perform one creatinine plasma measurement with enzymatic colorimetric assays. As capillary electrophoresis-mass spectrometry (CE-MS) utilizing a sheathless porous tip interface only requires limited amounts of sample for in-depth metabolic profiling studies, the aim of this work was to assess the utility of this method for the determination of creatinine in low amounts of plasma using residual blood samples from adults and infants. By using a starting amount of 5 µL of plasma and an injection volume of only 6.7 nL, a detection limit (S/N = 3) of 30 nM could be obtained for creatinine, and intra- and interday precisions (for peak area ratios) were below 3.2%. To shorten the electrophoretic separation time, a multi-segment injection (MSI) strategy was employed to analyze up to seven samples in one electrophoretic run. The findings obtained by CE-MS for creatinine in pretreated plasma were compared with the values acquired by an enzymatic colorimetric assay typically used in clinical laboratories for this purpose. The comparison revealed that CE-MS could be used in a reliable way for the determination of creatinine in residual plasma samples from infants and adults. Nevertheless, to underscore the clinical efficacy of this method, a subsequent investigation employing an expanded pool of plasma samples is imperative. This will not only enhance the method's diagnostic utility but also contribute to minimizing both the amount and frequency of blood collection required for diagnostic purposes.
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Affiliation(s)
- Marlien van Mever
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Bingshu He
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Mariam van Veen
- Department of Pediatrics, Spaarne Gasthuis, Haarlem/Hoofddorp, The Netherlands
- Amsterdam Universitair Medisch Centrum, Amsterdam, The Netherlands
| | - Jeroen Slaats
- Atalmedial Diagnostic Centers, Amsterdam, The Netherlands
| | | | - Joanne E Wieringa
- Department of Pediatrics, Spaarne Gasthuis, Haarlem/Hoofddorp, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Peter de Winter
- Department of Pediatrics, Spaarne Gasthuis, Haarlem/Hoofddorp, The Netherlands
- Leuven Child and Health Institute, KU Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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6
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Zhu P, Dubbelman AC, Hunter C, Genangeli M, Karu N, Harms A, Hankemeier T. Development of an Untargeted LC-MS Metabolomics Method with Postcolumn Infusion for Matrix Effect Monitoring in Plasma and Feces. J Am Soc Mass Spectrom 2024; 35:590-602. [PMID: 38379502 PMCID: PMC10921459 DOI: 10.1021/jasms.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Untargeted metabolomics based on reverse phase LC-MS (RPLC-MS) plays a crucial role in biomarker discovery across physiological and disease states. Standardizing the development process of untargeted methods requires paying attention to critical factors that are under discussed or easily overlooked, such as injection parameters, performance assessment, and matrix effect evaluation. In this study, we developed an untargeted metabolomics method for plasma and fecal samples with the optimization and evaluation of these factors. Our results showed that optimizing the reconstitution solvent and sample injection amount was critical for achieving the balance between metabolites coverage and signal linearity. Method validation with representative stable isotopically labeled standards (SILs) provided insights into the analytical performance evaluation of our method. To tackle the issue of the matrix effect, we implemented a postcolumn infusion (PCI) approach to monitor the overall absolute matrix effect (AME) and relative matrix effect (RME). The monitoring revealed distinct AME and RME profiles in plasma and feces. Comparing RME data obtained for SILs through postextraction spiking with those monitored using PCI compounds demonstrated the comparability of these two methods for RME assessment. Therefore, we applied the PCI approach to predict the RME of 305 target compounds covered in our in-house library and found that targets detected in the negative polarity were more vulnerable to the RME, regardless of the sample matrix. Given the value of this PCI approach in identifying the strengths and weaknesses of our method in terms of the matrix effect, we recommend implementing a PCI approach during method development and applying it routinely in untargeted metabolomics.
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Affiliation(s)
- Pingping Zhu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Anne-Charlotte Dubbelman
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | | | - Michele Genangeli
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Naama Karu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
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den Hartog I, Zwep LB, Meulman JJ, Hankemeier T, van de Garde EMW, van Hasselt JGC. Longitudinal metabolite profiling of Streptococcus pneumoniae-associated community-acquired pneumonia. Metabolomics 2024; 20:35. [PMID: 38441696 PMCID: PMC10914916 DOI: 10.1007/s11306-024-02091-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/17/2024] [Indexed: 03/07/2024]
Abstract
INTRODUCTION Longitudinal biomarkers in patients with community-acquired pneumonia (CAP) may help in monitoring of disease progression and treatment response. The metabolic host response could be a potential source of such biomarkers since it closely associates with the current health status of the patient. OBJECTIVES In this study we performed longitudinal metabolite profiling in patients with CAP for a comprehensive range of metabolites to identify potential host response biomarkers. METHODS Previously collected serum samples from CAP patients with confirmed Streptococcus pneumoniae infection (n = 25) were used. Samples were collected at multiple time points, up to 30 days after admission. A wide range of metabolites was measured, including amines, acylcarnitines, organic acids, and lipids. The associations between metabolites and C-reactive protein (CRP), procalcitonin, CURB disease severity score at admission, and total length of stay were evaluated. RESULTS Distinct longitudinal profiles of metabolite profiles were identified, including cholesteryl esters, diacyl-phosphatidylethanolamine, diacylglycerols, lysophosphatidylcholines, sphingomyelin, and triglycerides. Positive correlations were found between CRP and phosphatidylcholine (34:1) (cor = 0.63) and negative correlations were found for CRP and nine lysophosphocholines (cor = - 0.57 to - 0.74). The CURB disease severity score was negatively associated with six metabolites, including acylcarnitines (tau = - 0.64 to - 0.58). Negative correlations were found between the length of stay and six triglycerides (TGs), especially TGs (60:3) and (58:2) (cor = - 0.63 and - 0.61). CONCLUSION The identified metabolites may provide insight into biological mechanisms underlying disease severity and may be of interest for exploration as potential treatment response monitoring biomarker.
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Affiliation(s)
- Ilona den Hartog
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Laura B Zwep
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jacqueline J Meulman
- LUXs Data Science, Leiden, The Netherlands
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Thomas Hankemeier
- Metabolomics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Ewoudt M W van de Garde
- Division of Pharmacoepidemiology and Clinical Pharmacology, Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Department of Clinical Pharmacy, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - J G Coen van Hasselt
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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Hubers N, Hagenbeek FA, Pool R, Déjean S, Harms AC, Roetman PJ, van Beijsterveldt CEM, Fanos V, Ehli EA, Vermeiren RRJM, Bartels M, Hottenga JJ, Hankemeier T, van Dongen J, Boomsma DI. Integrative multi-omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention-Deficit/Hyperactivity Disorder. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32955. [PMID: 37534875 DOI: 10.1002/ajmg.b.32955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The evolving field of multi-omics combines data and provides methods for simultaneous analysis across several omics levels. Here, we integrated genomics (transmitted and non-transmitted polygenic scores [PGSs]), epigenomics, and metabolomics data in a multi-omics framework to identify biomarkers for Attention-Deficit/Hyperactivity Disorder (ADHD) and investigated the connections among the three omics levels. We first trained single- and next multi-omics models to differentiate between cases and controls in 596 twins (cases = 14.8%) from the Netherlands Twin Register (NTR) demonstrating reasonable in-sample prediction through cross-validation. The multi-omics model selected 30 PGSs, 143 CpGs, and 90 metabolites. We confirmed previous associations of ADHD with glucocorticoid exposure and the transmembrane protein family TMEM, show that the DNA methylation of the MAD1L1 gene associated with ADHD has a relation with parental smoking behavior, and present novel findings including associations between indirect genetic effects and CpGs of the STAP2 gene. However, out-of-sample prediction in NTR participants (N = 258, cases = 14.3%) and in a clinical sample (N = 145, cases = 51%) did not perform well (range misclassification was [0.40, 0.57]). The results highlighted connections between omics levels, with the strongest connections between non-transmitted PGSs, CpGs, and amino acid levels and show that multi-omics designs considering interrelated omics levels can help unravel the complex biology underlying ADHD.
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Affiliation(s)
- Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219, University of Toulouse, CNRS, Toulouse, France
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Peter J Roetman
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, USA
| | - Robert R J M Vermeiren
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
- Youz, Parnassia Group, the Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
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van Mever M, Mamani-Huanca M, Faught E, López-Gonzálvez Á, Hankemeier T, Barbas C, Schaaf MJM, Ramautar R. Application of a capillary electrophoresis-mass spectrometry metabolomics workflow in zebrafish larvae reveals new effects of cortisol. Electrophoresis 2024; 45:380-391. [PMID: 38072651 DOI: 10.1002/elps.202300186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 03/20/2024]
Abstract
In contemporary biomedical research, the zebrafish (Danio rerio) is increasingly considered a model system, as zebrafish embryos and larvae can (potentially) fill the gap between cultured cells and mammalian animal models, because they can be obtained in large numbers, are small and can easily be manipulated genetically. Given that capillary electrophoresis-mass spectrometry (CE-MS) is a useful analytical separation technique for the analysis of polar ionogenic metabolites in biomass-limited samples, the aim of this study was to develop and assess a CE-MS-based analytical workflow for the profiling of (endogenous) metabolites in extracts from individual zebrafish larvae and pools of small numbers of larvae. The developed CE-MS workflow was used to profile metabolites in extracts from pools of 1, 2, 4, 8, 12, 16, 20, and 40 zebrafish larvae. For six selected endogenous metabolites, a linear response (R2 > 0.98) for peak areas was obtained in extracts from these pools. The repeatability was satisfactory, with inter-day relative standard deviation values for peak area of 9.4%-17.7% for biological replicates (n = 3 over 3 days). Furthermore, the method allowed the analysis of over 70 endogenous metabolites in a pool of 12 zebrafish larvae, and 29 endogenous metabolites in an extract from only 1 zebrafish larva. Finally, we applied the optimized CE-MS workflow to identify potential novel targets of the mineralocorticoid receptor in mediating the effects of cortisol.
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Affiliation(s)
- Marlien van Mever
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Maricruz Mamani-Huanca
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Erin Faught
- Institute of Biology Leiden (IBL), Leiden University, Leiden, The Netherlands
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Marcel J M Schaaf
- Institute of Biology Leiden (IBL), Leiden University, Leiden, The Netherlands
| | - Rawi Ramautar
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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10
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Jurado-Fasoli L, Sanchez-Delgado G, Di X, Yang W, Kohler I, Villarroya F, Aguilera CM, Hankemeier T, Ruiz JR, Martinez-Tellez B. Cold-induced changes in plasma signaling lipids are associated with a healthier cardiometabolic profile independently of brown adipose tissue. Cell Rep Med 2024; 5:101387. [PMID: 38262411 PMCID: PMC10897514 DOI: 10.1016/j.xcrm.2023.101387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/27/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024]
Abstract
Cold exposure activates brown adipose tissue (BAT) and potentially improves cardiometabolic health through the secretion of signaling lipids by BAT. Here, we show that 2 h of cold exposure in young adults increases the levels of omega-6 and omega-3 oxylipins, the endocannabinoids (eCBs) anandamide and docosahexaenoylethanolamine, and lysophospholipids containing polyunsaturated fatty acids. Contrarily, it decreases the levels of the eCBs 1-LG and 2-LG and 1-OG and 2-OG, lysophosphatidic acids, and lysophosphatidylethanolamines. Participants overweight or obese show smaller increases in omega-6 and omega-3 oxylipins levels compared to normal weight. We observe that only a small proportion (∼4% on average) of the cold-induced changes in the plasma signaling lipids are slightly correlated with BAT volume. However, cold-induced changes in omega-6 and omega-3 oxylipins are negatively correlated with adiposity, glucose homeostasis, lipid profile, and liver parameters. Lastly, a 24-week exercise-based randomized controlled trial does not modify plasma signaling lipid response to cold exposure.
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Affiliation(s)
- Lucas Jurado-Fasoli
- Department of Physical Education and Sports, Faculty of Sports Science, Sport and Health University Research Institute (iMUDS), University of Granada, Carretera de Alfacar s/n, 18071 Granada, Spain; Department of Physiology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Guillermo Sanchez-Delgado
- Department of Physical Education and Sports, Faculty of Sports Science, Sport and Health University Research Institute (iMUDS), University of Granada, Carretera de Alfacar s/n, 18071 Granada, Spain; Department of Medicine, Division of Endocrinology, Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC, Canada; CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigación Biosanitaria, Ibs.Granada, Granada, Spain
| | - Xinyu Di
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Wei Yang
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Isabelle Kohler
- Vrije Universiteit Amsterdam, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of BioAnalytical Chemistry, Amsterdam, the Netherlands; Center for Analytical Sciences Amsterdam, Amsterdam, the Netherlands
| | - Francesc Villarroya
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine of the University of Barcelona, Barcelona, Spain
| | - Concepcion M Aguilera
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigación Biosanitaria, Ibs.Granada, Granada, Spain; Department of Biochemistry and Molecular Biology II, "José Mataix Verdú" Institute of Nutrition and Food Technology (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18016 Granada, Spain
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Jonatan R Ruiz
- Department of Physical Education and Sports, Faculty of Sports Science, Sport and Health University Research Institute (iMUDS), University of Granada, Carretera de Alfacar s/n, 18071 Granada, Spain; CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigación Biosanitaria, Ibs.Granada, Granada, Spain.
| | - Borja Martinez-Tellez
- Department of Physical Education and Sports, Faculty of Sports Science, Sport and Health University Research Institute (iMUDS), University of Granada, Carretera de Alfacar s/n, 18071 Granada, Spain; CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Department of Education, Faculty of Education Sciences and SPORT Research Group (CTS-1024), CERNEP Research Center, University of Almería, Almería, Spain.
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11
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Vanmaele A, Bouwens E, Hoeks SE, Kindt A, Lamont L, Fioole B, Moelker A, Ten Raa S, Hussain B, Oliveira-Pinto J, Ijpma AS, van Lier F, Akkerhuis KM, Majoor-Krakauer DF, Hankemeier T, de Rijke Y, Verhagen HJ, Boersma E, Kardys I. Targeted proteomics and metabolomics for biomarker discovery in abdominal aortic aneurysm and post-EVAR sac volume. Clin Chim Acta 2024; 554:117786. [PMID: 38246209 DOI: 10.1016/j.cca.2024.117786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
BACKGROUND AND AIMS Abdominal aortic aneurysm (AAA) patients undergo uniform surveillance programs both leading up to, and following surgery. Circulating biomarkers could play a pivotal role in individualizing surveillance. We applied a multi-omics approach to identify relevant biomarkers and gain pathophysiological insights. MATERIALS AND METHODS In this cross-sectional study, 108 AAA patients and 200 post-endovascular aneurysm repair (post-EVAR) patients were separately investigated. We performed partial least squares regression and ingenuity pathway analysis on circulating concentrations of 96 proteins (92 Olink Cardiovascular-III panel, 4 ELISA-assays) and 199 metabolites (measured by LC-TQMS), and their associations with CT-based AAA/sac volume. RESULTS The median (25th-75th percentile) maximal diameter was 50.0 mm (46.0, 53.0) in the AAA group, and 55.4 mm (45.0, 64.2) in the post-EVAR group. Correcting for clinical characteristics in AAA patients, the aneurysm volume Z-score differed 0.068 (95 %CI: (0.042, 0.093)), 0.066 (0.047, 0.085) and -0.051 (-0.064, -0.038) per Z-score valine, leucine and uPA, respectively. After correcting for clinical characteristics and orthogonalization in the post-EVAR group, the sac volume Z-score differed 0.049 (0.034, 0.063) per Z-score TIMP-4, -0.050 (-0.064, -0.037) per Z-score LDL-receptor, -0.051 (-0.062, -0.040) per Z-score 1-OG/2-OG and -0.056 (-0.066, -0.045) per Z-score 1-LG/2-LG. CONCLUSIONS The branched-chain amino acids and uPA were related to AAA volume. For post-EVAR patients, LDL-receptor, monoacylglycerols and TIMP-4 are potential biomarkers for sac volume. Additionally, distinct markers for sac change were identified.
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Affiliation(s)
- Alexander Vanmaele
- Department of Cardiology, Thorax Centre, Cardiovascular Institute, Erasmus MC, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus MC, Rotterdam, the Netherlands
| | - Elke Bouwens
- Department of Cardiology, Thorax Centre, Cardiovascular Institute, Erasmus MC, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus MC, Rotterdam, the Netherlands; Department of Anesthesiology, Erasmus MC, Rotterdam, the Netherlands
| | - Sanne E Hoeks
- Department of Anesthesiology, Erasmus MC, Rotterdam, the Netherlands
| | - Alida Kindt
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Lieke Lamont
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Bram Fioole
- Department of Vascular Surgery, Maasstad Hospital, Rotterdam, the Netherlands
| | - Adriaan Moelker
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Sander Ten Raa
- Department of Vascular Surgery, Erasmus MC, Rotterdam, the Netherlands
| | - Burhan Hussain
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands; Department of Radiology, Beatrix hospital, Gorinchem, the Netherlands
| | - José Oliveira-Pinto
- Department of Vascular Surgery, Erasmus MC, Rotterdam, the Netherlands; Department of Angiology and Vascular Surgery, Centro Hospitalar São João, Porto, Portugal; Department of Surgery and Physiology, Faculty of Medicine of Oporto, Porto, Portugal
| | - Arne S Ijpma
- Department of Pathology, Erasmus MC, Rotterdam, the Netherlands
| | - Felix van Lier
- Department of Anesthesiology, Erasmus MC, Rotterdam, the Netherlands
| | - K Martijn Akkerhuis
- Department of Cardiology, Thorax Centre, Cardiovascular Institute, Erasmus MC, Rotterdam, the Netherlands
| | | | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Yolanda de Rijke
- Department of Clinical Chemistry, Erasmus MC, Rotterdam, the Netherlands
| | - Hence Jm Verhagen
- Department of Vascular Surgery, Erasmus MC, Rotterdam, the Netherlands
| | - Eric Boersma
- Department of Cardiology, Thorax Centre, Cardiovascular Institute, Erasmus MC, Rotterdam, the Netherlands
| | - Isabella Kardys
- Department of Cardiology, Thorax Centre, Cardiovascular Institute, Erasmus MC, Rotterdam, the Netherlands.
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12
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Singh M, Kiyuna LA, Odendaal C, Bakker BM, Harms AC, Hankemeier T. Development of targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry method for acyl-Coenzyme A covering short- to long-chain species in a single analytical run. J Chromatogr A 2024; 1714:464524. [PMID: 38056390 DOI: 10.1016/j.chroma.2023.464524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/08/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Acyl-CoAs play a significant role in numerous physiological and metabolic processes making it important to assess their concentration levels for evaluating metabolic health. Considering the important role of acyl-CoAs, it is crucial to develop an analytical method that can analyze these compounds. Due to the structural variations of acyl-CoAs, multiple analytical methods are often required for comprehensive analysis of these compounds, which increases complexity and the analysis time. In this study, we have developed a method using a zwitterionic HILIC column that enables the coverage of free CoA and short- to long-chain acyl-CoA species in one analytical run. Initially, we developed the method using an LC-QTOF instrument for the identification of acyl-CoA species and optimizing their chromatography. Later, a targeted HILIC-MS/MS method was created in scheduled multiple reaction monitoring mode using a QTRAP MS detector. The performance of the method was evaluated based on various parameters such as linearity, precision, recovery and matrix effect. This method was applied to identify the difference in acyl-CoA profiles in HepG2 cells cultured in different conditions. Our findings revealed an increase in levels of acetyl-CoA, medium- and long-chain acyl-CoA while a decrease in the profiles of free CoA in the starved state, indicating a clear alteration in the fatty acid oxidation process.
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Affiliation(s)
- Madhulika Singh
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Ligia Akemi Kiyuna
- Laboratory of Paediatrics, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - Christoff Odendaal
- Laboratory of Paediatrics, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - Barbara M Bakker
- Laboratory of Paediatrics, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands.
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13
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Jiang M, Huizenga MCW, Wirt JL, Paloczi J, Amedi A, van den Berg RJBHN, Benz J, Collin L, Deng H, Di X, Driever WF, Florea BI, Grether U, Janssen APA, Hankemeier T, Heitman LH, Lam TW, Mohr F, Pavlovic A, Ruf I, van den Hurk H, Stevens AF, van der Vliet D, van der Wel T, Wittwer MB, van Boeckel CAA, Pacher P, Hohmann AG, van der Stelt M. A monoacylglycerol lipase inhibitor showing therapeutic efficacy in mice without central side effects or dependence. Nat Commun 2023; 14:8039. [PMID: 38052772 PMCID: PMC10698032 DOI: 10.1038/s41467-023-43606-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Monoacylglycerol lipase (MAGL) regulates endocannabinoid 2-arachidonoylglycerol (2-AG) and eicosanoid signalling. MAGL inhibition provides therapeutic opportunities but clinical potential is limited by central nervous system (CNS)-mediated side effects. Here, we report the discovery of LEI-515, a peripherally restricted, reversible MAGL inhibitor, using high throughput screening and a medicinal chemistry programme. LEI-515 increased 2-AG levels in peripheral organs, but not mouse brain. LEI-515 attenuated liver necrosis, oxidative stress and inflammation in a CCl4-induced acute liver injury model. LEI-515 suppressed chemotherapy-induced neuropathic nociception in mice without inducing cardinal signs of CB1 activation. Antinociceptive efficacy of LEI-515 was blocked by CB2, but not CB1, antagonists. The CB1 antagonist rimonabant precipitated signs of physical dependence in mice treated chronically with a global MAGL inhibitor (JZL184), and an orthosteric cannabinoid agonist (WIN55,212-2), but not with LEI-515. Our data support targeting peripheral MAGL as a promising therapeutic strategy for developing safe and effective anti-inflammatory and analgesic agents.
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Affiliation(s)
- Ming Jiang
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Mirjam C W Huizenga
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Jonah L Wirt
- Department of Psychological and Brain Sciences, Program in Neuroscience, Gill Center for Biomolecular Science, Indiana University, Bloomington, IN, USA
| | - Janos Paloczi
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute of Health/NIAAA, Rockville, MD, USA
| | - Avand Amedi
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | | | - Joerg Benz
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Ludovic Collin
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Hui Deng
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Xinyu Di
- Metabolomics and analytics center, Leiden University, Leiden, Netherlands
| | - Wouter F Driever
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Bogdan I Florea
- Department of Bio-organic Synthesis, Leiden University, Leiden, Netherlands
| | - Uwe Grether
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Thomas Hankemeier
- Metabolomics and analytics center, Leiden University, Leiden, Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden University & Oncode Institute, Leiden, Netherlands
| | | | - Florian Mohr
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Anto Pavlovic
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Iris Ruf
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | | | - Anna F Stevens
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Daan van der Vliet
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Tom van der Wel
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands
| | - Matthias B Wittwer
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | | | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute of Health/NIAAA, Rockville, MD, USA
| | - Andrea G Hohmann
- Department of Psychological and Brain Sciences, Program in Neuroscience, Gill Center for Biomolecular Science, Indiana University, Bloomington, IN, USA.
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden University & Oncode Institute, Leiden, Netherlands.
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14
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Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
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Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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15
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Zhang Z, Singh M, Kindt A, Wegrzyn AB, Pearson MJ, Ali A, Harms AC, Baker P, Hankemeier T. Development of a targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry based lipidomics platform applied to a coronavirus disease severity study. J Chromatogr A 2023; 1708:464342. [PMID: 37696124 DOI: 10.1016/j.chroma.2023.464342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
The importance of lipids seen in studies of metabolism, cancer, the recent COVID-19 pandemic and other diseases has brought the field of lipidomics to the forefront of clinical research. Quantitative and comprehensive analysis is required to understand biological interactions among lipid species. However, lipidomic analysis is often challenging due to the various compositional structures, diverse physicochemical properties, and wide dynamic range of concentrations of lipids in biological systems. To study the comprehensive lipidome, a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS)-based screening method with 1200 lipid features across 19 (sub)classes, including both nonpolar and polar lipids, has been developed. HILIC-MS/MS was selected due to its class separation property and fatty acyl chain level information. 3D models of class chromatographic retention behavior were established and evaluations of cross-class and within-class interferences were performed to avoid over-reporting these features. This targeted HILIC-MS/MS method was fully validated, with acceptable analytical parameters in terms of linearity, precision, reproducibility, and recovery. The accurate quantitation of 608 lipid species in the SRM 1950 NIST plasma was achieved using multi-internal standards per class and post-hoc correction, extending current databases by providing lipid concentrations resolved at fatty acyl chain level. The overall correlation coefficients (R2) of measured concentrations with values from literature range from 0.64 to 0.84. The applicability of the developed targeted lipidomics method was demonstrated by discovering 520 differential lipid features related to COVID-19 severity. This high coverage and targeted approach will aid in future investigations of the lipidome in various disease contexts.
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Affiliation(s)
- Zhengzheng Zhang
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Madhulika Singh
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Alida Kindt
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Agnieszka B Wegrzyn
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | | | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | | | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
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16
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Pandian K, Matsui M, Hankemeier T, Ali A, Okubo-Kurihara E. Advances in single-cell metabolomics to unravel cellular heterogeneity in plant biology. Plant Physiol 2023; 193:949-965. [PMID: 37338502 PMCID: PMC10517197 DOI: 10.1093/plphys/kiad357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
Single-cell metabolomics is a powerful tool that can reveal cellular heterogeneity and can elucidate the mechanisms of biological phenomena in detail. It is a promising approach in studying plants, especially when cellular heterogeneity has an impact on different biological processes. In addition, metabolomics, which can be regarded as a detailed phenotypic analysis, is expected to answer previously unrequited questions which will lead to expansion of crop production, increased understanding of resistance to diseases, and in other applications as well. In this review, we will introduce the flow of sample acquisition and single-cell techniques to facilitate the adoption of single-cell metabolomics. Furthermore, the applications of single-cell metabolomics will be summarized and reviewed.
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Affiliation(s)
- Kanchana Pandian
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Minami Matsui
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Emiko Okubo-Kurihara
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
- College of Science, Rikkyo University, Tokyo 171-8501, Japan
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17
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Fleming RMT, Haraldsdottir HS, Minh LH, Vuong PT, Hankemeier T, Thiele I. Cardinality optimization in constraint-based modelling: application to human metabolism. Bioinformatics 2023; 39:btad450. [PMID: 37697651 PMCID: PMC10495685 DOI: 10.1093/bioinformatics/btad450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/12/2023] [Indexed: 09/13/2023] Open
Abstract
MOTIVATION Several applications in constraint-based modelling can be mathematically formulated as cardinality optimization problems involving the minimization or maximization of the number of nonzeros in a vector. These problems include testing for stoichiometric consistency, testing for flux consistency, testing for thermodynamic flux consistency, computing sparse solutions to flux balance analysis problems and computing the minimum number of constraints to relax to render an infeasible flux balance analysis problem feasible. Such cardinality optimization problems are computationally complex, with no known polynomial time algorithms capable of returning an exact and globally optimal solution. RESULTS By approximating the zero-norm with nonconvex continuous functions, we reformulate a set of cardinality optimization problems in constraint-based modelling into a difference of convex functions. We implemented and numerically tested novel algorithms that approximately solve the reformulated problems using a sequence of convex programs. We applied these algorithms to various biochemical networks and demonstrate that our algorithms match or outperform existing related approaches. In particular, we illustrate the efficiency and practical utility of our algorithms for cardinality optimization problems that arise when extracting a model ready for thermodynamic flux balance analysis given a human metabolic reconstruction. AVAILABILITY AND IMPLEMENTATION Open source scripts to reproduce the results are here https://github.com/opencobra/COBRA.papers/2023_cardOpt with general purpose functions integrated within the COnstraint-Based Reconstruction and Analysis toolbox: https://github.com/opencobra/cobratoolbox.
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Affiliation(s)
- Ronan M T Fleming
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Wassenaarseweg 76, Leiden 2333 CC, The Netherlands
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, Belvaux L-4362, Luxembourg
- School of Medicine, National University of Ireland, University Rd, Galway H91 TK33, Ireland
| | - Hulda S Haraldsdottir
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, Belvaux L-4362, Luxembourg
| | - Le Hoai Minh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, Belvaux L-4362, Luxembourg
| | - Phan Tu Vuong
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, Belvaux L-4362, Luxembourg
- Mathematical Sciences School, University of Southampton, University Road, Southampton SO17 1BJ, United Kingdom
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Wassenaarseweg 76, Leiden 2333 CC, The Netherlands
| | - Ines Thiele
- School of Medicine, National University of Ireland, University Rd, Galway H91 TK33, Ireland
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18
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Zhang C, Le Dévédec SE, Ali A, Hankemeier T. Single-cell metabolomics by mass spectrometry: ready for primetime? Curr Opin Biotechnol 2023; 82:102963. [PMID: 37356380 DOI: 10.1016/j.copbio.2023.102963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/17/2023] [Accepted: 05/23/2023] [Indexed: 06/27/2023]
Abstract
Single-cell metabolomics (SCMs) is a powerful tool for studying cellular heterogeneity by providing insight into the differences between individual cells. With the development of a set of promising SCMs pipelines, this maturing technology is expected to be widely used in biomedical research. However, before SCMs is ready for primetime, there are some challenges to overcome. In this review, we summarize the trends and challenges in the development of SCMs. We also highlight the latest methodologies, applications, and sketch the perspective for integration with other omics and imaging approaches.
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Affiliation(s)
- Congrou Zhang
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands.
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands.
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19
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Zhang Z, Duri K, Duisters KLW, Schoeman JC, Chandiwana P, Lindenburg P, Jaeger J, Ziegler S, Altfeld M, Kohler I, Harms A, Gumbo FZ, Hankemeier T, Bunders MJ. Altered methionine-sulfone levels are associated with impaired growth in HIV-exposed-uninfected children. AIDS 2023; 37:1367-1376. [PMID: 37070556 DOI: 10.1097/qad.0000000000003574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
OBJECTIVE To determine immune-metabolic dysregulation in children born to women living with HIV. METHODS Longitudinal immune-metabolomic analyses of plasma of 32 pregnant women with HIV (WHIV) and 12 uninfected women and their children up to 1.5 years of age were performed. RESULTS Using liquid chromatography-mass spectrometry and a multiplex bead assay, 280 metabolites (57 amino acids, 116 positive lipids, 107 signalling lipids) and 24 immune mediators (e.g. cytokines) were quantified. combinational antiretroviral therapy (cART) exposure was categorized as cART initiation preconception (long), cART initiation postconception up to 4 weeks before birth (medium) and cART initiation within 3 weeks of birth (short). Plasma metabolite profiles differed between HIV-exposed-uninfected (HEU)-children with long cART exposure compared to HIV-unexposed-children (HUU). Specifically, higher levels of methionine-sulfone, which is associated with oxidative stress, were detected in HEU-children with long cART exposure compared to HUU-children. High infant methionine-sulfone levels were reflected by high prenatal plasma levels in the mother. Increased methionine-sulfone levels in the children were associated with decreased growth, including both weight and length. CONCLUSION These findings based on longitudinal data demonstrate that dysregulation of metabolite networks associated with oxidative stress in children born to WHIV is associated with restricted infant growth.
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Affiliation(s)
- Zhengzheng Zhang
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Kerina Duri
- Immunology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | - Johannes C Schoeman
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Panashe Chandiwana
- Immunology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Peter Lindenburg
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
- Research Group Metabolomics, Faculty Science & Technology, University of Applied Sciences Leiden, Hogeschool Leiden, Leiden, The Netherlands
| | | | | | | | - Isabelle Kohler
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Felicity Z Gumbo
- Department of Primary Health Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Madeleine J Bunders
- Leibniz Institute of Virology, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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20
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Theel WB, Boxma-de Klerk BM, Dirksmeier-Harinck F, van Rossum EF, Kanhai DA, Apers JA, van Dalen BM, De Knegt RJ, Neecke B, van der Zwan EM, Grobbee DE, Hankemeier T, Wiebolt J, Castro Cabezas M. Effect of bariatric surgery on NAFLD/NASH: a single-centre observational prospective cohort study. BMJ Open 2023; 13:e070431. [PMID: 37400234 DOI: 10.1136/bmjopen-2022-070431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Abstract
INTRODUCTION The prevalence of non-alcoholic fatty liver disease (NAFLD) ranges from 25% in the general population to 90% in patients with obesity scheduled for bariatric surgery. NAFLD can progress towards non-alcoholic steatohepatitis (NASH) associated with complications such as cirrhosis, hepatocellular carcinoma and cardiovascular disease. To date, losing weight and lifestyle modifications are the best known treatments for NASH. Bariatric surgery significantly improves NAFLD/NASH in the short term. However, the extent of this improvement is not yet clear and long-term data on the natural course of NAFLD/NASH after bariatric surgery are lacking. The factors involved in NAFLD/NASH regression after bariatric surgery have not been elucidated. METHODS AND ANALYSIS This is an observational prospective cohort study including patients scheduled for bariatric surgery. Extensive metabolic and cardiovascular analyses will be carried out including measurements of carotid intima media thickness and pulse wave velocity. Genomic, proteomic, lipidomic and metabolomic studies will be done. Microbioma analyses before and 1 year after surgery will be done. Transient elastography measurements will be performed before and at 1, 3 and 5 years after surgery. For those with an elevated preoperative transient elastography measurement by Fibroscan, a laparoscopic liver biopsy will be performed during surgery. Primary outcome measures are the change of steatosis and liver fibrosis 5 years after surgery. Secondary outcome measure is the comparison of the transient elastography measurements with the NAFLD Activity Score from the biopsies. ETHICS AND DISSEMINATION The protocol has been approved by the Medical Research Ethics Committees United, Nieuwegein, on 1 March 2022 (registration code R21.103/NL79423.100.21). The study results will be submitted for publication in peer-reviewed journals and data will be presented at scientific meetings. TRIAL REGISTRATION NUMBER NCT05499949.
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Affiliation(s)
- Willy B Theel
- Internal Medicine, Franciscus Gasthuis en Vlietland, Rotterdam, The Netherlands
- Centrum Gezond Gewicht, Rotterdam, The Netherlands
- Endocrinology, Erasmus MC, Rotterdam, The Netherlands
| | - Bianca M Boxma-de Klerk
- Statistics and Education, Franciscus Gasthuis en Vlietland, Rotterdam, The Netherlands
- Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Elisabeth Fc van Rossum
- Centrum Gezond Gewicht, Rotterdam, The Netherlands
- Endocrinology, Erasmus MC, Rotterdam, The Netherlands
| | - Danny A Kanhai
- Pediatrics, Franciscus Gasthuis en Vlietland, Rotterdam, The Netherlands
| | - Jan A Apers
- Bariatric Surgery, Franciscus Gasthuis en Vlietland, Rotterdam, The Netherlands
| | - Bas M van Dalen
- Cardiology, Franciscus Gasthuis en Vlietland, Rotterdam, The Netherlands
| | - Robert J De Knegt
- Gastroenterology and Hepatology, Erasmus Universiteit Rotterdam, Rotterdam, The Netherlands
| | - Bojou Neecke
- Pathology, Franciscus Gasthuis en Vlietland, Rotterdam, The Netherlands
| | - Ellen M van der Zwan
- Clinical Chemistry, Franciscus Gasthuis en Vlietland, Rotterdam, The Netherlands
| | - Diederick E Grobbee
- Julius Global Health, Julius Centrum for Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - Thomas Hankemeier
- Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | | | - Manuel Castro Cabezas
- Endocrinology, Erasmus MC, Rotterdam, The Netherlands
- Internal Medicine, Franciscus Gasthuis & Vlietland Berkel, Rotterdam, The Netherlands
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21
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Hetzel LA, Ali A, Corbo V, Hankemeier T. Microfluidics and Organoids, the Power Couple of Developmental Biology and Oncology Studies. Int J Mol Sci 2023; 24:10882. [PMID: 37446057 DOI: 10.3390/ijms241310882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Organoids are an advanced cell model that hold the key to unlocking a deeper understanding of in vivo cellular processes. This model can be used in understanding organ development, disease progression, and treatment efficacy. As the scientific world embraces the model, it must also establish the best practices for cultivating organoids and utilizing them to the greatest potential in assays. Microfluidic devices are emerging as a solution to overcome the challenges of organoids and adapt assays. Unfortunately, the various applications of organoids often depend on specific features in a device. In this review, we discuss the options and considerations for features and materials depending on the application and development of the organoid.
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Affiliation(s)
- Laura Ann Hetzel
- Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Ahmed Ali
- Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, ARC-Net Research Centre, University of Verona, 37134 Verona, Italy
| | - Thomas Hankemeier
- Leiden Academic Center for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
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22
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den Hartog I, Karu N, Zwep LB, Voorn GP, van de Garde EM, Hankemeier T, van Hasselt JC. Differential metabolic host response to pathogens associated with community-acquired pneumonia. Metabol Open 2023; 18:100239. [PMID: 37025095 PMCID: PMC10070890 DOI: 10.1016/j.metop.2023.100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Background Metabolic changes induced by the host immune response to pathogens found in patients with community-acquired pneumonia (CAP) may provide insight into its pathogenesis. In this study, we characterized differences in the host metabolic response to common CAP-associated pathogens. Method Targeted metabolomic profiling was performed on serum samples obtained from hospitalized CAP patients (n = 119) at admission. We quantified 347 unique metabolites across multiple biochemical classes, including amines, acylcarnitines, and signaling lipids. We evaluated if unique associations between metabolite levels and specific CAP-associated pathogens could be identified. Results Several acylcarnitines were found to be elevated in C. burnetii and herpes simplex virus and lowered in M. pneumoniae as compared to other pathogens. Phenylalanine and kynurenine were found elevated in L. pneumophila as compared to other pathogens. S-methylcysteine was elevated in patients with M. pneumoniae, and these patients also showed lowered cortisol levels in comparison to almost all other pathogens. For the herpes simplex virus, we observed a unique elevation of eicosanoids and several amines. Many lysophosphatidylcholines showed an altered profile in C. burnetii versus S. pneumoniae, L. pneumophila, and respiratory syncytial virus. Finally, phosphatidylcholines were negatively affected by the influenza virus in comparison to S. pneumoniae. Conclusions In this exploratory analysis, metabolites from different biochemical classes were found to be altered in serum samples from patients with different CAP-associated pathogens, which may be used for hypothesis generation in studies on differences in pathogen host response and pathogenesis of CAP.
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Affiliation(s)
- Ilona den Hartog
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Naama Karu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Laura B. Zwep
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - G. Paul Voorn
- Department of Medical Microbiology and Immunology, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Ewoudt M.W. van de Garde
- Division of Pharmacoepidemiology and Clinical Pharmacology, Department of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
- Department of Clinical Pharmacy, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - J.G. Coen van Hasselt
- Division of Systems Pharmacology & Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
- Corresponding author.
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23
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Yin C, Harms AC, Hankemeier T, Kindt A, de Lange ECM. Status of Metabolomic Measurement for Insights in Alzheimer's Disease Progression-What Is Missing? Int J Mol Sci 2023; 24:ijms24054960. [PMID: 36902391 PMCID: PMC10003384 DOI: 10.3390/ijms24054960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Alzheimer's disease (AD) is an aging-related neurodegenerative disease, leading to the progressive loss of memory and other cognitive functions. As there is still no cure for AD, the growth in the number of susceptible individuals represents a major emerging threat to public health. Currently, the pathogenesis and etiology of AD remain poorly understood, while no efficient treatments are available to slow down the degenerative effects of AD. Metabolomics allows the study of biochemical alterations in pathological processes which may be involved in AD progression and to discover new therapeutic targets. In this review, we summarized and analyzed the results from studies on metabolomics analysis performed in biological samples of AD subjects and AD animal models. Then this information was analyzed by using MetaboAnalyst to find the disturbed pathways among different sample types in human and animal models at different disease stages. We discuss the underlying biochemical mechanisms involved, and the extent to which they could impact the specific hallmarks of AD. Then we identify gaps and challenges and provide recommendations for future metabolomics approaches to better understand AD pathogenesis.
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Affiliation(s)
- Chunyuan Yin
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Amy C. Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Alida Kindt
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Elizabeth C. M. de Lange
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
- Correspondence:
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24
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Huang L, Drouin N, Causon J, Wegrzyn A, Castro-Perez J, Fleming R, Harms A, Hankemeier T. Reconstruction of Glutathione Metabolism in the Neuronal Model of Rotenone-Induced Neurodegeneration Using Mass Isotopologue Analysis with Hydrophilic Interaction Liquid Chromatography-Zeno High-Resolution Multiple Reaction Monitoring. Anal Chem 2023; 95:3255-3266. [PMID: 36735349 PMCID: PMC9933045 DOI: 10.1021/acs.analchem.2c04231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Accurate reconstruction of metabolic pathways is an important prerequisite for interpreting metabolomics changes and understanding the diverse biological processes in disease models. A tracer-based metabolomics strategy utilizes stable isotope-labeled precursors to resolve complex pathways by tracing the labeled atom(s) to downstream metabolites through enzymatic reactions. Isotope enrichment analysis is informative and achieved by counting total labeled atoms and acquiring the mass isotopologue distribution (MID) of the intact metabolite. However, quantitative analysis of labeled metabolite substructures/moieties (MS2 fragments) can offer more valuable insights into the reaction connections through measuring metabolite transformation. In order to acquire the isotopic labeling information at the intact metabolite and moiety level simultaneously, we developed a method that couples hydrophilic interaction liquid chromatography (HILIC) with Zeno trap-enabled high-resolution multiple reaction monitoring (MRMHR). The method enabled accurate and reproducible MID quantification for intact metabolites as well as their fragmented moieties, with notably high sensitivity in the MS2 fragmentation mode based on the measurement of 13C- or 15N-labeled cellular samples. The method was applied to human-induced pluripotent stem cell-derived neurons to trace the fate of 13C/15N atoms from D-13C6-glucose/L-15N2-glutamine added to the media. With the MID analysis of both intact metabolites and fragmented moieties, we validated the pathway reconstruction of de novo glutathione synthesis in mid-brain neurons. We discovered increased glutathione oxidization from both basal and newly synthesized glutathione pools under neuronal oxidative stress. Furthermore, the significantly decreased de novo glutathione synthesis was investigated and associated with altered activities of several key enzymes, as evidenced by suppressed glutamate supply via glucose metabolism and a diminished flux of glutathione synthetic reaction in the neuronal model of rotenone-induced neurodegeneration.
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Affiliation(s)
- Luojiao Huang
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Nicolas Drouin
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | | | - Agnieszka Wegrzyn
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | | | - Ronan Fleming
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands,School
of Medicine, National University of Ireland, University Rd, Galway H91 TK33, Ireland
| | - Amy Harms
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Thomas Hankemeier
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands,
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25
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Hagenbeek FA, van Dongen J, Pool R, Roetman PJ, Harms AC, Hottenga JJ, Kluft C, Colins OF, van Beijsterveldt CEM, Fanos V, Ehli EA, Hankemeier T, Vermeiren RRJM, Bartels M, Déjean S, Boomsma DI. Integrative Multi-omics Analysis of Childhood Aggressive Behavior. Behav Genet 2023; 53:101-117. [PMID: 36344863 PMCID: PMC9922241 DOI: 10.1007/s10519-022-10126-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
Abstract
This study introduces and illustrates the potential of an integrated multi-omics approach in investigating the underlying biology of complex traits such as childhood aggressive behavior. In 645 twins (cases = 42%), we trained single- and integrative multi-omics models to identify biomarkers for subclinical aggression and investigated the connections among these biomarkers. Our data comprised transmitted and two non-transmitted polygenic scores (PGSs) for 15 traits, 78,772 CpGs, and 90 metabolites. The single-omics models selected 31 PGSs, 1614 CpGs, and 90 metabolites, and the multi-omics model comprised 44 PGSs, 746 CpGs, and 90 metabolites. The predictive accuracy for these models in the test (N = 277, cases = 42%) and independent clinical data (N = 142, cases = 45%) ranged from 43 to 57%. We observed strong connections between DNA methylation, amino acids, and parental non-transmitted PGSs for ADHD, Autism Spectrum Disorder, intelligence, smoking initiation, and self-reported health. Aggression-related omics traits link to known and novel risk factors, including inflammation, carcinogens, and smoking.
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Affiliation(s)
- Fiona A. Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands ,Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Peter J. Roetman
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands
| | - Amy C. Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands ,The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands
| | | | - Olivier F. Colins
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands ,Department Special Needs Education, Ghent University, Ghent, Belgium
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota USA
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands ,The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Robert R. J. M. Vermeiren
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands ,Youz, Parnassia Psychiatric Institute, The Hague, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, University of Toulouse, CNRS, Toulouse, France
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands ,Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
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26
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Van Puyvelde B, Van Uytfanghe K, Van Oudenhove L, Gabriels R, Van Royen T, Matthys A, Razavi M, Yip R, Pearson T, Drouin N, Claereboudt J, Foley D, Wardle R, Wyndham K, Hankemeier T, Jones D, Saelens X, Martens G, Stove CP, Deforce D, Martens L, Vissers JPC, Anderson NL, Dhaenens M. Cov 2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein. Anal Chem 2022; 94:17379-17387. [PMID: 36490367 PMCID: PMC9773173 DOI: 10.1021/acs.analchem.2c01610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pandemic readiness toolbox needs to be extended, targeting different biomolecules, using orthogonal experimental set-ups. Here, we build on our Cov-MS effort using LC-MS, adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma and has increased sensitivity into the attomole range, a 1000-fold improvement compared to direct detection in a matrix. A strong positive correlation was observed with qPCR detection beyond a quantification cycle of 30-31, the level where no live virus can be cultured. The automatable sample preparation and reduced LC dependency allow analysis of up to 500 samples per day per instrument. Importantly, peptide enrichment allows detection of the N protein in pooled samples without sensitivity loss. Easily multiplexed, we detect variants and propose targets for Influenza A and B detection. Thus, the Cov2MS assay can be adapted to test for many different pathogens in pooled samples, providing longitudinal epidemiological monitoring of large numbers of pathogens within a population as an early warning system.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Uytfanghe
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | | | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tessa Van Royen
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Arne Matthys
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Richard Yip
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | | | - Dominic Foley
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Robert Wardle
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Kevin Wyndham
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Donald Jones
- Leicester Cancer Research Centre, RKCSB, Cardiovascular Research Centre, Glenfield Hospital, University of Leicester, Leicester LE1 7RH, United Kingdom.,John and Lucille van Geest Biomarker Facility, Leicester LE3 9QP, United Kingdom.,The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Level 4, Sandringham Building, Leicester LE1 7RH, United Kingdom
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Geert Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Johannes P C Vissers
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - N Leigh Anderson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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27
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Onderwater GLJ, van Dongen RM, Harms AC, Zielman R, van Oosterhout WPJ, van Klinken JB, Goeman JJ, Terwindt GM, van den Maagdenberg AMJM, Hankemeier T, Ferrari MD. Cerebrospinal Fluid and Plasma Amine Profiles in Interictal Migraine. Ann Neurol 2022; 93:715-728. [PMID: 36511835 DOI: 10.1002/ana.26576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 11/18/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Impaired amine metabolism has been associated with the etiology of migraine, that is, why patients continue to get migraine attacks. However, evidence from cerebrospinal fluid (CSF) is lacking. Here, we evaluated individual amine levels, global amine profiles, and amine pathways in CSF and plasma of interictal migraine patients and healthy controls. METHODS CSF and plasma were sampled between 8:30 am and 1:00 pm, randomly and interchangeably over the time span to avoid any diurnal and seasonal influences, from healthy volunteers and interictal migraine patients, matched for age, sex, and sampling time. The study was approved by the local medical ethics committee. Individual amines (n = 31), global amine profiles, and specific amine pathways were analyzed using a validated ultraperformance liquid chromatography mass spectrometry platform. RESULTS We analyzed n = 99 participants with migraine with aura, n = 98 with migraine without aura, and n = 96 healthy volunteers. Univariate analysis with Bonferroni correction indicated that CSF L-arginine was reduced in migraine with aura (10.4%, p < 0.001) and without aura (5.0%, p = 0.03). False discovery rate-corrected CSF L-phenylalanine was also lower in migraine with aura (6.9%, p = 0.011) and without aura (8.1%, p = 0.001), p = 0.088 after Bonferroni correction. Multivariate analysis revealed that CSF global amine profiles were similar for both types of migraine (p = 0.64), but distinct from controls (p = 0.009). Global profile analyses were similar in plasma. The strongest associated pathways with migraine were related to L-arginine metabolism. INTERPRETATION L-Arginine was decreased in the CSF (but not in plasma) of interictal patients with migraine with or without aura, and associated pathways were altered. This suggests that dysfunction of nitric oxide signaling is involved in susceptibility to getting migraine attacks. ANN NEUROL 2023.
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Affiliation(s)
| | - Robin M van Dongen
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden, the Netherlands
| | - Ronald Zielman
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jan B van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jelle J Goeman
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arn M J M van den Maagdenberg
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden, the Netherlands
| | - Michel D Ferrari
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
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28
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He Y, Miggiels P, Drouin N, Lindenburg PW, Wouters B, Hankemeier T. An automated online three-phase electro-extraction setup with machine-vision process monitoring hyphenated to LC-MS analysis. Anal Chim Acta 2022; 1235:340521. [DOI: 10.1016/j.aca.2022.340521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022]
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29
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Leygeber S, Grossmann JL, Diez-Simon C, Karu N, Dubbelman AC, Harms AC, Westerhuis JA, Jacobs DM, Lindenburg PW, Hendriks MMWB, Ammerlaan BCH, van den Berg MA, van Doorn R, Mumm R, Hall RD, Smilde AK, Hankemeier T. Flavor Profiling Using Comprehensive Mass Spectrometry Analysis of Metabolites in Tomato Soups. Metabolites 2022; 12:metabo12121194. [PMID: 36557232 PMCID: PMC9788410 DOI: 10.3390/metabo12121194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Trained sensory panels are regularly used to rate food products but do not allow for data-driven approaches to steer food product development. This study evaluated the potential of a molecular-based strategy by analyzing 27 tomato soups that were enhanced with yeast-derived flavor products using a sensory panel as well as LC-MS and GC-MS profiling. These data sets were used to build prediction models for 26 different sensory attributes using partial least squares analysis. We found driving separation factors between the tomato soups and metabolites predicting different flavors. Many metabolites were putatively identified as dipeptides and sulfur-containing modified amino acids, which are scientifically described as related to umami or having "garlic-like" and "onion-like" attributes. Proposed identities of high-impact sensory markers (methionyl-proline and asparagine-leucine) were verified using MS/MS. The overall results highlighted the strength of combining sensory data and metabolomics platforms to find new information related to flavor perception in a complex food matrix.
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Affiliation(s)
- Simon Leygeber
- Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Justus L. Grossmann
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Carmen Diez-Simon
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Naama Karu
- Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Anne-Charlotte Dubbelman
- Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Amy C. Harms
- Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Johan A. Westerhuis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Doris M. Jacobs
- Unilever’s Foods Innovation Centre, Bronland 14, 6708 WH Wageningen, The Netherlands
| | - Peter W. Lindenburg
- Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Leiden Centre for Applied Bioscience, University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden, The Netherlands
| | | | - Brenda C. H. Ammerlaan
- DSM Center for Biodata & Translation, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | | | - Rudi van Doorn
- DSM Food & Beverages, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Roland Mumm
- Wageningen Research (Bioscience), Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Robert D. Hall
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Research (Bioscience), Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Age K. Smilde
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Correspondence:
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30
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Jurado-Fasoli L, Di X, Sanchez-Delgado G, Yang W, Osuna-Prieto FJ, Ortiz-Alvarez L, Krekels E, Harms AC, Hankemeier T, Schönke M, Aguilera CM, Llamas-Elvira JM, Kohler I, Rensen PCN, Ruiz JR, Martinez-Tellez B. Acute and long-term exercise differently modulate plasma levels of oxylipins, endocannabinoids, and their analogues in young sedentary adults: A sub-study and secondary analyses from the ACTIBATE randomized controlled-trial. EBioMedicine 2022; 85:104313. [PMID: 36374769 PMCID: PMC9626892 DOI: 10.1016/j.ebiom.2022.104313] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Fatty acid-derived lipid mediators including oxylipins, endocannabinoids (eCBs), and their analogues, have emerged as key metabolites in the inflammatory and immune response to physiological stressors. METHODS This report was based on a sub-study and secondary analyses the ACTIBATE single-center unblinded randomized controlled trial (ClinicalTrials.gov ID: NCT02365129). The study was performed in the Sport and Health University Research Institute and the Virgen de las Nieves University Hospital of the University of Granada. Eligible participants were young, sedentary adults with no chronic diseases. Here, we performed both an acute endurance and resistance exercise sub-studies (n.ß=.ß14 and 17 respectively), and a 24-week supervised exercise intervention, combining endurance and resistance exercise training at moderate-intensity (MOD-EX) or vigorous-intensity (VIG-EX) exercise groups, in young sedentary adults. Randomization was performed by unrestricted randomization. Plasma levels of oxylipins, eCBs, and their analogues were measured using liquid chromatography-tandem mass spectrometry. FINDINGS Both endurance and resistance exercise increased by.ß+50% the plasma levels of dihomo-..-linolenic acid and arachidonic acid (AA) omega-6 derived oxylipins, as well as eicosapentaenoic acid and docosahexaenoic acid omega-3 derived after 3 and 120.ßmin of the bout of exercise (all ..2.ß....ß0.219 and P.ß..±.ß0.039). These exercise modalities also increased the levels of anandamide and eCBs analogues (+25%). 145 young sedentary adults were assigned to a control (CON, n.ß=.ß54), a MOD-EX (n.ß=.ß48) or a VIG-EX (n.ß=.ß43). 102 participants were included in the final long-term analyses (CON, n.ß=.ß36; MOD-EX, n.ß=.ß33; and VIG-EX, n.ß=.ß33) of the trial. After 24-week of supervised exercise, MOD-EX decreased plasma levels of omega-6 oxylipins, concretely linoleic acid (LA) and adrenic acid derived oxylipins, and the eCBs analogues OEA and LEA in comparison to the CON (all P.ß..±.ß0.021). VIG-EX decreased LA-derived oxylipins and LEA compared to CON. No relevant adverse events were recorded. INTERPRETATION Endurance and resistance exercises acutely increased plasma levels of oxylipins, eCBs, and their analogues, whereas 24 weeks of exercise training decreased fasting plasma levels of omega-6 oxylipins, and eCBs analogues in young, sedentary adults. FUNDING See Acknowledgments section.
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Affiliation(s)
- Lucas Jurado-Fasoli
- PROmoting FITness and Health Through Physical Activity Research Group (PROFITH), Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain; Department of Physiology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Xinyu Di
- Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Guillermo Sanchez-Delgado
- PROmoting FITness and Health Through Physical Activity Research Group (PROFITH), Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain; Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Wei Yang
- Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Francisco J Osuna-Prieto
- PROmoting FITness and Health Through Physical Activity Research Group (PROFITH), Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain; Department of Analytical Chemistry, University of Granada, Granada, Spain; Research and Development of Functional Food Centre (CIDAF), Granada, Spain
| | - Lourdes Ortiz-Alvarez
- PROmoting FITness and Health Through Physical Activity Research Group (PROFITH), Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain; Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | - Elke Krekels
- Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Amy C Harms
- Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Thomas Hankemeier
- Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Milena Schönke
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Centre, Leiden, the Netherlands
| | - Concepcion M Aguilera
- Department of Biochemistry and Molecular Biology II, ..úJos.. Mataix Verd....Ñ Institute of Nutrition and Food Technology (INYTA), Biomedical Research Centre (CIBM), University of Granada, Granada 18016, Spain; Instituto de Investigaci..n Biosanitaria, ibs.Granada, Granada, Spain; CIBER Fisiopatolog.ía de la Obesidad y la Nutrici..n (CIBEROBN), Madrid 28029, Spain
| | - Jose M Llamas-Elvira
- Instituto de Investigaci..n Biosanitaria, ibs.Granada, Granada, Spain; Servicio de Medicina Nuclear, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Isabelle Kohler
- Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam, the Netherlands; Center for Analytical Sciences Amsterdam, Amsterdam, the Netherlands
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Centre, Leiden, the Netherlands
| | - Jonatan R Ruiz
- PROmoting FITness and Health Through Physical Activity Research Group (PROFITH), Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain; Instituto de Investigaci..n Biosanitaria, ibs.Granada, Granada, Spain.
| | - Borja Martinez-Tellez
- PROmoting FITness and Health Through Physical Activity Research Group (PROFITH), Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain; Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Centre, Leiden, the Netherlands; Department of Education, Faculty of Education Sciences and SPORT Research Group (CTS-1024), CERNEP Research Center, University of Almer.ía, Almer.ía, Spain.
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31
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Wouters B, Miggiels P, Bezemer R, van der Cruijsen EA, van Leeuwen E, Gauvin J, Houben K, Babu Sai Sankar Gupta K, Zuijdwijk P, Harms A, Carvalho de Souza A, Hankemeier T. Automated Segmented-Flow Analysis – NMR with a Novel Fluoropolymer Flow Cell for High-Throughput Screening. Anal Chem 2022; 94:15350-15358. [DOI: 10.1021/acs.analchem.2c03038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bert Wouters
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Paul Miggiels
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Roland Bezemer
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands
| | | | - Erik van Leeuwen
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands
| | - John Gauvin
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands
| | - Klaartje Houben
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands
| | | | - Paul Zuijdwijk
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AXDelft, The Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | | | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
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32
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Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
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Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
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33
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Kindt A, Kraus Y, Rasp D, Foerster KM, Ahmidi N, Flemmer AW, Herber-Jonat S, Heinen F, Weigand H, Hankemeier T, Koletzko B, Krumsiek J, Babl J, Hilgendorff A. Improved Macro- and Micronutrient Supply for Favorable Growth and Metabolomic Profile with Standardized Parenteral Nutrition Solutions for Very Preterm Infants. Nutrients 2022; 14:3912. [PMID: 36235563 PMCID: PMC9572167 DOI: 10.3390/nu14193912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Very preterm infants are at high risk for suboptimal nutrition in the first weeks of life leading to insufficient weight gain and complications arising from metabolic imbalances such as insufficient bone mineral accretion. We investigated the use of a novel set of standardized parenteral nutrition (PN; MUC PREPARE) solutions regarding improving nutritional intake, accelerating termination of parenteral feeding, and positively affecting growth in comparison to individually prescribed and compounded PN solutions. We studied the effect of MUC PREPARE on macro- and micronutrient intake, metabolism, and growth in 58 very preterm infants and compared results to a historic reference group of 58 very preterm infants matched for clinical characteristics. Infants receiving MUC PREPARE demonstrated improved macro- and micronutrient intake resulting in balanced electrolyte levels and stable metabolomic profiles. Subsequently, improved energy supply was associated with up to 1.5 weeks earlier termination of parenteral feeding, while simultaneously reaching up to 1.9 times higher weight gain at day 28 in extremely immature infants (<27 GA weeks) as well as overall improved growth at 2 years of age for all infants. The use of the new standardized PN solution MUC PREPARE improved nutritional supply and short- and long-term growth and reduced PN duration in very preterm infants and is considered a superior therapeutic strategy.
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Affiliation(s)
- Alida Kindt
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Oberschleißheim, Germany
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Yvonne Kraus
- Center for Comprehensive Developmental Care (CDeCLMU), Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr von Hauner Children's Hospital, Munich University Hospital, Ludwig Maximilians University, 80336 Munich, Germany
- Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Lung Research Center (DZL), 81377 Munich, Germany
| | - David Rasp
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Kai M. Foerster
- Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Lung Research Center (DZL), 81377 Munich, Germany
- Department of Neonatology, Perinatal Center, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians University, 80337 Munich, Germany
| | - Narges Ahmidi
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Oberschleißheim, Germany
| | - Andreas W. Flemmer
- Department of Neonatology, Perinatal Center, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians University, 80337 Munich, Germany
| | - Susanne Herber-Jonat
- Department of Neonatology, Perinatal Center, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians University, 80337 Munich, Germany
| | - Florian Heinen
- Center for Comprehensive Developmental Care (CDeCLMU), Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr von Hauner Children's Hospital, Munich University Hospital, Ludwig Maximilians University, 80336 Munich, Germany
| | - Heike Weigand
- Center for Comprehensive Developmental Care (CDeCLMU), Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr von Hauner Children's Hospital, Munich University Hospital, Ludwig Maximilians University, 80336 Munich, Germany
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Department of Paediatrics, Dr. von Hauner Children’s Hospital University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Oberschleißheim, Germany
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Juergen Babl
- Pharmacy of the University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Anne Hilgendorff
- Center for Comprehensive Developmental Care (CDeCLMU), Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr von Hauner Children's Hospital, Munich University Hospital, Ludwig Maximilians University, 80336 Munich, Germany
- Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Lung Research Center (DZL), 81377 Munich, Germany
- Department of Neonatology, Perinatal Center, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians University, 80337 Munich, Germany
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He Y, van Mever M, Yang W, Huang L, Ramautar R, Rijksen Y, Vermeij WP, Hoeijmakers JHJ, Harms AC, Lindenburg PW, Hankemeier T. A Sample Preparation Method for the Simultaneous Profiling of Signaling Lipids and Polar Metabolites in Small Quantities of Muscle Tissues from a Mouse Model for Sarcopenia. Metabolites 2022; 12:metabo12080742. [PMID: 36005613 PMCID: PMC9413361 DOI: 10.3390/metabo12080742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
The metabolic profiling of a wide range of chemical classes relevant to understanding sarcopenia under conditions in which sample availability is limited, e.g., from mouse models, small muscles, or muscle biopsies, is desired. Several existing metabolomics platforms that include diverse classes of signaling lipids, energy metabolites, and amino acids and amines would be informative for suspected biochemical pathways involved in sarcopenia. The sample limitation requires an optimized sample preparation method with minimal losses during isolation and handling and maximal accuracy and reproducibility. Here, two developed sample preparation methods, BuOH-MTBE-Water (BMW) and BuOH-MTBE-More-Water (BMMW), were evaluated and compared with previously reported methods, Bligh-Dyer (BD) and BuOH-MTBE-Citrate (BMC), for their suitability for these classes. The most optimal extraction was found to be the BMMW method, with the highest extraction recovery of 63% for the signaling lipids and 81% for polar metabolites, and an acceptable matrix effect (close to 1.0) for all metabolites of interest. The BMMW method was applied on muscle tissues as small as 5 mg (dry weight) from the well-characterized, prematurely aging, DNA repair-deficient Ercc1∆/- mouse mutant exhibiting multiple-morbidities, including sarcopenia. We successfully detected 109 lipids and 62 polar targeted metabolites. We further investigated whether fast muscle tissue isolation is necessary for mouse sarcopenia studies. A muscle isolation procedure involving 15 min at room temperature revealed a subset of metabolites to be unstable; hence, fast sample isolation is critical, especially for more oxidative muscles. Therefore, BMMW and fast muscle tissue isolation are recommended for future sarcopenia studies. This research provides a sensitive sample preparation method for the simultaneous extraction of non-polar and polar metabolites from limited amounts of muscle tissue, supplies a stable mouse muscle tissue collection method, and methodologically supports future metabolomic mechanistic studies of sarcopenia.
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Affiliation(s)
- Yupeng He
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marlien van Mever
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Wei Yang
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Luojiao Huang
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Yvonne Rijksen
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Jan H. J. Hoeijmakers
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
- Institute for Genome Stability in Aging and Disease, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Amy C. Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Peter W. Lindenburg
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Research Group Metabolomics, Leiden Center for Applied Bioscience, University of Applied Sciences Leiden, 2333 CK Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Correspondence: ; Tel.: +31-71-527-1340
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Ding Y, Haks MC, van den Eeden SJF, Ottenhoff THM, Harms AC, Hankemeier T, Eeza MNH, Matysik J, Alia A, Spaink HP. Leptin mutation and mycobacterial infection lead non-synergistically to a similar metabolic syndrome. Metabolomics 2022; 18:67. [PMID: 35933481 PMCID: PMC9356939 DOI: 10.1007/s11306-022-01921-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The leptin signaling pathway plays an important role as a key regulator of glucose homeostasis, metabolism control and systemic inflammatory responses. However, the metabolic effects of leptin on infectious diseases, for example tuberculosis (TB), are still little known. OBJECTIVES In this study, we aim to investigate the role of leptin on metabolism in the absence and presence of mycobacterial infection in zebrafish larvae and mice. METHODS Metabolites in entire zebrafish larvae and the blood of mice were studied using high-resolution magic-angle-spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy and mass spectrometry, respectively. For transcriptome studies of zebrafish larvae, deep RNA sequencing was used. RESULTS The results show that leptin mutation leads to a similar metabolic syndrome as caused by mycobacterial infection in the two species, characterized by the decrease of 11 amine metabolites. In both species, this metabolic syndrome was not aggravated further when the leptin mutant was infected by mycobacteria. Therefore, we conclude that leptin and mycobacterial infection are both impacting metabolism non-synergistically. In addition, we studied the transcriptomes of lepbibl54 mutant zebrafish larvae and wild type (WT) siblings after mycobacterial infection. These studies showed that mycobacteria induced a very distinct transcriptome signature in the lepbibl54 mutant zebrafish compared to WT sibling control larvae. Furthermore, lepbibl55 Tg (pck1:luc1) zebrafish line was constructed and confirmed this difference in transcriptional responses. CONCLUSIONS Leptin mutation and TB lead non-synergistically to a similar metabolic syndrome. Moreover, different transcriptomic responses in the lepbibl54 mutant and TB can lead to the similar metabolic end states.
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Affiliation(s)
- Yi Ding
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Mariëlle C Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan J F van den Eeden
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Amy C Harms
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Muhamed N H Eeza
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Jörg Matysik
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - A Alia
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Abstract
Postcolumn infusion has been widely used to study the matrix effect of analytical methods based on liquid chromatography coupled to mass spectrometry (LC-MS). Nevertheless, this methodology is usually only applied during a method development or validation. With this application note, we aim to demonstrate that the continuous use of postcolumn infusion can be also a very useful tool to monitor the quality of LC-MS analyses and easily detect flaws in the analytical method performance. Here we propose a protocol that can be transferred to other LC-MS platforms, and we show some real situations in bioanalysis in which postcolumn infusion proved to be extremely helpful in, for example, the evaluation of a sample treatment or the detection of unexpected sources of the matrix effect.
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Affiliation(s)
| | - Anne-Charlotte Dubbelman
- Analytical BioSciences and
Metabolomics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Thomas Hankemeier
- Analytical BioSciences and
Metabolomics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
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Ortiz-Alvarez L, Xu H, Di X, Kohler I, Osuna-Prieto FJ, Acosta FM, Vilchez-Vargas R, Link A, Plaza-Díaz J, van der Stelt M, Hankemeier T, Clemente-Postigo M, Tinahones FJ, Gil A, Rensen PCN, Ruiz JR, Martinez-Tellez B. Plasma Levels of Endocannabinoids and Their Analogues Are Related to Specific Fecal Bacterial Genera in Young Adults: Role in Gut Barrier Integrity. Nutrients 2022; 14:2143. [PMID: 35631284 PMCID: PMC9143287 DOI: 10.3390/nu14102143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To investigate the association of plasma levels of endocannabinoids with fecal microbiota. METHODS Plasma levels of endocannabinoids, anandamide (AEA) and 2-arachidonoylglycerol (2-AG), as well as their eleven analogues, and arachidonic acid (AA), were measured using liquid chromatography-tandem mass spectrometry in 92 young adults. DNA extracted from stool samples was analyzed using 16S rRNA gene sequencing. Lipopolysaccharide levels were measured in plasma samples. RESULTS Plasma levels of endocannabinoids and their analogues were not related to beta or alpha diversity indexes. Plasma levels of AEA and related N-acylethanolamines correlated positively with the relative abundance of Faecalibacterium genus (all rho ≥ 0.26, p ≤ 0.012) and Akkermansia genus (all rho ≥ 0.22, p ≤ 0.036), and negatively with the relative abundance of Bilophila genus (all rho ≤ -0.23, p ≤ 0.031). Moreover, plasma levels of 2-AG and other acylglycerols correlated positively with the relative abundance of Parasutterella (all rho ≥ 0.24, p ≤ 0.020) and Odoribacter genera (all rho ≥ 0.27, p ≤ 0.011), and negatively with the relative abundance of Prevotella genus (all rho ≤ -0.24, p ≤ 0.023). In participants with high lipopolysaccharide values, the plasma levels of AEA and related N-acylethanolamines, as well as AA and 2-AG, were negatively correlated with plasma levels of lipopolysaccharide (all rho ≤ -0.24, p ≤ 0.020). CONCLUSION Plasma levels of endocannabinoids and their analogues are correlated to specific fecal bacterial genera involved in maintaining gut barrier integrity in young adults. This suggests that plasma levels of endocannabinoids and their analogues may play a role in the gut barrier integrity in young adults.
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Affiliation(s)
- Lourdes Ortiz-Alvarez
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
| | - Huiwen Xu
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
| | - Xinyu Di
- Leiden Academic Centre for Drug Research, Division of Systems Biomedicine and Pharmacology, Leiden University, 2300 Leiden, The Netherlands;
| | - Isabelle Kohler
- Division of BioAnalytical Chemistry, Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 Amsterdam, The Netherlands;
- Center for Analytical Sciences Amsterdam, 1098 Amsterdam, The Netherlands
| | - Francisco J. Osuna-Prieto
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Center for Biomedical Research, Department of Analytical Chemistry, Institute of Nutrition and Food Technology, University of Granada, 18071 Granada, Spain
- Research and Development of Functional Food Center (CIDAF), Health Sciences Technology Park, 18071 Granada, Spain
| | - Francisco M. Acosta
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Turku PET Centre, University of Turku, 20014 Turku, Finland
- Turku PET Centre, Turku University Hospital, 20521 Turku, Finland
- InFLAMES Research Flagship Centre, University of Turku, 20014 Turku, Finland
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany; (R.V.-V.); (A.L.)
| | - Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, 2300 Leiden, The Netherlands;
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Department of Systems Biomedicine and Pharmacology, Leiden University, 2300 Leiden, The Netherlands;
| | - Mercedes Clemente-Postigo
- Department of Cell Biology, Physiology and Immunology, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain;
- Unidad de Gestión Clínica Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29016 Malaga, Spain;
- Centro de Investigación Biomédica En Red (CIBER), Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Malaga, Spain
| | - Francisco J. Tinahones
- Unidad de Gestión Clínica Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29016 Malaga, Spain;
- Centro de Investigación Biomédica En Red (CIBER), Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Malaga, Spain
| | - Angel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (J.P.-D.); (A.G.)
- Centro de Investigación Biomédica En Red (CIBER), Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Malaga, Spain
- Biomedical Research Center, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Parque Tecnológico Ciencias de la Salud, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria, 18014 Granada, Spain
| | - Patrick C. N. Rensen
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands;
| | - Jonatan R. Ruiz
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Instituto de Investigación Biosanitaria, 18014 Granada, Spain
- Department of Physical and Sports Education, School of Sports Science, University of Granada, 18071 Granada, Spain
| | - Borja Martinez-Tellez
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, 18071 Granada, Spain; (L.O.-A.); (H.X.); (F.J.O.-P.); (F.M.A.); (B.M.-T.)
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands;
- CERNEP Research Center, Department of Education, Faculty of Education Sciences and SPORT Research Group (CTS-1024), University of Almería, 04120 Almeria, Spain
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Schultes E, Roos M, Bonino da Silva Santos LO, Guizzardi G, Bouwman J, Hankemeier T, Baak A, Mons B. FAIR Digital Twins for Data-Intensive Research. Front Big Data 2022; 5:883341. [PMID: 35647536 PMCID: PMC9130601 DOI: 10.3389/fdata.2022.883341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Although all the technical components supporting fully orchestrated Digital Twins (DT) currently exist, what remains missing is a conceptual clarification and analysis of a more generalized concept of a DT that is made FAIR, that is, universally machine actionable. This methodological overview is a first step toward this clarification. We present a review of previously developed semantic artifacts and how they may be used to compose a higher-order data model referred to here as a FAIR Digital Twin (FDT). We propose an architectural design to compose, store and reuse FDTs supporting data intensive research, with emphasis on privacy by design and their use in GDPR compliant open science.
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Machushynets NV, Elsayed SS, Du C, Siegler MA, de la Cruz M, Genilloud O, Hankemeier T, van Wezel GP. Discovery of actinomycin L, a new member of the actinomycin family of antibiotics. Sci Rep 2022; 12:2813. [PMID: 35181725 PMCID: PMC8857259 DOI: 10.1038/s41598-022-06736-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/01/2022] [Indexed: 12/25/2022] Open
Abstract
Streptomycetes are major producers of bioactive natural products, including the majority of the naturally produced antibiotics. While much of the low-hanging fruit has been discovered, it is predicted that less than 5% of the chemical space of natural products has been mined. Here, we describe the discovery of the novel actinomycins L1 and L2 produced by Streptomyces sp. MBT27, via application of metabolic analysis and molecular networking. Actinomycins L1 and L2 are diastereomers, and the structure of actinomycin L2 was resolved using NMR and single crystal X-ray crystallography. Actinomycin L is formed via spirolinkage of anthranilamide to the 4-oxoproline moiety of actinomycin X2, prior to the condensation of the actinomycin halves. Such a structural feature has not previously been identified in naturally occurring actinomycins. Adding anthranilamide to cultures of the actinomycin X2 producer Streptomyces antibioticus, which has the same biosynthetic gene cluster as Streptomyces sp. MBT27, resulted in the production of actinomycin L. This supports a biosynthetic pathway whereby actinomycin L is produced from two distinct metabolic routes, namely those for actinomycin X2 and for anthranilamide. Actinomycins L1 and L2 showed significant antimicrobial activity against Gram-positive bacteria. Our work shows how new molecules can still be identified even in the oldest of natural product families.
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Affiliation(s)
- Nataliia V Machushynets
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Chao Du
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Mercedes de la Cruz
- Fundación MEDINA, Health Sciences Technology Park, Avda Conocimiento 34, 18016, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, Avda Conocimiento 34, 18016, Granada, Spain
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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40
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Bakker B, Vaes RDW, Aberle MR, Welbers T, Hankemeier T, Rensen SS, Olde Damink SWM, Heeren RMA. Preparing ductal epithelial organoids for high-spatial-resolution molecular profiling using mass spectrometry imaging. Nat Protoc 2022; 17:962-979. [PMID: 35181767 DOI: 10.1038/s41596-021-00661-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022]
Abstract
Organoid culture systems are self-renewing, three-dimensional (3D) models derived from pluripotent stem cells, adult derived stem cells or cancer cells that recapitulate key molecular and structural characteristics of their tissue of origin. They generally form into hollow structures with apical-basolateral polarization. Mass spectrometry imaging (MSI) is a powerful analytical method for detecting a wide variety of molecules in a single experiment while retaining their spatiotemporal distribution. Here we describe a protocol for preparing organoids for MSI that (1) preserves the 3D morphological structure of hollow organoids, (2) retains the spatiotemporal distribution of a vast array of molecules (3) and enables accurate molecular identification based on tandem mass spectrometry. The protocol specifically focuses on the collection and embedding of the organoids in gelatin, and gives recommendations for MSI-specific sample preparation, data acquisition and molecular identification by tandem mass spectrometry. This method is applicable to a wide range of organoids from different origins, and takes 1 d from organoid collection to MSI data acquisition.
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Affiliation(s)
- Brenda Bakker
- Maastricht MultiModal Molecular Imaging institute (M4I), Maastricht University, Maastricht, the Netherlands
| | - Rianne D W Vaes
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Merel R Aberle
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Tessa Welbers
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Thomas Hankemeier
- Leiden Academic Center for Drug Research, Division of System Biomedicine and Pharmacology, Leiden University, Leiden, the Netherlands
| | - Sander S Rensen
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Steven W M Olde Damink
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands.,Department of General, Visceral and Transplant Surgery, University Hospital Aachen, Aachen, Germany
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging institute (M4I), Maastricht University, Maastricht, the Netherlands.
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Hosseinkhani F, Huang L, Dubbelman AC, Guled F, Harms AC, Hankemeier T. Systematic Evaluation of HILIC Stationary Phases for Global Metabolomics of Human Plasma. Metabolites 2022; 12:metabo12020165. [PMID: 35208239 PMCID: PMC8875576 DOI: 10.3390/metabo12020165] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
Polar hydrophilic metabolites have been identified as important actors in many biochemical pathways. Despite continuous improvement and refinement of hydrophilic interaction liquid chromatography (HILIC) platforms, its application in global polar metabolomics has been underutilized. In this study, we aimed to systematically evaluate polar stationary phases for untargeted metabolomics by using HILIC columns (neutral and zwitterionic) that have been exploited widely in targeted approaches. To do so, high-resolution mass spectrometry was applied to thoroughly investigate selectivity, repeatability and matrix effect at three pH conditions for 9 classes of polar compounds using 54 authentic standards and plasma matrix. The column performance for utilization in untargeted metabolomics was assessed using plasma samples with diverse phenotypes. Our results indicate that the ZIC-c HILIC column operated at neutral pH exhibited several advantages, including superior performance for different classes of compounds, better isomer separation, repeatability and high metabolic coverage. Regardless of the column type, the retention of inorganic ions in plasma leads to extensive adduct formation and co-elution with analytes, which results in ion-suppression as part of the overall plasma matrix effect. In ZIC-c HILIC, the sodium chloride ion effect was particularly observed for amino acids and amine classes. Successful performance of HILIC for separation of plasma samples with different phenotypes highlights this mode of separation as a valuable approach in global profiling of plasma sample and discovering the metabolic changes associated with health and disease.
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de Jong LM, Zhang Z, den Hartog Y, Sijsenaar TJP, Martins Cardoso R, Manson ML, Hankemeier T, Lindenburg PW, Salvatori DCF, Van Eck M, Hoekstra M. PRMT3 inhibitor SGC707 reduces triglyceride levels and induces pruritus in Western-type diet-fed LDL receptor knockout mice. Sci Rep 2022; 12:483. [PMID: 35013582 PMCID: PMC8748717 DOI: 10.1038/s41598-021-04524-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/20/2021] [Indexed: 11/29/2022] Open
Abstract
Protein arginine methyltransferase 3 (PRMT3) is a co-activator of liver X receptor capable of selectively modulating hepatic triglyceride synthesis. Here we investigated whether pharmacological PRMT3 inhibition can diminish the hepatic steatosis extent and lower plasma lipid levels and atherosclerosis susceptibility. Hereto, male hyperlipidemic low-density lipoprotein receptor knockout mice were fed an atherogenic Western-type diet and injected 3 times per week intraperitoneally with PRMT3 inhibitor SGC707 or solvent control. Three weeks into the study, SGC707-treated mice developed severe pruritus and scratching-associated skin lesions, leading to early study termination. SGC707-treated mice exhibited 50% lower liver triglyceride stores as well as 32% lower plasma triglyceride levels. Atherosclerotic lesions were virtually absent in all experimental mice. Plasma metabolite analysis revealed that levels of taurine-conjugated bile acids were ~ threefold increased (P < 0.001) in response to SGC707 treatment, which was paralleled by systemically higher bile acid receptor TGR5 signalling. In conclusion, we have shown that SGC707 treatment reduces hepatic steatosis and plasma triglyceride levels and induces pruritus in Western-type diet-fed LDL receptor knockout mice. These findings suggest that pharmacological PRMT3 inhibition can serve as therapeutic approach to treat non-alcoholic fatty liver disease and dyslipidemia/atherosclerosis, when unwanted effects on cholesterol and bile acid metabolism can be effectively tackled.
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Affiliation(s)
- Laura M de Jong
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Gorlaeus Laboratories, 2333CC, Leiden, The Netherlands
| | - Zhengzheng Zhang
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Yvette den Hartog
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Gorlaeus Laboratories, 2333CC, Leiden, The Netherlands
| | - Timothy J P Sijsenaar
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Gorlaeus Laboratories, 2333CC, Leiden, The Netherlands
| | - Renata Martins Cardoso
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Gorlaeus Laboratories, 2333CC, Leiden, The Netherlands
| | - Martijn L Manson
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Gorlaeus Laboratories, 2333CC, Leiden, The Netherlands
| | - Thomas Hankemeier
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Peter W Lindenburg
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.,Research Group Metabolomics, Leiden Center for Applied Bioscience, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Daniela C F Salvatori
- Central Laboratory Animal Facility, Leiden University Medical Center, Leiden, The Netherlands.,Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Miranda Van Eck
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Gorlaeus Laboratories, 2333CC, Leiden, The Netherlands
| | - Menno Hoekstra
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Gorlaeus Laboratories, 2333CC, Leiden, The Netherlands.
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43
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Ronde E, Frerichs NM, Brantenaar S, El Manouni El Hassani S, Wicaksono AN, Covington JA, De Boer NKH, De Meij TG, Hankemeier T, Reiss IKM, Schoenmakers S. Detection of spontaneous preterm birth by maternal urinary volatile organic compound analysis: A prospective cohort study. Front Pediatr 2022; 10:1063248. [PMID: 36578660 PMCID: PMC9791099 DOI: 10.3389/fped.2022.1063248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Accurate prediction of preterm birth is currently challenging, resulting in unnecessary maternal hospital admittance and fetal overexposure to antenatal corticosteroids. Novel biomarkers like volatile organic compounds (VOCs) hold potential for predictive, bed-side clinical applicability. In a proof of principle study, we aimed to assess the predictive potential of urinary volatile organic compounds in the identification of pregnant women at risk for preterm birth. Urine samples of women with a high risk for preterm birth (≧24 + 0 until 36 + 6 weeks) were collected prospectively and analyzed for VOCs using gas chromatography coupled with an ion mobility spectrometer (GS-IMS). Urinary VOCs of women delivering preterm were compared with urine samples of women with suspicion of preterm birth collected at the same gestation period but delivering at term. Additionally, the results were also interpreted in combination with patient characteristics, such as physical examination at admission, microbial cultures, and placental pathology. In our cohort, we found that urinary VOCs of women admitted for imminent preterm birth were not significantly different in the overall group of women delivering preterm vs. term. However, urinary VOCs of women admitted for imminent preterm birth and delivering between 28 + 0 until 36 + 6 weeks compared to women with a high risk for preterm birth during the same gestation period and eventually delivering at term (>37 + 0 weeks) differed significantly (area under the curve: 0.70). In addition, based on the same urinary VOCs, we could identify women with a confirmed chorioamnionitis (area under the curve: 0.72) and urinary tract infection (area under the curve: 0.97). In conclusion, urinary VOCs hold potential for non-invasive, bedside prediction of preterm birth and on the spot identification of intra-uterine infection and urinary tract infections. We suggest these observations are further explored in larger populations.
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Affiliation(s)
- Emma Ronde
- Division of Obstetrics and Prenatal Diagnosis, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Nina M Frerichs
- Department of Pediatric Gastroenterology, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Shauni Brantenaar
- Division of Obstetrics and Prenatal Diagnosis, Erasmus University Medical Centre, Rotterdam, Netherlands
| | | | | | - James A Covington
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Nanne K H De Boer
- Department of Pediatric Gastroenterology, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Tim G De Meij
- Department of Pediatric Gastroenterology, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Irwin K M Reiss
- Department of Pediatrics, Division of Neonatology, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Sam Schoenmakers
- Division of Obstetrics and Prenatal Diagnosis, Erasmus University Medical Centre, Rotterdam, Netherlands
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44
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Jurado‐Fasoli L, Di X, Kohler I, Osuna‐Prieto FJ, Hankemeier T, Krekels E, Harms AC, Yang W, Garcia‐Lario JV, Fernández‐Veledo S, Ruiz JR, Rensen PCN, Martinez‐Tellez B. Omega-6 and omega-3 oxylipins as potential markers of cardiometabolic risk in young adults. Obesity (Silver Spring) 2022; 30:50-61. [PMID: 34898010 PMCID: PMC9299871 DOI: 10.1002/oby.23282] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/29/2021] [Accepted: 08/04/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Omega-6 and omega-3 oxylipins are known to play a role in inflammation and cardiometabolic diseases in preclinical models. The associations between plasma levels of omega-6 and omega-3 polyunsaturated fatty acid-derived oxylipins and body composition and cardiometabolic risk factors in young adults were assessed. METHODS Body composition, brown adipose tissue, traditional serum cardiometabolic risk factors, inflammatory markers, and a panel of 83 oxylipins were analyzed in 133 young adults (age 22.1[SD 2.2] years, 67% women). RESULTS Plasma levels of four omega-6 oxylipins (15-HeTrE, 5-HETE, 14,15-EpETrE, and the oxidative stress-derived 8,12-iso-iPF2α -VI) correlated positively with adiposity, prevalence of metabolic syndrome, fatty liver index, and homeostatic model assessment of insulin resistance index and lipid parameters. By contrast, the plasma levels of three omega-3 oxylipins (14,15-DiHETE, 17,18-DiHETE, and 19,20-DiHDPA) were negatively correlated with adiposity, prevalence of metabolic syndrome, fatty liver index, homeostatic model assessment of insulin resistance index, and lipid parameters. The panel of seven oxylipins predicted adiposity better than traditional inflammatory markers such as interferon gamma or tumor necrosis factor-alpha. Pathway analyses revealed that individuals with obesity had higher plasma levels of omega-6 and lower plasma levels of omega-3 oxylipins than normal-weight individuals. CONCLUSION Plasma levels of seven omega-6 and omega-3 oxylipins may have utility as early markers of cardiometabolic risk in young adults.
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Affiliation(s)
- Lucas Jurado‐Fasoli
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH)Department of Physical Education and SportsFaculty of Sport SciencesSport and Health University Research Institute (iMUDS)University of GranadaGranadaSpain
| | - Xinyu Di
- Department of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenthe Netherlands
| | - Isabelle Kohler
- Division of BioAnalytical ChemistryVrije Universiteit AmsterdamAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdamthe Netherlands
- Center for Analytical Sciences AmsterdamAmsterdamthe Netherlands
| | - Francisco J. Osuna‐Prieto
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH)Department of Physical Education and SportsFaculty of Sport SciencesSport and Health University Research Institute (iMUDS)University of GranadaGranadaSpain
- Department of Analytical ChemistryUniversity of GranadaGranadaSpain
- Research and Development of Functional Food Centre (CIDAF)GranadaSpain
| | - Thomas Hankemeier
- Department of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenthe Netherlands
| | - Elke Krekels
- Department of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenthe Netherlands
| | - Amy C. Harms
- Department of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenthe Netherlands
| | - Wei Yang
- Department of Systems Biomedicine and PharmacologyLeiden Academic Centre for Drug Research (LACDR)Leiden UniversityLeidenthe Netherlands
| | | | - Sonia Fernández‐Veledo
- Departament of Endocrinology and Nutrition and Research UnitUniversity Hospital of Tarragona Joan XXIII‐Institut d ´Investigació Sanitària Pere Virgili (IISPV)TarragonaSpain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)‐Instituto de Salud Carlos IIIMadridSpain
| | - Jonatan R. Ruiz
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH)Department of Physical Education and SportsFaculty of Sport SciencesSport and Health University Research Institute (iMUDS)University of GranadaGranadaSpain
| | - Patrick C. N. Rensen
- Department of MedicineDivision of Endocrinology, and Einthoven Laboratory for Experimental Vascular MedicineLeiden University Medical Centrethe Netherlands
| | - Borja Martinez‐Tellez
- PROmoting FITness and Health through Physical Activity Research Group (PROFITH)Department of Physical Education and SportsFaculty of Sport SciencesSport and Health University Research Institute (iMUDS)University of GranadaGranadaSpain
- Department of MedicineDivision of Endocrinology, and Einthoven Laboratory for Experimental Vascular MedicineLeiden University Medical Centrethe Netherlands
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45
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He B, Zhang W, Guled F, Harms A, Ramautar R, Hankemeier T. Analytical techniques for biomass-restricted metabolomics: An overview of the state-of-the-art. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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46
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Batra R, Heinken A, Karu N, Arnold M, Kastenmüller G, Hankemeier T, Bennett DA, Knight R, Krumsiek J, Thiele I, Kaddurah‐Daouk RF. Mapping the human brain metabolome and influences of gut microbiome. Alzheimers Dement 2021. [DOI: 10.1002/alz.056270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Almut Heinken
- National University of Ireland Galway Galway Ireland
| | - Naama Karu
- Leiden Academic Centre for Drug Research Leiden Netherlands
| | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- German Center for Diabetes Research (DZD) Neuherberg Germany
- Duke University Durham NC USA
| | | | | | | | - Rob Knight
- University of California at San Diego San Diego CA USA
| | | | - Ines Thiele
- National University of Ireland Galway Ireland
| | - Rima F. Kaddurah‐Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- Duke Institute for Brain Sciences, Duke University Durham NC USA
- Department of Medicine, Duke University Durham NC USA
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47
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Ahmad S, Arnold M, Hankemeier T, Ghanbari M, Uitterlinden AG, Kraaij R, Van Duijn CM, Kaddurah‐Daouk RF, Kastenmüller G, Ikram MA. Gut microbiome‐related metabolites in plasma are associated with general cognition. Alzheimers Dement 2021. [DOI: 10.1002/alz.056142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Center Rotterdam Netherlands
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research Leiden Netherlands
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research Leiden Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus Medical Centre Rotterdam Netherlands
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam Netherlands
| | - Cornelia M. Van Duijn
- Department of Epidemiology, Erasmus Medical Center Rotterdam Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford United Kingdom
| | - Rima F. Kaddurah‐Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- Duke Institute for Brain Sciences, Duke University Durham NC USA
- Department of Medicine, Duke University Durham NC USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
- German Center for Diabetes Research (DZD) Neuherberg Germany
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center Rotterdam Netherlands
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48
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Kanhai KMS, Goulooze SC, van der Grond J, Harms AC, Hankemeier T, Verma A, Dent G, Chavez J, Meijering H, Groeneveld GJ. Kinetics of myelin breakdown products: A labeling study in patients with progressive multiple sclerosis. Clin Transl Sci 2021; 15:638-648. [PMID: 34799987 PMCID: PMC8932820 DOI: 10.1111/cts.13181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 05/10/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
The majority of disease modifying therapies for multiple sclerosis (MS) reduce inflammation, but do no’t target remyelination. Development of remyelinating therapies will benefit from a method to quantify myelin kinetics in patients with MS. We labeled myelin in vivo with deuterium, and modeled kinetics of myelin breakdown products β‐galactosylceramide (β‐GalC) and N‐Octadecanoyl‐sulfatide (NO‐Sulf). Five patients with MS received 120 ml 70% D2O daily for 70 days and were compared with six healthy subjects who previously received the same procedure. Mass spectrometry and compartmental modeling were used to quantify the turnover rate of β‐GalC and NO‐Sulf in cerebrospinal fluid (CSF). Turnover rate constants of the fractions of β‐GalC and NO‐Sulf with non‐negligible turnover were 0.00186 and 0.00714, respectively, in both healthy subjects and patients with MS. The turnover half‐life of β‐GalC and NO‐Sulf was calculated as 373 days and 96.5 days, respectively. The effect of MS on the NO‐Sulf (49.4% lower fraction with non‐negligible turnover) was more pronounced compared to the effect on β‐GalC turnover (18.3% lower fraction with non‐negligible turnover). Kinetics of myelin breakdown products in the CSF are different in patients with MS compared with healthy subjects. This may be caused by slower myelin production in these patients, by a higher level of degradation of a more stable component of myelin, or, most likely, by a combination of these two processes. Labeling myelin breakdown products is a useful method that can be used to quantify myelin turnover in patients with progressive MS and can therefore be used in proof‐of‐concept studies with remyelination therapies.
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Affiliation(s)
- Kawita M S Kanhai
- Centre for Human Drug Research, Leiden, The Netherlands.,Prothya Biosolutions, Amsterdam, The Netherlands
| | - Sebastiaan C Goulooze
- Centre for Human Drug Research, Leiden, The Netherlands.,Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | | | - Amy C Harms
- Prothya Biosolutions, Amsterdam, The Netherlands.,Radiology Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Hankemeier
- Department of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.,Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Ajay Verma
- Yumanity Pharmaceuticals, Boston, Massachusetts, USA
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49
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Vormann MK, Tool LM, Ohbuchi M, Gijzen L, van Vught R, Hankemeier T, Kiyonaga F, Kawabe T, Goto T, Fujimori A, Vulto P, Lanz HL, Tetsuka K. Modelling and Prevention of Acute Kidney Injury through Ischemia and Reperfusion in a Combined Human Renal Proximal Tubule/Blood Vessel-on-a-Chip. Kidney360 2021; 3:217-231. [PMID: 35373131 PMCID: PMC8967632 DOI: 10.34067/kid.0003622021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/29/2021] [Indexed: 01/10/2023]
Abstract
Background Renal ischemia/reperfusion injury (rIRI) is one of the major causes of AKI. Although animal models are suitable for investigating systemic symptoms of AKI, they are limited in translatability. Human in vitro models are crucial in giving mechanistic insights into rIRI; however, they miss out on crucial aspects such as reperfusion injury and the multitissue aspect of AKI. Methods We advanced the current renal proximal tubule-on-a-chip model to a coculture model with a perfused endothelial vessel separated by an extracellular matrix. The coculture was characterized for its three-dimensional structure, protein expression, and response to nephrotoxins. Then, rIRI was captured through control of oxygen levels, nutrient availability, and perfusion flow settings. Injury was quantified through morphologic assessment, caspase-3/7 activation, and cell viability. Results The combination of low oxygen, reduced glucose, and interrupted flow was potent to disturb the proximal tubules. This effect was strongly amplified upon reperfusion. Endothelial vessels were less sensitive to the ischemia-reperfusion parameters. Adenosine treatment showed a protective effect on the disruption of the epithelium and on the caspase-3/7 activation. Conclusions A human in vitro rIRI model was developed using a coculture of a proximal tubule and blood vessel on-a-chip, which was used to characterize the renoprotective effect of adenosine. The robustness of the model and assays in combination with the throughput of the platform make it ideal to advance pathophysiological research and enable the development of novel therapeutic modalities.
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Affiliation(s)
| | | | - Masato Ohbuchi
- Analysis and Pharmacokinetics Research Labs, Astellas Pharma, Inc., Ibaraki, Japan
| | | | | | | | - Fumiko Kiyonaga
- Innovation and Incubation Research Labs, Astellas Pharma, Inc., Ibaraki, Japan
| | | | - Takayuki Goto
- Modality Research Labs, Astellas Pharma, Inc., Ibaraki, Japan
| | - Akira Fujimori
- Research Portfolio Planning, Astellas Pharma, Inc., Ibaraki, Japan
| | | | | | - Kazuhiro Tetsuka
- Analysis and Pharmacokinetics Research Labs, Astellas Pharma, Inc., Ibaraki, Japan
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50
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Wouters B, Currivan S, Abdulhussain N, Hankemeier T, Schoenmakers P. Immobilized-enzyme reactors integrated into analytical platforms: Recent advances and challenges. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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