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Santos AA, Delgado TC, Marques V, Ramirez-Moncayo C, Alonso C, Vidal-Puig A, Hall Z, Martínez-Chantar ML, Rodrigues CM. Spatial metabolomics and its application in the liver. Hepatology 2024; 79:1158-1179. [PMID: 36811413 PMCID: PMC11020039 DOI: 10.1097/hep.0000000000000341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023]
Abstract
Hepatocytes work in highly structured, repetitive hepatic lobules. Blood flow across the radial axis of the lobule generates oxygen, nutrient, and hormone gradients, which result in zoned spatial variability and functional diversity. This large heterogeneity suggests that hepatocytes in different lobule zones may have distinct gene expression profiles, metabolic features, regenerative capacity, and susceptibility to damage. Here, we describe the principles of liver zonation, introduce metabolomic approaches to study the spatial heterogeneity of the liver, and highlight the possibility of exploring the spatial metabolic profile, leading to a deeper understanding of the tissue metabolic organization. Spatial metabolomics can also reveal intercellular heterogeneity and its contribution to liver disease. These approaches facilitate the global characterization of liver metabolic function with high spatial resolution along physiological and pathological time scales. This review summarizes the state of the art for spatially resolved metabolomic analysis and the challenges that hinder the achievement of metabolome coverage at the single-cell level. We also discuss several major contributions to the understanding of liver spatial metabolism and conclude with our opinion on the future developments and applications of these exciting new technologies.
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Affiliation(s)
- André A. Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa C. Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Congenital Metabolic Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Vanda Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Carmen Ramirez-Moncayo
- Institute of Clinical Sciences, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | | | - Antonio Vidal-Puig
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Centro Investigation Principe Felipe, Valencia, Spain
| | - Zoe Hall
- Division of Systems Medicine, Imperial College London, London, UK
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Cecilia M.P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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Schwaiger-Haber M, Stancliffe E, Anbukumar DS, Sells B, Yi J, Cho K, Adkins-Travis K, Chheda MG, Shriver LP, Patti GJ. Using mass spectrometry imaging to map fluxes quantitatively in the tumor ecosystem. Nat Commun 2023; 14:2876. [PMID: 37208361 DOI: 10.1038/s41467-023-38403-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 04/26/2023] [Indexed: 05/21/2023] Open
Abstract
Tumors are comprised of a multitude of cell types spanning different microenvironments. Mass spectrometry imaging (MSI) has the potential to identify metabolic patterns within the tumor ecosystem and surrounding tissues, but conventional workflows have not yet fully integrated the breadth of experimental techniques in metabolomics. Here, we combine MSI, stable isotope labeling, and a spatial variant of Isotopologue Spectral Analysis to map distributions of metabolite abundances, nutrient contributions, and metabolic turnover fluxes across the brains of mice harboring GL261 glioma, a widely used model for glioblastoma. When integrated with MSI, the combination of ion mobility, desorption electrospray ionization, and matrix assisted laser desorption ionization reveals alterations in multiple anabolic pathways. De novo fatty acid synthesis flux is increased by approximately 3-fold in glioma relative to surrounding healthy tissue. Fatty acid elongation flux is elevated even higher at 8-fold relative to surrounding healthy tissue and highlights the importance of elongase activity in glioma.
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Affiliation(s)
- Michaela Schwaiger-Haber
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Ethan Stancliffe
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Dhanalakshmi S Anbukumar
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Blake Sells
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jia Yi
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Kayla Adkins-Travis
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
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4
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Müller WH, De Pauw E, Far J, Malherbe C, Eppe G. Imaging lipids in biological samples with surface-assisted laser desorption/ionization mass spectrometry: A concise review of the last decade. Prog Lipid Res 2021; 83:101114. [PMID: 34217733 DOI: 10.1016/j.plipres.2021.101114] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023]
Abstract
Knowing the spatial location of the lipid species present in biological samples is of paramount importance for the elucidation of pathological and physiological processes. In this context, mass spectrometry imaging (MSI) has emerged as a powerful technology allowing the visualization of the spatial distributions of biomolecules, including lipids, in complex biological samples. Among the different ionization methods available, the emerging surface-assisted laser desorption/ionization (SALDI) MSI offers unique capabilities for the study of lipids. This review describes the specific advantages of SALDI-MSI for lipid analysis, including the ability to perform analyses in both ionization modes with the same nanosubstrate, the detection of lipids characterized by low ionization efficiency in MALDI-MS, and the possibilities of surface modification to improve the detection of lipids. The complementarity of SALDI and MALDI-MSI is also discussed. Finally, this review presents data processing strategies applied in SALDI-MSI of lipids, as well as examples of applications of SALDI-MSI in biomedical lipidomics.
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Affiliation(s)
- Wendy H Müller
- Mass Spectrometry Laboratory, MolSys RU, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys RU, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys RU, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000 Liège, Belgium
| | - Cedric Malherbe
- Mass Spectrometry Laboratory, MolSys RU, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000 Liège, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys RU, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000 Liège, Belgium.
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Wilkinson DJ, Brook MS, Smith K. Principles of stable isotope research - with special reference to protein metabolism. CLINICAL NUTRITION OPEN SCIENCE 2021; 36:111-125. [PMID: 33969338 PMCID: PMC8083121 DOI: 10.1016/j.nutos.2021.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
The key to understanding the mechanisms regulating disease stems from the ability to accurately quantify the dynamic nature of the metabolism underlying the physiological and pathological changes occurring as a result of the disease. Stable isotope tracer technologies have been at the forefront of this for almost 80 years now, and through a combination of both intense theoretical and technological development over these decades, it is now possible to utilise stable isotope tracers to investigate the complexities of in vivo human metabolism from a whole body perspective, down to the regulation of sub-nanometer cellular components (i.e organelles, nucleotides and individual proteins). This review therefore aims to highlight; 1) the advances made in these stable isotope tracer approaches - with special reference given to their role in understanding the nutritional regulation of protein metabolism, 2) some considerations required for the appropriate application of these stable isotope techniques to study protein metabolism, 3) and finally how new stable isotopes approaches and instrument/technical developments will help to deliver greater clinical insight in the near future.
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Key Words
- A-V, Arterial Venous
- AA, Amino Acids
- AP(E), Atom percent (excess)
- FBR, Fractional Breakdown Rate
- FSR, Fractional Synthesis Rate
- GC-MS, Gas Chromatography Mass Spectrometry
- LC-MS, Liquid Chromatography Mass Spectrometry
- MPS, Muscle Protein Synthesis
- Muscle
- Protein turnover
- Ra, Rate of Appearance
- Rd, Rate of Disappearance
- Stable isotope tracers
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Affiliation(s)
- Daniel J. Wilkinson
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Health Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby, UK
| | - Matthew S. Brook
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Ken Smith
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Health Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby, UK
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