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Vandenbosch M, van Hove ERA, Mohren R, Vermeulen I, Dijkman H, Heeren RMA, Leonards PEG, Hughes S. Combined matrix-assisted laser desorption/ionisation-mass spectrometry imaging with liquid chromatography-tandem mass spectrometry for observing spatial distribution of lipids in whole Caenorhabditis elegans. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9850. [PMID: 39034751 DOI: 10.1002/rcm.9850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 07/23/2024]
Abstract
RATIONALE Matrix-assisted laser desorption/ionisation-mass spectrometry imaging (MALDI-MSI) is a powerful label-free technique for biomolecule detection (e.g., lipids), within tissue sections across various biological species. However, despite its utility in many applications, the nematode Caenorhabditis elegans is not routinely used in combination with MALDI-MSI. The lack of studies exploring spatial distribution of biomolecules in nematodes is likely due to challenges with sample preparation. METHODS This study developed a sample preparation method for whole intact nematodes, evaluated using cryosectioning of nematodes embedded in a 10% gelatine solution to obtain longitudinal cross sections. The slices were then subjected to MALDI-MSI, using a RapifleX Tissuetyper in positive and negative polarities. Samples were also prepared for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis using an Exploris 480 coupled to a HPLC Vanquish system to confirm the MALDI-MSI results. RESULTS An optimised embedding method was developed for longitudinal cross-sectioning of individual worms. To obtain longitudinal cross sections, nematodes were frozen at -80°C so that all worms were rod shaped. Then, the samples were defrosted and transferred to a 10% gelatine matrix in a cryomold; the worms aligned, and the whole cryomold submerged in liquid nitrogen. Using MALDI-MSI, we were able to observe the distribution of lipids within C. elegans, with clear differences in their spatial distribution at a resolution of 5 μm. To confirm the lipids from MALDI-MSI, age-matched nematodes were subjected to LC-MS/MS. Here, 520 lipids were identified using LC-MS/MS, indicating overlap with MALDI-MSI data. CONCLUSIONS This optimised sample preparation technique enabled (un)targeted analysis of spatially distributed lipids within individual nematodes. The possibility to detect other biomolecules using this method thus laid the basis for prospective preclinical and toxicological studies on C. elegans.
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Affiliation(s)
- Michiel Vandenbosch
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Erika R Amstalden van Hove
- Amsterdam Institute for Life and Environment, Chemistry for Environment and Health, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ronny Mohren
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Isabeau Vermeulen
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Henry Dijkman
- HAN University of Applied Sciences, Nijmegen, The Netherlands
| | - Ron M A Heeren
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, Maastricht, The Netherlands
| | - Pim E G Leonards
- Amsterdam Institute for Life and Environment, Chemistry for Environment and Health, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Samantha Hughes
- Amsterdam Institute for Life and Environment, Environmental Health and Toxicology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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2
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Nguyen BT, Le QV, Ahn J, Nguyen KA, Nguyen HT, Kang JS, Long NP, Kim HM. Omics analysis unveils changes in the metabolome and lipidome of Caenorhabditis elegans upon polydopamine exposure. J Pharm Biomed Anal 2024; 244:116126. [PMID: 38581931 DOI: 10.1016/j.jpba.2024.116126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Polydopamine (PDA) is an insoluble biopolymer with a dark brown-black color that forms through the autoxidation of dopamine. Because of its outstanding biocompatibility and durability, PDA holds enormous promise for various applications, both in the biomedical and non-medical domains. To ensure human safety, protect health, and minimize environmental impacts, the assessment of PDA toxicity is important. In this study, metabolomics and lipidomics assessed the impact of acute PDA exposure on Caenorhabditis elegans (C. elegans). The findings revealed a pronounced perturbation in the metabolome and lipidome of C. elegans at the L4 stage following 24 hours of exposure to 100 µg/mL PDA. The changes in lipid composition varied based on lipid classes. Increased lipid classes included lysophosphatidylethanolamine, triacylglycerides, and fatty acids, while decreased species involved in several sub-classes of glycerophospholipids and sphingolipids. Besides, we detected 37 significantly affected metabolites in the positive and 8 in the negative ion modes due to exposure to PDA in C. elegans. The metabolites most impacted by PDA exposure were associated with purine metabolism, biosynthesis of valine, leucine, and isoleucine; aminoacyl-tRNA biosynthesis; and cysteine and methionine metabolism, along with pantothenate and CoA biosynthesis; the citrate cycle (TCA cycle); and beta-alanine metabolism. In conclusion, PDA exposure may intricately influence the metabolome and lipidome of C. elegans. The combined application of metabolomics and lipidomics offers additional insights into the metabolic perturbations involved in PDA-induced biological effects and presents potential biomarkers for the assessment of PDA safety.
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Affiliation(s)
- Bao Tan Nguyen
- College of Pharmacy, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Quoc-Viet Le
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Jeongjun Ahn
- College of Pharmacy, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ky Anh Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Huy Truong Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Jong Seong Kang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Republic of Korea.
| | - Hyung Min Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Republic of Korea.
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3
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Nollet EE, Schuldt M, Sequeira V, Binek A, Pham TV, Schoonvelde SA, Jansen M, Schomakers BV, van Weeghel M, Vaz FM, Houtkooper RH, Van Eyk JE, Jimenez CR, Michels M, Bedi KC, Margulies KB, dos Remedios CG, Kuster DW, van der Velden J. Integrating Clinical Phenotype With Multiomics Analyses of Human Cardiac Tissue Unveils Divergent Metabolic Remodeling in Genotype-Positive and Genotype-Negative Patients With Hypertrophic Cardiomyopathy. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004369. [PMID: 38853772 PMCID: PMC11188634 DOI: 10.1161/circgen.123.004369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/31/2024] [Indexed: 06/11/2024]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is caused by sarcomere gene mutations (genotype-positive HCM) in ≈50% of patients and occurs in the absence of mutations (genotype-negative HCM) in the other half of patients. We explored how alterations in the metabolomic and lipidomic landscape are involved in cardiac remodeling in both patient groups. METHODS We performed proteomics, metabolomics, and lipidomics on myectomy samples (genotype-positive N=19; genotype-negative N=22; and genotype unknown N=6) from clinically well-phenotyped patients with HCM and on cardiac tissue samples from sex- and age-matched and body mass index-matched nonfailing donors (N=20). These data sets were integrated to comprehensively map changes in lipid-handling and energy metabolism pathways. By linking metabolomic and lipidomic data to variability in clinical data, we explored patient group-specific associations between cardiac and metabolic remodeling. RESULTS HCM myectomy samples exhibited (1) increased glucose and glycogen metabolism, (2) downregulation of fatty acid oxidation, and (3) reduced ceramide formation and lipid storage. In genotype-negative patients, septal hypertrophy and diastolic dysfunction correlated with lowering of acylcarnitines, redox metabolites, amino acids, pentose phosphate pathway intermediates, purines, and pyrimidines. In contrast, redox metabolites, amino acids, pentose phosphate pathway intermediates, purines, and pyrimidines were positively associated with septal hypertrophy and diastolic impairment in genotype-positive patients. CONCLUSIONS We provide novel insights into both general and genotype-specific metabolic changes in HCM. Distinct metabolic alterations underlie cardiac disease progression in genotype-negative and genotype-positive patients with HCM.
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Affiliation(s)
- Edgar E. Nollet
- Department of Physiology (E.E.N., M.S., D.W.D.K., J.v.d.V.), Amsterdam UMC, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, the Netherlands (E.E.N., M.S., D.W.D.K., J.v.d.V.)
| | - Maike Schuldt
- Department of Physiology (E.E.N., M.S., D.W.D.K., J.v.d.V.), Amsterdam UMC, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, the Netherlands (E.E.N., M.S., D.W.D.K., J.v.d.V.)
| | - Vasco Sequeira
- Department of Translational Science Universitätsklinikum, Deutsches Zentrum für Herzinsuffizienz, Würzburg, Germany (V.S.)
| | - Aleksandra Binek
- Advanced Clinical Biosystems Research Institute (A.B., J.E.V.E.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Thang V. Pham
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, OncoProteomics Laboratory (T.V.P., C.R.J.), Amsterdam UMC, the Netherlands
| | | | - Mark Jansen
- Division of Genetics and Department of Cardiology, UMC Utrecht, the Netherlands (M.J.)
| | - Bauke V. Schomakers
- Laboratory Genetic Metabolic Diseases (B.V.S., M.v.W., F.M.V., R.H.H.), Amsterdam UMC, the Netherlands
- Core Facility Metabolomics (B.V.S., M.v.W., F.M.V.), Amsterdam UMC, the Netherlands
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases (B.V.S., M.v.W., F.M.V., R.H.H.), Amsterdam UMC, the Netherlands
- Core Facility Metabolomics (B.V.S., M.v.W., F.M.V.), Amsterdam UMC, the Netherlands
| | - Fred M. Vaz
- Laboratory Genetic Metabolic Diseases (B.V.S., M.v.W., F.M.V., R.H.H.), Amsterdam UMC, the Netherlands
- Core Facility Metabolomics (B.V.S., M.v.W., F.M.V.), Amsterdam UMC, the Netherlands
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases (B.V.S., M.v.W., F.M.V., R.H.H.), Amsterdam UMC, the Netherlands
- Emma Center for Personalized Medicine (R.H.H.), Amsterdam UMC, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, the Netherlands (R.H.H.)
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute (A.B., J.E.V.E.), Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Smidt Heart Institute (J.E.V.E.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Connie R. Jimenez
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, OncoProteomics Laboratory (T.V.P., C.R.J.), Amsterdam UMC, the Netherlands
| | - Michelle Michels
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands (S.A.C.S., M.M.)
| | - Kenneth C. Bedi
- Cardiovascular Institute, Perelman School of Medicine, Philadelphia, PA (K.C.B., K.B.M.)
| | - Kenneth B. Margulies
- Cardiovascular Institute, Perelman School of Medicine, Philadelphia, PA (K.C.B., K.B.M.)
| | - Cristobal G. dos Remedios
- Sydney Heart Bank, Discipline of Anatomy, Bosch Institute, University of Sydney, NSW, Australia (C.G.d.R.)
| | - Diederik W.D. Kuster
- Department of Physiology (E.E.N., M.S., D.W.D.K., J.v.d.V.), Amsterdam UMC, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, the Netherlands (E.E.N., M.S., D.W.D.K., J.v.d.V.)
| | - Jolanda van der Velden
- Department of Physiology (E.E.N., M.S., D.W.D.K., J.v.d.V.), Amsterdam UMC, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, the Netherlands (E.E.N., M.S., D.W.D.K., J.v.d.V.)
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4
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Janssens GE, Molenaars M, Herzog K, Grevendonk L, Remie CME, Vervaart MAT, Elfrink HL, Wever EJM, Schomakers BV, Denis SW, Waterham HR, Pras-Raves ML, van Weeghel M, van Kampen AHC, Tammaro A, Butter LM, van der Rijt S, Florquin S, Jongejan A, Moerland PD, Hoeks J, Schrauwen P, Vaz FM, Houtkooper RH. A conserved complex lipid signature marks human muscle aging and responds to short-term exercise. NATURE AGING 2024; 4:681-693. [PMID: 38609524 DOI: 10.1038/s43587-024-00595-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2024] [Indexed: 04/14/2024]
Abstract
Studies in preclinical models suggest that complex lipids, such as phospholipids, play a role in the regulation of longevity. However, identification of universally conserved complex lipid changes that occur during aging, and how these respond to interventions, is lacking. Here, to comprehensively map how complex lipids change during aging, we profiled ten tissues in young versus aged mice using a lipidomics platform. Strikingly, from >1,200 unique lipids, we found a tissue-wide accumulation of bis(monoacylglycero)phosphate (BMP) during mouse aging. To investigate translational value, we assessed muscle tissue of young and older people, and found a similar marked BMP accumulation in the human aging lipidome. Furthermore, we found that a healthy-aging intervention consisting of moderate-to-vigorous exercise was able to lower BMP levels in postmenopausal female research participants. Our work implicates complex lipid biology as central to aging, identifying a conserved aging lipid signature of BMP accumulation that is modifiable upon a short-term healthy-aging intervention.
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Affiliation(s)
- Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands.
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
| | - Katharina Herzog
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
| | - Lotte Grevendonk
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Carlijn M E Remie
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Martin A T Vervaart
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Hyung L Elfrink
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric J M Wever
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Bauke V Schomakers
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Simone W Denis
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
| | - Mia L Pras-Raves
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Antoine H C van Kampen
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Methodology, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - Alessandra Tammaro
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Amsterdam, the Netherlands
| | - Loes M Butter
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Amsterdam, the Netherlands
| | - Sanne van der Rijt
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
| | - Sandrine Florquin
- Pathology Department, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Methodology, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - Perry D Moerland
- Epidemiology and Data Science, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Methodology, Amsterdam, the Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, the Netherlands
| | - Joris Hoeks
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Patrick Schrauwen
- Department of Nutrition and Human Movement Sciences, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
- TI Food and Nutrition, Wageningen, the Netherlands
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands.
- Core Facility Metabolomics, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC location, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam, the Netherlands.
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands.
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5
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Harber KJ, Neele AE, van Roomen CP, Gijbels MJ, Beckers L, Toom MD, Schomakers BV, Heister DA, Willemsen L, Griffith GR, de Goede KE, van Dierendonck XA, Reiche ME, Poli A, L-H Mogensen F, Michelucci A, Verberk SG, de Vries H, van Weeghel M, Van den Bossche J, de Winther MP. Targeting the ACOD1-itaconate axis stabilizes atherosclerotic plaques. Redox Biol 2024; 70:103054. [PMID: 38309122 PMCID: PMC10848031 DOI: 10.1016/j.redox.2024.103054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/05/2024] Open
Abstract
Inflammatory macrophages are key drivers of atherosclerosis that can induce rupture-prone vulnerable plaques. Skewing the plaque macrophage population towards a more protective phenotype and reducing the occurrence of clinical events is thought to be a promising method of treating atherosclerotic patients. In the current study, we investigate the immunomodulatory properties of itaconate, an immunometabolite derived from the TCA cycle intermediate cis-aconitate and synthesised by the enzyme Aconitate Decarboxylase 1 (ACOD1, also known as IRG1), in the context of atherosclerosis. Ldlr-/- atherogenic mice transplanted with Acod1-/- bone marrow displayed a more stable plaque phenotype with smaller necrotic cores and showed increased recruitment of monocytes to the vessel intima. Macrophages from Acod1-/- mice contained more lipids whilst also displaying reduced induction of apoptosis. Using multi-omics approaches, we identify a metabolic shift towards purine metabolism, in addition to an altered glycolytic flux towards production of glycerol for triglyceride synthesis. Overall, our data highlight the potential of therapeutically blocking ACOD1 with the aim of stabilizing atherosclerotic plaques.
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Affiliation(s)
- Karl J Harber
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, the Netherlands; Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands; Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands
| | - Annette E Neele
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, the Netherlands; Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands
| | - Cindy Paa van Roomen
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Marion Jj Gijbels
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands; Department of Pathology, CARIM, Cardiovascular Research Institute Maastricht, GROW-School for Oncology and Developmental Biology, Maastricht UMC, University of Maastricht, 6229 HX, Maastricht, the Netherlands
| | - Linda Beckers
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Myrthe den Toom
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Bauke V Schomakers
- Department of Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Daan Af Heister
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands
| | - Lisa Willemsen
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, the Netherlands; Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands
| | - Guillermo R Griffith
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands
| | - Kyra E de Goede
- Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands; Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, the Netherlands
| | - Xanthe Amh van Dierendonck
- Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands; Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, the Netherlands
| | - Myrthe E Reiche
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, the Netherlands; Department of Medical Cell Biology, Uppsala University, 75236, Uppsala, Sweden
| | - Aurélie Poli
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, 6A Rue Nicolas-Ernest Barblé, L-1210, Luxembourg, Luxembourg
| | - Frida L-H Mogensen
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, 6A Rue Nicolas-Ernest Barblé, L-1210, Luxembourg, Luxembourg
| | - Alessandro Michelucci
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, 6A Rue Nicolas-Ernest Barblé, L-1210, Luxembourg, Luxembourg
| | - Sanne Gs Verberk
- Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, the Netherlands; Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands; Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands
| | - Helga de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Michel van Weeghel
- Department of Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jan Van den Bossche
- Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, the Netherlands; Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands; Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, the Netherlands.
| | - Menno Pj de Winther
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences (ACS), Atherosclerosis & Ischemic Syndromes, Amsterdam UMC, the Netherlands; Amsterdam Institute for Infection and Immunity (AII), Inflammatory Diseases, Amsterdam UMC, the Netherlands.
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6
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Christen M, Oevermann A, Rupp S, Vaz FM, Wever EJM, Braus BK, Jagannathan V, Kehl A, Hytönen MK, Lohi H, Leeb T. PCYT2 deficiency in Saarlooswolfdogs with progressive retinal, central, and peripheral neurodegeneration. Mol Genet Metab 2024; 141:108149. [PMID: 38277988 DOI: 10.1016/j.ymgme.2024.108149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
We investigated a syndromic disease comprising blindness and neurodegeneration in 11 Saarlooswolfdogs. Clinical signs involved early adult onset retinal degeneration and adult-onset neurological deficits including gait abnormalities, hind limb weakness, tremors, ataxia, cognitive decline and behavioral changes such as aggression towards the owner. Histopathology in one affected dog demonstrated cataract, retinal degeneration, central and peripheral axonal degeneration, and severe astroglial hypertrophy and hyperplasia in the central nervous system. Pedigrees indicated autosomal recessive inheritance. We mapped the suspected genetic defect to a 15 Mb critical interval by combined linkage and autozygosity analysis. Whole genome sequencing revealed a private homozygous missense variant, PCYT2:c.4A>G, predicted to change the second amino acid of the encoded ethanolamine-phosphate cytidylyltransferase 2, XP_038402224.1:(p.Ile2Val). Genotyping of additional Saarlooswolfdogs confirmed the homozygous genotype in all eleven affected dogs and demonstrated an allele frequency of 9.9% in the population. This experiment also identified three additional homozygous mutant young dogs without overt clinical signs. Subsequent examination of one of these dogs revealed early-stage progressive retinal atrophy (PRA) and expansion of subarachnoid CSF spaces in MRI. Dogs homozygous for the pathogenic variant showed ether lipid accumulation, confirming a functional PCYT2 deficiency. The clinical and metabolic phenotype in affected dogs shows some parallels with human patients, in whom PCYT2 variants lead to a rare form of spastic paraplegia or axonal motor and sensory polyneuropathy. Our results demonstrate that PCYT2:c.4A>G in dogs cause PCYT2 deficiency. This canine model with histopathologically documented retinal, central, and peripheral neurodegeneration further deepens the knowledge of PCYT2 deficiency.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Anna Oevermann
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Stefan Rupp
- Neurology Department, Tierklinik Hofheim, IVC Evidensia, Hofheim am Taunus 65719, Germany
| | - Frédéric M Vaz
- Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric J M Wever
- Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, University of Amsterdam, 1100 DE Amsterdam UMC, the Netherlands
| | - Barbara K Braus
- Ophthalmology Department, Tierklinik Hofheim, IVC Evidensia, Hofheim am Taunus 65719, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Alexandra Kehl
- Laboklin GmbH & Co. KG, Steubenstraße 4, Bad Kissingen 97688, Germany; Comparative Experimental Pathology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki 00014, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland; Folkhälsan Research Center, Helsinki 00290, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki 00014, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland; Folkhälsan Research Center, Helsinki 00290, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland.
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7
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Schwantje M, Mosegaard S, Knottnerus SJG, van Klinken JB, Wanders RJ, van Lenthe H, Hermans J, IJlst L, Denis SW, Jaspers YRJ, Fuchs SA, Houtkooper RH, Ferdinandusse S, Vaz FM. Tracer-based lipidomics enables the discovery of disease-specific candidate biomarkers in mitochondrial β-oxidation disorders. FASEB J 2024; 38:e23478. [PMID: 38372965 DOI: 10.1096/fj.202302163r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/05/2024] [Accepted: 01/26/2024] [Indexed: 02/20/2024]
Abstract
Carnitine derivatives of disease-specific acyl-CoAs are the diagnostic hallmark for long-chain fatty acid β-oxidation disorders (lcFAOD), including carnitine shuttle deficiencies, very-long-chain acyl-CoA dehydrogenase deficiency (VLCADD), long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (LCHADD) and mitochondrial trifunctional protein deficiency (MPTD). The exact consequence of accumulating lcFAO-intermediates and their influence on cellular lipid homeostasis is, however, still unknown. To investigate the fate and cellular effects of the accumulating lcFAO-intermediates and to explore the presence of disease-specific markers, we used tracer-based lipidomics with deuterium-labeled oleic acid (D9-C18:1) in lcFAOD patient-derived fibroblasts. In line with previous studies, we observed a trend towards neutral lipid accumulation in lcFAOD. In addition, we detected a direct connection between the chain length and patterns of (un)saturation of accumulating acylcarnitines and the various enzyme deficiencies. Our results also identified two disease-specific candidate biomarkers. Lysophosphatidylcholine(14:1) (LPC(14:1)) was specifically increased in severe VLCADD compared to mild VLCADD and control samples. This was confirmed in plasma samples showing an inverse correlation with enzyme activity, which was better than the classic diagnostic marker C14:1-carnitine. The second candidate biomarker was an unknown lipid class, which we identified as S-(3-hydroxyacyl)cysteamines. We hypothesized that these were degradation products of the CoA moiety of accumulating 3-hydroxyacyl-CoAs. S-(3-hydroxyacyl)cysteamines were significantly increased in LCHADD compared to controls and other lcFAOD, including MTPD. Our findings suggest extensive alternative lipid metabolism in lcFAOD and confirm that lcFAOD accumulate neutral lipid species. In addition, we present two disease-specific candidate biomarkers for VLCADD and LCHADD, that may have significant relevance for disease diagnosis, prognosis, and monitoring.
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Affiliation(s)
- Marit Schwantje
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Signe Mosegaard
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, the Netherlands
| | - Suzan J G Knottnerus
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam, the Netherlands
| | - Jan Bert van Klinken
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Ronald J Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam, the Netherlands
| | - Henk van Lenthe
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jill Hermans
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam, the Netherlands
| | - Simone W Denis
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Yorrick R J Jaspers
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Sabine A Fuchs
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam, the Netherlands
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam, the Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, the Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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8
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Valdés A, Sánchez-Martínez JD, Gallego R, Ibáñez E, Herrero M, Cifuentes A. In vivo neuroprotective capacity of a Dunaliella salina extract - comprehensive transcriptomics and metabolomics study. NPJ Sci Food 2024; 8:4. [PMID: 38200022 PMCID: PMC10782027 DOI: 10.1038/s41538-023-00246-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
In this study, an exhaustive chemical characterization of a Dunaliella salina (DS) microalga extract obtained using supercritical fluids has been performed, and its neuroprotective capacity has been evaluated in vivo using an Alzheimer's disease (AD) transgenic model of Caenorhabditis elegans (strain CL4176). More than 350 compounds were annotated in the studied DS extract, with triacylglycerols, free fatty acids (FAs), carotenoids, apocarotenoids and glycerol being the most abundant. DS extract significantly protects C. elegans in a dose-dependent manner against Aβ-peptide paralysis toxicity, after 32 h, 53% of treated worms at 50 µg/mL were not paralyzed. This concentration was selected to further evaluate the transcriptomics and metabolomics changes after 26 h by using advanced analytical methodologies. The RNA-Seq data showed an alteration of 150 genes, mainly related to the stress and detoxification responses, and the retinol and lipid metabolism. The comprehensive metabolomics and lipidomics analyses allowed the identification of 793 intracellular metabolites, of which 69 were significantly altered compared to non-treated control animals. Among them, different unsaturated FAs, lysophosphatidylethanolamines, nucleosides, dipeptides and modified amino acids that have been previously reported as beneficial during AD progression, were assigned. These compounds could explain the neuroprotective capacity observed, thus, providing with new evidences of the protection mechanisms of this promising extract.
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Affiliation(s)
- Alberto Valdés
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC-UAM), Calle Nicolás Cabrera 9, 28049, Madrid, Spain.
| | - José David Sánchez-Martínez
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC-UAM), Calle Nicolás Cabrera 9, 28049, Madrid, Spain
| | - Rocío Gallego
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC-UAM), Calle Nicolás Cabrera 9, 28049, Madrid, Spain
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC-UAM), Calle Nicolás Cabrera 9, 28049, Madrid, Spain
| | - Miguel Herrero
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC-UAM), Calle Nicolás Cabrera 9, 28049, Madrid, Spain
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC-UAM), Calle Nicolás Cabrera 9, 28049, Madrid, Spain
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9
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Barros YVR, de Andrade AO, da Silva LPD, Pedroza LAL, Bezerra IC, Cavalcanti IDL, de Britto Lira Nogueira MC, Mousinho KC, Antoniolli AR, Alves LC, de Lima Filho JL, Moura AV, Rosini Silva ÁA, de Melo Porcari A, Gubert P. Bee Venom Toxic Effect on MDA-MB-231 Breast Cancer Cells and Caenorhabditis Elegans. Anticancer Agents Med Chem 2024; 24:798-811. [PMID: 38500290 DOI: 10.2174/0118715206291634240312062957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
INTRODUCTION Bee venom has therapeutics and pharmacological properties. Further toxicological studies on animal models are necessary due to the severe allergic reactions caused by this product. METHOD Here, Caenorhabditis elegans was used as an in vivo toxicity model, while breast cancer cells were used to evaluate the pharmacological benefits. The bee venom utilized in this research was collected from Apis mellifera species found in Northeast Brazil. The cytotoxicity caused by bee venom was measured by MTT assay on MDA-MB-231 and J774 A.1 cells during 24 - 72 hours of exposure. C. elegans at the L4 larval stage were exposed for three hours to M9 buffer or bee venom. Survival, behavioral parameters, reproduction, DAF-16 transcription factor translocation, the expression of superoxide dismutase (SOD), and metabolomics were analyzed. Bee venom suppressed the growth of MDA-MB-231 cancer cells and exhibited cytotoxic effects on macrophages. Also, decreased C. elegans survival impacted its behaviors by decreasing C. elegans feeding behavior, movement, and reproduction. RESULTS Bee venom did not increase the expression of SOD-3, but it enhanced DAF-16 translocation from the cytoplasm to the nucleus. C. elegans metabolites differed after bee venom exposure, primarily related to aminoacyl- tRNA biosynthesis, glycine, serine and threonine metabolism, and sphingolipid and purine metabolic pathways. Our findings indicate that exposure to bee venom resulted in harmful effects on the cells and animal models examined. CONCLUSION Thus, due to its potential toxic effect and induction of allergic reactions, using bee venom as a therapeutic approach has been limited. The development of controlled-release drug strategies to improve this natural product's efficacy and safety should be intensified.
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Affiliation(s)
| | | | | | | | | | - Iago Dillion Lima Cavalcanti
- Keizo Asami Institute, iLIKA, Federal University of Pernambuco, Recife, Brazil
- Postgraduate Program in Biological Science, Federal University of Pernambuco, Pernambuco, Recife, Brazil
| | - Mariane Cajuba de Britto Lira Nogueira
- Keizo Asami Institute, iLIKA, Federal University of Pernambuco, Recife, Brazil
- Academic Center of Vitória, Federal University of Pernambuco, Pernambuco, Brazil
| | | | | | - Luiz Carlos Alves
- Keizo Asami Institute, iLIKA, Federal University of Pernambuco, Recife, Brazil
- Postgraduate Program in Biological Science, Federal University of Pernambuco, Pernambuco, Recife, Brazil
- Oswaldo Cruz Foundation, Aggeu Magalhães Institute, Department of Virology and Experimental Therapy, Recife, Brazil.cr
| | - José Luiz de Lima Filho
- Keizo Asami Institute, iLIKA, Federal University of Pernambuco, Recife, Brazil
- Postgraduate Program in Biological Science, Federal University of Pernambuco, Pernambuco, Recife, Brazil
- Postgraduate Program in Pure and Applied Chemistry, Federal University of Western of Bahia, Bahia, Brazil
| | - Alexandre Varão Moura
- MS4Life Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista, São Paulo 12916-900, Brazil
| | - Álex Aparecido Rosini Silva
- MS4Life Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista, São Paulo 12916-900, Brazil
| | - Andréia de Melo Porcari
- MS4Life Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista, São Paulo 12916-900, Brazil
| | - Priscila Gubert
- Keizo Asami Institute, iLIKA, Federal University of Pernambuco, Recife, Brazil
- Department of Biochemistry, Federal University of Pernambuco, Pernambuco, Recife, Brazil
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10
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Uthailak N, Adisakwattana P, Chienwichai P, Tipthara P, Tarning J, Thawornkuno C, Thiangtrongjit T, Reamtong O. Metabolite profiling of Trichinella spiralis adult worms and muscle larvae identifies their excretory and secretory products. Front Cell Infect Microbiol 2023; 13:1306567. [PMID: 38145042 PMCID: PMC10749202 DOI: 10.3389/fcimb.2023.1306567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Human trichinellosis is a parasitic infection caused by roundworms belonging to the genus Trichinella, especially Trichinella spiralis. Early and accurate clinical diagnoses of trichinellosis are required for efficacious prognosis and treatment. Current drug therapies are limited by antiparasitic resistance, poor absorption, and an inability to kill the encapsulating muscle-stage larvae. Therefore, reliable biomarkers and drug targets for novel diagnostic approaches and anthelmintic drugs are required. In this study, metabolite profiles of T. spiralis adult worms and muscle larvae were obtained using mass spectrometry-based metabolomics. In addition, metabolite-based biomarkers of T. spiralis excretory-secretory products and their related metabolic pathways were characterized. The metabolic profiling identified major, related metabolic pathways involving adenosine monophosphate (AMP)-dependent synthetase/ligase and glycolysis/gluconeogenesis in T. spiralis adult worms and muscle larvae, respectively. These pathways are potential drug targets for the treatment of the intestinal and muscular phases of infection. The metabolome of larva excretory-secretory products was characterized, with amino acid permease and carbohydrate kinase being identified as key metabolic pathways. Among six metabolites, decanoyl-l-carnitine and 2,3-dinor-6-keto prostaglandin F1α-d9 were identified as potential metabolite-based biomarkers that might be related to the host inflammatory processes. In summary, this study compared the relationships between the metabolic profiles of two T. spiralis growth stages. Importantly, the main metabolites and metabolic pathways identified may aid the development of novel clinical diagnostics and therapeutics for human trichinellosis and other related helminthic infections.
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Affiliation(s)
- Naphatsamon Uthailak
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Peerut Chienwichai
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Phornpimon Tipthara
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Joel Tarning
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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11
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Sánchez-Martínez JD, Cifuentes A, Valdés A. Omics approaches to investigate the neuroprotective capacity of a Citrus sinensis (sweet orange) extract in a Caenorhabditis elegans Alzheimer's model. Food Res Int 2023; 172:113128. [PMID: 37689893 DOI: 10.1016/j.foodres.2023.113128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 09/11/2023]
Abstract
Citrus sinensis by-products are a promising source of neuroprotective molecules. In this study, a pressurized liquid extract of Citrus by-products (PLE100) has been extensively characterized, and its neuroprotective capacity tested in the Caenorhabditis elegans strain CL4176, a validated in vivo model of Alzheimer's disease (AD). More than 450 compounds have been annotated in the extract, being triacylglycerols (TGs), stigmastanes, fatty acids (FAs) and carbohydrates the most abundant. The results demonstrate that worms PLE100-treated are significantly protected in a dose-dependent manner against the Aβ-peptide paralysis toxicity. The RNA-Seq data showed an alteration of 294 genes mainly related to the stress response defense along with genes involved in the lipid transport and metabolism. Moreover, the comprehensive metabolomics study allowed the identification of 818 intracellular metabolites, of which 54 were significantly altered (mainly lipids). The integration of these and previous results provides with new evidences of the protection mechanisms of this promising extract.
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Affiliation(s)
| | - Alejandro Cifuentes
- Foodomics Laboratory, CIAL, CSIC-UAM, Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Alberto Valdés
- Foodomics Laboratory, CIAL, CSIC-UAM, Nicolás Cabrera 9, 28049 Madrid, Spain.
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12
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Zhu Y, Jen A, Overmyer KA, Gao AW, Shishkova E, Auwerx J, Coon JJ. Mass Spectrometry-Based Multi-omics Integration with a Single Set of C. elegans Samples. Anal Chem 2023; 95:10930-10938. [PMID: 37432911 PMCID: PMC10863427 DOI: 10.1021/acs.analchem.3c00734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Mass spectrometry-based large-scale multi-omics research has proven to be powerful in answering biological questions; nonetheless, it faces many challenges from sample preparation to downstream data integration. To efficiently extract biomolecules of different physicochemical properties, preparation of various sample type needs specific tailoring, especially of difficult ones, such as Caenorhabditis elegans. In this study, we sought to develop a multi-omics sample preparation method starting with a single set ofC. elegans samples to save time, minimize variability, expand biomolecule coverage, and promote multi-omics integration. We investigated tissue disruption methods to effectively release biomolecules and optimized extraction strategies to achieve broader and more reproducible biomolecule coverage in proteomics, lipidomics, and metabolomics workflows. In our assessment, we also considered speediness and usability of the approaches. The developed method was validated through a study of 16C. elegans samples designed to shine light on mitochondrial unfolded protein response (UPRmt), induced by three unique stressors─knocking down electron transfer chain element cco-1, mitochondrial ribosome protein S5 mrps-5, and antibiotic treatment Doxycycline. Our findings suggested that the method achieved great coverage of proteome, lipidome, and metabolome with high reproducibility and validated that all stressors triggered UPRmt in C. elegans, although generating unique molecular signatures. Innate immune response was activated, and triglycerides were decreased under all three stressor conditions. Additionally, Doxycycline treatment elicited more distinct proteomic, lipidomic, and metabolomic response than the other two treatments. This method has been successfully used to process Saccharomyces cerevisiae (data not shown) and can likely be applied to other organisms for multi-omics research.
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Affiliation(s)
- Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Katherine A Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Arwen W Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
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13
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Scott A, Willis CR, Muratani M, Higashitani A, Etheridge T, Szewczyk NJ, Deane CS. Caenorhabditis elegans in microgravity: An omics perspective. iScience 2023; 26:107189. [PMID: 37456835 PMCID: PMC10344948 DOI: 10.1016/j.isci.2023.107189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
The application of omics to study Caenorhabditis elegans (C. elegans) in the context of spaceflight is increasing, illuminating the wide-ranging biological impacts of spaceflight on physiology. In this review, we highlight the application of omics, including transcriptomics, genomics, proteomics, multi-omics, and integrated omics in the study of spaceflown C. elegans, and discuss the impact, use, and future direction of this branch of research. We highlight the variety of molecular alterations that occur in response to spaceflight, most notably changes in metabolic and neuromuscular gene regulation. These transcriptional features are reproducible and evident across many spaceflown species (e.g., mice and astronauts), supporting the use of C. elegans as a model organism to study spaceflight physiology with translational capital. Integrating tissue-specific, spatial, and multi-omics approaches, which quantitatively link molecular responses to phenotypic adaptations, will facilitate the identification of candidate regulatory molecules for therapeutic intervention and thus represents the next frontiers in C. elegans space omics research.
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Affiliation(s)
- Amanda Scott
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Craig R.G. Willis
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
| | - Masafumi Muratani
- Transborder Medical Research Center and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | | | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Nathaniel J. Szewczyk
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
- Ohio Musculoskeletal and Neurological Institute, Ohio University, Athens, OH, USA
| | - Colleen S. Deane
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
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14
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Polak I, Stryiński R, Majewska M, Łopieńska-Biernat E. Metabolomic analysis reveals a differential adaptation process of the larval stages of Anisakis simplex to the host environment. Front Mol Biosci 2023; 10:1233586. [PMID: 37520327 PMCID: PMC10373882 DOI: 10.3389/fmolb.2023.1233586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction: Anisakis simplex are parasitic nematodes that cause anisakiasis. The possibility of infection with this parasite is through consumption of raw or undercooked fish products. A. simplex infections are often misdiagnosed, especially in subclinical cases that do not present with typical symptoms such as urticaria, angioedema, and gastrointestinal allergy. The resulting allergic reactions range from rapid-onset and potentially fatal anaphylactic reactions to chronic, debilitating conditions. While there have been numerous published studies on the genomes and proteomes of A. simplex, less attention has been paid to the metabolomes. Metabolomics is concerned with the composition of metabolites in biological systems. Dynamic responses to endogenous and exogenous stimuli are particularly well suited for the study of holistic metabolic responses. In addition, metabolomics can be used to determine metabolic activity at different stages of development or during growth. Materials and methods: In this study, we reveal for the first time the metabolomes of infectious stages (L3 and L4) of A. simplex using untargeted metabolomics by ultra-performance liquid chromatography-mass spectrometry. Results: In the negative ionization mode (ESI-), we identified 172 different compounds, whereas in the positive ionization mode (ESI+), 186 metabolites were found. Statistical analysis showed that 60 metabolites were found in the ESI- mode with different concentration in each group, of which 21 were more enriched in the L3 larvae and 39 in the L4 stage of A. simplex. Comparison of the individual developmental stages in the ESI + mode also revealed a total of 60 differential metabolites, but 32 metabolites were more enriched in the L3 stage larvae, and 28 metabolites were more concentrated in the L4 stage. Discussion: The metabolomics study revealed that the developmental stages of A. simplex differed in a number of metabolic pathways, including nicotinate and nicotinamide metabolism. In addition, molecules responsible for successful migration within their host, such as pyridoxine and prostaglandins (E1, E2, F1a) were present in the L4 stage. In contrast, metabolic pathways for amino acids, starch, and sucrose were mainly activated in the L3 stage. Our results provide new insights into the comparative metabolome profiles of two different developmental stages of A. simplex.
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Affiliation(s)
- Iwona Polak
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Robert Stryiński
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marta Majewska
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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15
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Long NP, Kang JS, Kim HM. Caenorhabditis elegans: a model organism in the toxicity assessment of environmental pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:39273-39287. [PMID: 36745349 DOI: 10.1007/s11356-023-25675-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/29/2023] [Indexed: 02/07/2023]
Abstract
The unfavorable effects of environmental pollutants are becoming increasingly evident. In recent years, Caenorhabditis elegans (C. elegans) has been used as a powerful terrestrial model organism for environmental toxicity studies owing to its various advantages, including ease of culture, short lifespan, small size, transparent body, and well-characterized genome. In vivo bioassays and field studies can analyze and evaluate various toxic effects of the toxicants on the model organism, while emerging technologies allow profound insights into molecular disturbances underlying the observed phenotypes. In this review, we discuss the applications of C. elegans as a model organism in environmental toxicity studies and delineate apical assays such as lifespan, growth rate, reproduction, and locomotion, which are widely used in toxicity evaluation. In addition to phenotype assays, a comprehensive understanding of the toxic mode of action and mechanism can be achieved through a highly sensitive multi-omics approach, including the expression levels of genes and endogenous metabolites. Recent studies on environmental toxicity using these approaches have been summarized. This review highlights the practicality and advantages of C. elegans in evaluating the toxicity of environmental pollutants and presents the findings of recent toxicity studies performed using this model organism. Finally, we propose crucial technical considerations to escalate the appropriate use of C. elegans in examining the toxic effects of environmental pollutants.
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Affiliation(s)
- Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 614-735, Korea
| | - Jong Seong Kang
- College of Pharmacy, Chungnam National University, Daejeon, 34134, Korea
| | - Hyung Min Kim
- College of Pharmacy, Chungnam National University, Daejeon, 34134, Korea.
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16
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Hermans ME, van Weeghel M, Vaz FM, Ferdinandusse S, Hollak CEM, Huidekoper HH, Janssen MCH, van Kuilenburg ABP, Pras-Raves ML, Wamelink MMC, Wanders RJA, Welsink-Karssies MM, Bosch AM. Multi-omics in classical galactosemia: Evidence for the involvement of multiple metabolic pathways. J Inherit Metab Dis 2022; 45:1094-1105. [PMID: 36053831 DOI: 10.1002/jimd.12548] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 11/12/2022]
Abstract
Classical galactosemia (CG) is one of the more frequent inborn errors of metabolism affecting approximately 1:40.000 people. Despite a life-saving galactose-restricted diet, patients develop highly variable long-term complications including intellectual disability and movement disorders. The pathophysiology of these complications is still poorly understood and development of new therapies is hampered by a lack of valid prognostic biomarkers. Multi-omics approaches may discover new biomarkers and improve prediction of patient outcome. In the current study, (semi-)targeted mass-spectrometry based metabolomics and lipidomics were performed in erythrocytes of 40 patients with both classical and variant phenotypes and 39 controls. Lipidomics did not show any significant changes or deficiencies. The metabolomics analysis revealed that CG does not only compromise the Leloir pathway, but also involves other metabolic pathways including glycolysis, the pentose phosphate pathway, and nucleotide metabolism in the erythrocyte. Moreover, the energy status of the cell appears to be compromised, with significantly decreased levels of ATP and ADP. This possibly is the consequence of two different mechanisms: impaired formation of ATP from ADP possibly due to reduced flux though the glycolytic pathway and trapping of phosphate in galactose-1-phosphate (Gal-1P) which accumulates in CG. Our findings are in line with the current notion that the accumulation of Gal-1P plays a key role in the pathophysiology of CG not only by depletion of intracellular phosphate levels but also by decreasing metabolite abundance downstream in the glycolytic pathway and affecting other pathways. New therapeutic options for CG could be directed towards the restoration of intracellular phosphate homeostasis.
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Affiliation(s)
- Merel E Hermans
- Department of Pediatrics, Division of Metabolic Diseases, Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
| | - Michel van Weeghel
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Frédéric M Vaz
- Department of Pediatrics, Division of Metabolic Diseases, Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
- United for Metabolic Diseases, The Netherlands
| | - Sacha Ferdinandusse
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Carla E M Hollak
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Hidde H Huidekoper
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Mirian C H Janssen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - André B P van Kuilenburg
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Mia L Pras-Raves
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
- Epidemiology and Data Science, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Mirjam M C Wamelink
- Department of Clinical Chemistry, Metabolic Unit, Gastroenterology Endocrinology Metabolism, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Mendy M Welsink-Karssies
- Department of Pediatrics, Division of Metabolic Diseases, Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
| | - Annet M Bosch
- Department of Pediatrics, Division of Metabolic Diseases, Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, The Netherlands
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17
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Abstract
The publication of Resource articles is essential for the dissemination of novel, or substantially enhanced, tools, techniques, disease models, datasets and resources. By sharing knowledge and resources in a globally accessible manner, we can support human disease research to accelerate the translation of fundamental discoveries to effective treatments or diagnostics for diverse patient populations. To promote and encourage excellence in Resource articles, Disease Models & Mechanisms (DMM) is launching a new 'Outstanding Resource Paper Prize'. To celebrate this, we highlight recent outstanding DMM Resource articles that have the ultimate goal of benefitting of human health.
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Affiliation(s)
- Kirsty M. Hooper
- The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
| | - Julija Hmeljak
- The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
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18
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Soria LR, Makris G, D'Alessio AM, De Angelis A, Boffa I, Pravata VM, Rüfenacht V, Attanasio S, Nusco E, Arena P, Ferenbach AT, Paris D, Cuomo P, Motta A, Nitzahn M, Lipshutz GS, Martínez-Pizarro A, Richard E, Desviat LR, Häberle J, van Aalten DMF, Brunetti-Pierri N. O-GlcNAcylation enhances CPS1 catalytic efficiency for ammonia and promotes ureagenesis. Nat Commun 2022; 13:5212. [PMID: 36064721 PMCID: PMC9445089 DOI: 10.1038/s41467-022-32904-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Life-threatening hyperammonemia occurs in both inherited and acquired liver diseases affecting ureagenesis, the main pathway for detoxification of neurotoxic ammonia in mammals. Protein O-GlcNAcylation is a reversible and nutrient-sensitive post-translational modification using as substrate UDP-GlcNAc, the end-product of hexosamine biosynthesis pathway. Here we show that increased liver UDP-GlcNAc during hyperammonemia increases protein O-GlcNAcylation and enhances ureagenesis. Mechanistically, O-GlcNAcylation on specific threonine residues increased the catalytic efficiency for ammonia of carbamoyl phosphate synthetase 1 (CPS1), the rate-limiting enzyme in ureagenesis. Pharmacological inhibition of O-GlcNAcase, the enzyme removing O-GlcNAc from proteins, resulted in clinically relevant reductions of systemic ammonia in both genetic (hypomorphic mouse model of propionic acidemia) and acquired (thioacetamide-induced acute liver failure) mouse models of liver diseases. In conclusion, by fine-tuned control of ammonia entry into ureagenesis, hepatic O-GlcNAcylation of CPS1 increases ammonia detoxification and is a novel target for therapy of hyperammonemia in both genetic and acquired diseases.
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Affiliation(s)
- Leandro R Soria
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
| | - Georgios Makris
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | | | | | - Iolanda Boffa
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | | | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Paola Arena
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Debora Paris
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - Paola Cuomo
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - Andrea Motta
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - Matthew Nitzahn
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Gerald S Lipshutz
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ainhoa Martínez-Pizarro
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, CIBERER, IdiPaz, Universidad Autónoma, Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, CIBERER, IdiPaz, Universidad Autónoma, Madrid, Spain
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, CIBERER, IdiPaz, Universidad Autónoma, Madrid, Spain
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | | | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
- Department of Translational Medicine, Federico II University, Naples, Italy.
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy.
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19
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Kunst RF, de Waart DR, Wolters F, Duijst S, Vogels EW, Bolt I, Verheij J, Beuers U, Oude Elferink RP, van de Graaf SF. Systemic ASBT inactivation protects against liver damage in obstructive cholestasis in mice. JHEP REPORTS : INNOVATION IN HEPATOLOGY 2022; 4:100573. [PMID: 36160754 PMCID: PMC9494276 DOI: 10.1016/j.jhepr.2022.100573] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 02/08/2023]
Abstract
Background & Aims Non-absorbable inhibitors of the apical sodium-dependent bile acid transporter (ASBT; also called ileal bile acid transporter [IBAT]) are recently approved or in clinical development for multiple cholestatic liver disorders and lead to a reduction in pruritus and (markers for) liver injury. Unfortunately, non-absorbable ASBT inhibitors (ASBTi) can induce diarrhoea or may be ineffective if cholestasis is extensive and largely precludes intestinal excretion of bile acids. Systemically acting ASBTi that divert bile salts towards renal excretion may alleviate these issues. Methods Bile duct ligation (BDL) was performed in ASBT-deficient (ASBT knockout [KO]) mice as a model for chronic systemic ASBT inhibition in obstructive cholestasis. Co-infusion of radiolabelled taurocholate and inulin was used to quantify renal bile salt excretion after BDL. In a second (wild-type) mouse model, a combination of obeticholic acid (OCA) and intestine-restricted ASBT inhibition was used to lower the bile salt pool size before BDL. Results After BDL, ASBT KO mice had reduced plasma bilirubin and alkaline phosphatase compared with wild-type mice with BDL and showed a marked reduction in liver necrotic areas at histopathological analysis, suggesting decreased BDL-induced liver damage. Furthermore, ASBT KO mice had reduced bile salt pool size, lower plasma taurine-conjugated polyhydroxylated bile salt, and increased urinary bile salt excretion. Pretreatment with OCA + ASBTi in wild-type mice reduced the pool size and greatly improved liver injury markers and liver histology. Conclusions A reduced bile salt pool at the onset of cholestasis effectively lowers cholestatic liver injury in mice. Systemic ASBT inhibition may be valuable as treatment for cholestatic liver disease by lowering the pool size and increasing renal bile salt output even under conditions of minimal faecal bile salt secretion. Lay summary Novel treatment approaches against cholestatic liver disease (resulting in reduced or blocked flow of bile) involve non-absorbable inhibitors of the bile acid transport protein ASBT, but these are not always effective and/or can cause unwanted side effects. In this study, we demonstrate that systemic inhibition/inactivation of ASBT protects mice against developing severe cholestatic liver injury after bile duct ligation, by reducing bile salt pool size and increasing renal bile salt excretion.
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Key Words
- ALT, alanine transaminase
- ASBT, apical sodium-dependent bile acid transporter
- ASBTi, ASBT inhibitors
- AST, aspartate transaminase
- Alagille
- Apical sodium-dependent bile acid transporter (ASBT)
- BDL, bile duct ligation
- BSEP
- Bile salt pool size
- CCl4, carbon tetrachloride
- CK7, cytokeratin 7
- Cholestasis
- FRET, Förster resonance energy transfer
- G-OCA, glycine-conjugated OCA
- HepG2 cell, hepatocarcinoma cell
- IBAT
- MDR2, multidrug resistance protein 2
- NASH, non-alcoholic steatohepatitis
- NGM282, non-tumorigenic fibroblast growth factor 19 analogue
- NTCP
- NTCP, Na+/taurocholate cotransporting polypeptide
- NucleoBAS, nuclear Bile Acid Sensor
- OCA, obeticholic acid
- PBC, primary biliary cholangitis
- PFIC
- PentaOH, pentahydroxylated
- RT-qPCR, real-time quantitative PCR
- Renal excretion
- T-OCA, taurine-conjugated OCA
- TCA, taurocholic acid
- TetraOH, tetrahydroxylated
- U2OS, osteosarcoma cell
- UHPLC-MS, ultrahigh-performance liquid chromatography mass spectrometry
- WT, wild-type
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Affiliation(s)
- Roni F. Kunst
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands
| | - Dirk R. de Waart
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands
| | - Frank Wolters
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands
| | - Suzanne Duijst
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands
| | - Esther W. Vogels
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands
| | - Isabelle Bolt
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands
| | - Joanne Verheij
- Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands,Department of Pathology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ulrich Beuers
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ronald P.J. Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Stan F.J. van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Amsterdam Gastroenterology, Endocrinology and Metabolism (AGEM), Amsterdam University Medical Centers, The Netherlands,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands,Corresponding author. Address: Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands. Tel.: +31-020-5668832; Fax: +31-020-5669190.
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20
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Schuurman AR, Léopold V, Pereverzeva L, Chouchane O, Reijnders TDY, Brabander JD, Douma RA, Weeghel MV, Wever E, Schomaker BV, Vaz FM, Wiersinga WJ, Veer CV, Poll TVD. The Platelet Lipidome Is Altered in Patients with COVID-19 and Correlates with Platelet Reactivity. Thromb Haemost 2022; 122:1683-1692. [PMID: 35850149 PMCID: PMC9512584 DOI: 10.1055/s-0042-1749438] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Activated platelets have been implicated in the proinflammatory and prothrombotic phenotype of coronavirus disease 2019 (COVID-19). While it is increasingly recognized that lipids have important structural and signaling roles in platelets, the lipidomic landscape of platelets during infection has remained unexplored. OBJECTIVE To investigate the platelet lipidome of patients hospitalized for COVID-19. METHODS We performed untargeted lipidomics in platelets of 25 patients hospitalized for COVID-19 and 23 noninfectious controls with similar age and sex characteristics, and with comparable comorbidities. RESULTS Twenty-five percent of the 1,650 annotated lipids were significantly different between the groups. The significantly altered part of the platelet lipidome mostly comprised lipids that were less abundant in patients with COVID-19 (20.4% down, 4.6% up, 75% unchanged). Platelets from COVID-19 patients showed decreased levels of membrane plasmalogens, and a distinct decrease of long-chain, unsaturated triacylglycerols. Conversely, platelets from patients with COVID-19 displayed class-wide higher abundances of bis(monoacylglycero)phosphate and its biosynthetic precursor lysophosphatidylglycerol. Levels of these classes positively correlated with ex vivo platelet reactivity-as measured by P-selectin expression after PAR1 activation-irrespective of disease state. CONCLUSION Taken together, this investigation provides the first exploration of the profound impact of infection on the human platelet lipidome, and reveals associations between the lipid composition of platelets and their reactivity. These results warrant further lipidomic research in other infections and disease states involving platelet pathophysiology.
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Affiliation(s)
- Alex R Schuurman
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Valentine Léopold
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Anesthesia and Intensive Care, Hôpital Lariboisière, INSERM U942S MASCOT, Université de Paris, Paris, France
| | - Liza Pereverzeva
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Osoul Chouchane
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Justin de Brabander
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Renée A Douma
- Department of Internal Medicine, Flevo Hospital, Almere, The Netherlands
| | - Michel van Weeghel
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Eric Wever
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands.,Department of Epidemiology & Data Science, Bioinformatics Laboratory, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Bauke V Schomaker
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Frédéric M Vaz
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Willem Joost Wiersinga
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Cornelis Van't Veer
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, The Netherlands
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21
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Anh NH, Yoon YC, Min YJ, Long NP, Jung CW, Kim SJ, Kim SW, Lee EG, Wang D, Wang X, Kwon SW. Caenorhabditis elegans deep lipidome profiling by using integrative mass spectrometry acquisitions reveals significantly altered lipid networks. J Pharm Anal 2022; 12:743-754. [PMID: 36320604 PMCID: PMC9615529 DOI: 10.1016/j.jpha.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/02/2022] Open
Abstract
Lipidomics coverage improvement is essential for functional lipid and pathway construction. A powerful approach to discovering organism lipidome is to combine various data acquisitions, such as full scan mass spectrometry (full MS), data-dependent acquisition (DDA), and data-independent acquisition (DIA). Caenorhabditis elegans (C. elegans) is a useful model for discovering toxic-induced metabolism, high-throughput drug screening, and a variety of human disease pathways. To determine the lipidome of C. elegans and investigate lipid disruption from the molecular level to the system biology level, we used integrative data acquisition. The methyl-tert-butyl ether method was used to extract L4 stage C. elegans after exposure to triclosan (TCS), perfluorooctanoic acid, and nanopolystyrene (nPS). Full MS, DDA, and DIA integrations were performed to comprehensively profile the C. elegans lipidome by Q-Exactive Plus MS. All annotated lipids were then analyzed using lipid ontology and pathway analysis. We annotated up to 940 lipids from 20 lipid classes involved in various functions and pathways. The biological investigations revealed that when C. elegans were exposed to nPS, lipid droplets were disrupted, whereas plasma membrane-functionalized lipids were likely to be changed in the TCS treatment group. The nPS treatment caused a significant disruption in lipid storage. Triacylglycerol, glycerophospholipid, and ether class lipids were those primarily hindered by toxicants. Finally, toxicant exposure frequently involved numerous lipid-related pathways, including the phosphoinositide 3-kinase/protein kinase B pathway. In conclusion, an integrative data acquisition strategy was used to characterize the C. elegans lipidome, providing valuable biological insights into hypothesis generation and validation. Multiple data acquisitions were used to profile the lipidome of C. elegans. 940 detected lipids of 20 main classes involved in various pathways. Relevant hypotheses were generated using high-coverable lipidomics and pathways analysis.
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22
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Schomakers BV, Hermans J, Jaspers YR, Salomons G, Vaz FM, van Weeghel M, Houtkooper RH. Polar metabolomics in human muscle biopsies using a liquid-liquid extraction and full-scan LC-MS. STAR Protoc 2022; 3:101302. [PMID: 35479116 PMCID: PMC9035783 DOI: 10.1016/j.xpro.2022.101302] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe here a user-friendly analysis protocol for semi-targeted polar metabolomics in human muscle biopsies using Zwitterionic Hydrophilic Interaction Liquid Chromatography and high-resolution full-scan mass spectrometry. Previously, this protocol has been used for Caenorhabditis elegans. Here we show that it can be successfully applied to human muscle biopsies with minor adjustments. Summarized instructions for other matrices are also provided. As peak integration in metabolomics can be challenging, we provide expected retention times and extensive peak descriptions to aid this process. For complete details on the use and execution of this protocol, please refer to Molenaars et al. (2021). Protocol for polar metabolomics using liquid-liquid extraction and full-scan MS Semiquantitative analysis of 150 metabolites in human muscle biopsies Full peak integration and data processing instructions Additional instructions on 32 more biological matrices provided
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The evolving role of the Caenorhabditis elegans model as a tool to advance studies in nutrition and health. Nutr Res 2022; 106:47-59. [DOI: 10.1016/j.nutres.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 12/29/2022]
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Gao AW, El Alam G, Lalou A, Li TY, Molenaars M, Zhu Y, Overmyer KA, Shishkova E, Hof K, Bou Sleiman M, Houtkooper RH, Coon JJ, Auwerx J. Multi-omics analysis identifies essential regulators of mitochondrial stress response in two wild-type C. elegans strains. iScience 2022; 25:103734. [PMID: 35118355 PMCID: PMC8792074 DOI: 10.1016/j.isci.2022.103734] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/02/2021] [Accepted: 12/31/2021] [Indexed: 11/28/2022] Open
Abstract
The mitochondrial unfolded protein response (UPRmt) is a promising pharmacological target for aging and age-related diseases. However, the integrative analysis of the impact of UPRmt activation on different signaling layers in animals with different genetic backgrounds is lacking. Here, we applied systems approaches to investigate the effect of UPRmt induced by doxycycline (Dox) on transcriptome, proteome, and lipidome in two genetically divergent worm strains, named N2 and CB4856. From the integrated omics datasets, we found that Dox prolongs lifespan of both worm strains through shared and strain-specific mechanisms. Specifically, Dox strongly impacts mitochondria, upregulates defense response, and lipid metabolism, while decreasing triglycerides. We further validated that lipid genes acs-2/20 and fat-7/6 were required for Dox-induced UPRmt and longevity in N2 and CB4856 worms, respectively. Our data have translational value as they indicate that the beneficial effects of Dox-induced UPRmt on lifespan are consistent across different genetic backgrounds through different regulators. Dox extends lifespan of N2 and CB4856 via shared and strain-specific mechanisms Dox controls mitochondria, defense responses, and lipid metabolism in both strains Dox-mediated longevity requires acs-2/20 in N2 and fat-7/6 in CB4856 worms
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Affiliation(s)
- Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Amélia Lalou
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Terytty Yang Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, AZ, the Netherlands
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Katherine A. Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
| | - Kevin Hof
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, AZ, the Netherlands
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Corresponding author
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25
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Haal S, Guman MSS, Acherman YIZ, Jansen JPG, van Weeghel M, van Lenthe H, Wever EJM, Gerdes VEA, Voermans RP, Groen AK. Gallstone Formation Follows a Different Trajectory in Bariatric Patients Compared to Nonbariatric Patients. Metabolites 2021; 11:682. [PMID: 34677397 PMCID: PMC8541369 DOI: 10.3390/metabo11100682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 12/20/2022] Open
Abstract
Since obese patients form cholesterol gallstones very rapidly after bariatric surgery, in patients who did not form gallstones during preceding years, we hypothesized that gallstone formation follows a different trajectory in bariatric patients compared to nonbariatric patients. We therefore analyzed the lipid composition of gallbladder bile derived from 18 bariatric gallstone patients and 17 nonbariatric gallstone patients (median (IQR) age, 46.0 (28.0-54.0) years; 33 (94%) female) during laparoscopic cholecystectomy using an enzymatic and lipidomics approach. We observed a higher concentration of total lipids (9.9 vs. 5.8 g/dL), bile acids (157.7 vs. 81.5 mM), cholesterol (10.6 vs. 5.4 mM), and phospholipids (30.4 vs. 21.8 mM) in bariatric gallstone patients compared to nonbariatric gallstone patients. The cholesterol saturation index did not significantly differ between the two groups. Lipidomics analysis revealed an interesting pattern. Enhanced amounts of a number of lipid species were found in the gallbladder bile of nonbariatric gallstone patients. Most striking was a fivefold higher amount of triglyceride. A concomitant ninefold increase of apolipoprotein B was found, suggesting secretion of triglyceride-rich lipoproteins (TRLs) at the canalicular pole of the hepatocyte in livers from nonbariatric gallstone patients. These findings suggest that gallstone formation follows a different trajectory in bariatric patients compared to nonbariatric patients. Impaired gallbladder emptying might explain the rapid gallstone formation after bariatric surgery, while biliary TRL secretion might contribute to gallstone formation in nonbariatric patients.
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Affiliation(s)
- Sylke Haal
- Department of Internal Medicine, Spaane Gasthuis, 2134 TM Hoofddorp, The Netherlands; (M.S.S.G.); (V.E.A.G.)
- Department of Gastroenterology and Hepatology, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands;
| | - Maimoena S. S. Guman
- Department of Internal Medicine, Spaane Gasthuis, 2134 TM Hoofddorp, The Netherlands; (M.S.S.G.); (V.E.A.G.)
- Department of Internal and Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.P.G.J.); (A.K.G.)
| | - Yair I. Z. Acherman
- Department of Surgery, Spaarne Gasthuis, 2134 TM Hoofddorp, The Netherlands;
| | - Johannes P. G. Jansen
- Department of Internal and Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.P.G.J.); (A.K.G.)
| | - Michel van Weeghel
- Laboratory of Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, 1105 AZ Amsterdam, The Netherlands; (M.v.W.); (H.v.L.); (E.J.M.W.)
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Henk van Lenthe
- Laboratory of Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, 1105 AZ Amsterdam, The Netherlands; (M.v.W.); (H.v.L.); (E.J.M.W.)
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Eric J. M. Wever
- Laboratory of Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, 1105 AZ Amsterdam, The Netherlands; (M.v.W.); (H.v.L.); (E.J.M.W.)
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, 1105 AZ Amsterdam, The Netherlands
| | - Victor E. A. Gerdes
- Department of Internal Medicine, Spaane Gasthuis, 2134 TM Hoofddorp, The Netherlands; (M.S.S.G.); (V.E.A.G.)
- Department of Internal and Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.P.G.J.); (A.K.G.)
| | - Rogier P. Voermans
- Department of Gastroenterology and Hepatology, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands;
| | - Albert K. Groen
- Department of Internal and Vascular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.P.G.J.); (A.K.G.)
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First person – Marte Molenaars and Bauke Schomakers. Dis Model Mech 2021. [PMCID: PMC8106958 DOI: 10.1242/dmm.049009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
First Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping early-career researchers promote themselves alongside their papers. Marte Molenaars and Bauke Schomakers are co-first authors on ‘Metabolomics and lipidomics in Caenorhabditis elegans using a single-sample preparation’, published in DMM. Marte conducted the research described in the article while a PhD student in the lab of Riekelt Houtkooper at Amsterdam UMC, Amsterdam, The Netherlands, and is now a postdoc in the lab of Richard Possemato at New York University School of Medicine, New York, NY, USA. During her PhD, she was investigating cellular metabolic pathways and how to use them to target ageing and age-related diseases, and currently she focuses on metabolic pathways in cancer cells as a postdoc. Bauke is a Research Analyst in the lab of Riekelt Houtkooper at Amsterdam UMC, Amsterdam, The Netherlands, investigating liquid chromatography–mass spectrometry-based omics methods for the comprehensive analysis of biological samples.
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