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Veličković M, Wu R, Gao Y, Thairu MW, Veličković D, Munoz N, Clendinen CS, Bilbao A, Chu RK, Lalli PM, Zemaitis K, Nicora CD, Kyle JE, Orton D, Williams S, Zhu Y, Zhao R, Monroe ME, Moore RJ, Webb-Robertson BJM, Bramer LM, Currie CR, Piehowski PD, Burnum-Johnson KE. Mapping microhabitats of lignocellulose decomposition by a microbial consortium. Nat Chem Biol 2024; 20:1033-1043. [PMID: 38302607 PMCID: PMC11288888 DOI: 10.1038/s41589-023-01536-7] [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: 08/27/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.
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Affiliation(s)
- Marija Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margaret W Thairu
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dušan Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathalie Munoz
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chaevien S Clendinen
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aivett Bilbao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rosalie K Chu
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Priscila M Lalli
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Zemaitis
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarai Williams
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ying Zhu
- Department of Microchemistry, Proteomics, Lipidomics, and Next Generation Sequencing, Genentech, San Francisco, CA, USA
| | - Rui Zhao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Paul D Piehowski
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
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Veličković D, Zemaitis KJ, Bhattacharjee A, Anderton CR. Mass spectrometry imaging of natural carbonyl products directly from agar-based microbial interactions using 4-APEBA derivatization. mSystems 2024; 9:e0080323. [PMID: 38064548 PMCID: PMC10804984 DOI: 10.1128/msystems.00803-23] [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: 08/10/2023] [Accepted: 10/31/2023] [Indexed: 01/24/2024] Open
Abstract
Aliphatic carboxylic acids, aldehydes, and ketones play diverse roles in microbial adaptation to their microenvironment, from excretion as toxins to adaptive metabolites for membrane fluidity. However, the spatial distribution of these molecules throughout biofilms and how microbes in these environments exchange these molecules remain elusive for many of these bioactive species due to inefficient molecular imaging strategies. Herein, we apply on-tissue chemical derivatization (OTCD) using 4-(2-((4-bromophenethyl)dimethylammonio)ethoxy)benzenaminium dibromide (4-APEBA) on a co-culture of a soil bacterium (Bacillus subtilis NCIB 3610) and fungus (Fusarium sp. DS 682) grown on agar as our model system. Using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), we spatially resolved more than 300 different metabolites containing carbonyl groups within this model system. Various spatial patterns are observable in these species, which indicate possible extracellular or intercellular processes of the metabolites and their up- or downregulation during microbial interaction. The unique chemistry of our approach allowed us to bring additional confidence in accurate carbonyl identification, especially when multiple isomeric candidates were possible, and this provided the ability to generate hypotheses about the potential role of some aliphatic carbonyls in this B. subtilis/Fusarium sp. interaction. The results shown here demonstrate the utility of 4-ABEBA-based OTCD MALDI-MSI in probing interkingdom interactions directly from microbial co-cultures, and these methods will enable future microbial interaction studies with expanded metabolic coverage.IMPORTANCEThe metabolic profiles within microbial biofilms and interkingdom interactions are extremely complex and serve a variety of functions, which include promoting colonization, growth, and survival within competitive and symbiotic environments. However, measuring and differentiating many of these molecules, especially in an in situ fashion, remains a significant analytical challenge. We demonstrate a chemical derivatization strategy that enabled highly sensitive, multiplexed mass spectrometry imaging of over 300 metabolites from a model microbial co-culture. Notably, this approach afforded us to visualize over two dozen classes of ketone-, aldehyde-, and carboxyl-containing molecules, which were previously undetectable from colonies grown on agar. We also demonstrate that this chemical derivatization strategy can enable the discrimination of isobaric and isomeric metabolites without the need for orthogonal separation (e.g., online chromatography or ion mobility). We anticipate that this approach will further enhance our knowledge of metabolic regulation within microbiomes and microbial systems used in bioengineering applications.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kevin J. Zemaitis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Arunima Bhattacharjee
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
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3
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Wheeler AM, Eberhard CD, Mosher EP, Yuan Y, Wilkins HN, Seneviratne HK, Orsburn BC, Bumpus NN. Achieving a Deeper Understanding of Drug Metabolism and Responses Using Single-Cell Technologies. Drug Metab Dispos 2023; 51:350-359. [PMID: 36627162 PMCID: PMC10029823 DOI: 10.1124/dmd.122.001043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 01/12/2023] Open
Abstract
Recent advancements in single-cell technologies have enabled detection of RNA, proteins, metabolites, and xenobiotics in individual cells, and the application of these technologies has the potential to transform pharmacological research. Single-cell data has already resulted in the development of human and model species cell atlases, identifying different cell types within a tissue, further facilitating the characterization of tumor heterogeneity, and providing insight into treatment resistance. Research discussed in this review demonstrates that distinct cell populations express drug metabolizing enzymes to different extents, indicating there may be variability in drug metabolism not only between organs, but within tissue types. Additionally, we put forth the concept that single-cell analyses can be used to expose underlying variability in cellular response to drugs, providing a unique examination of drug efficacy, toxicity, and metabolism. We will outline several of these techniques: single-cell RNA-sequencing and mass cytometry to characterize and distinguish different cell types, single-cell proteomics to quantify drug metabolizing enzymes and characterize cellular responses to drug, capillary electrophoresis-ultrasensitive laser-induced fluorescence detection and single-probe single-cell mass spectrometry for detection of drugs, and others. Emerging single-cell technologies such as these can comprehensively characterize heterogeneity in both cell-type-specific drug metabolism and response to treatment, enhancing progress toward personalized and precision medicine. SIGNIFICANCE STATEMENT: Recent technological advances have enabled the analysis of gene expression and protein levels in single cells. These types of analyses are important to investigating mechanisms that cannot be elucidated on a bulk level, primarily due to the variability of cell populations within biological systems. Here, we summarize cell-type-specific drug metabolism and how pharmacologists can utilize single-cell approaches to obtain a comprehensive understanding of drug metabolism and cellular heterogeneity in response to drugs.
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Affiliation(s)
- Abigail M Wheeler
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Colten D Eberhard
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Eric P Mosher
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Yuting Yuan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Hannah N Wilkins
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Herana Kamal Seneviratne
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Benjamin C Orsburn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
| | - Namandjé N Bumpus
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (A.M.W., C.D.E., E.P.M., Y.Y., H.N.W., H.K.S., B.C.O., N.N.B.) and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland (H.K.S.)
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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5
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Ajith A, Milnes PJ, Johnson GN, Lockyer NP. Mass Spectrometry Imaging for Spatial Chemical Profiling of Vegetative Parts of Plants. PLANTS 2022; 11:plants11091234. [PMID: 35567235 PMCID: PMC9102225 DOI: 10.3390/plants11091234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 11/23/2022]
Abstract
The detection of chemical species and understanding their respective localisations in tissues have important implications in plant science. The conventional methods for imaging spatial localisation of chemical species are often restricted by the number of species that can be identified and is mostly done in a targeted manner. Mass spectrometry imaging combines the ability of traditional mass spectrometry to detect numerous chemical species in a sample with their spatial localisation information by analysing the specimen in a 2D manner. This article details the popular mass spectrometry imaging methodologies which are widely pursued along with their respective sample preparation and the data analysis methods that are commonly used. We also review the advancements through the years in the usage of the technique for the spatial profiling of endogenous metabolites, detection of xenobiotic agrochemicals and disease detection in plants. As an actively pursued area of research, we also address the hurdles in the analysis of plant tissues, the future scopes and an integrated approach to analyse samples combining different mass spectrometry imaging methods to obtain the most information from a sample of interest.
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Affiliation(s)
- Akhila Ajith
- Department of Chemistry, Photon Science Institute, University of Manchester, Manchester M13 9PL, UK;
| | - Phillip J. Milnes
- Syngenta, Jeolott’s Hill International Research Centre, Bracknell RG42 6EY, UK;
| | - Giles N. Johnson
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PY, UK;
| | - Nicholas P. Lockyer
- Department of Chemistry, Photon Science Institute, University of Manchester, Manchester M13 9PL, UK;
- Correspondence:
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Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism. THE ISME JOURNAL 2022; 16:1074-1085. [PMID: 34845335 PMCID: PMC8941135 DOI: 10.1038/s41396-021-01136-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022]
Abstract
Interactions between Sphagnum (peat moss) and cyanobacteria play critical roles in terrestrial carbon and nitrogen cycling processes. Knowledge of the metabolites exchanged, the physiological processes involved, and the environmental conditions allowing the formation of symbiosis is important for a better understanding of the mechanisms underlying these interactions. In this study, we used a cross-feeding approach with spatially resolved metabolite profiling and metatranscriptomics to characterize the symbiosis between Sphagnum and Nostoc cyanobacteria. A pH gradient study revealed that the Sphagnum–Nostoc symbiosis was driven by pH, with mutualism occurring only at low pH. Metabolic cross-feeding studies along with spatially resolved matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) identified trehalose as the main carbohydrate source released by Sphagnum, which were depleted by Nostoc along with sulfur-containing choline-O-sulfate, taurine and sulfoacetate. In exchange, Nostoc increased exudation of purines and amino acids. Metatranscriptome analysis indicated that Sphagnum host defense was downregulated when in direct contact with the Nostoc symbiont, but not as a result of chemical contact alone. The observations in this study elucidated environmental, metabolic, and physiological underpinnings of the widespread plant–cyanobacterial symbioses with important implications for predicting carbon and nitrogen cycling in peatland ecosystems as well as the basis of general host-microbe interactions.
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Samarah LZ, Vertes A, Anderton CR. Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures. Methods Mol Biol 2022; 2437:61-75. [PMID: 34902140 DOI: 10.1007/978-1-0716-2030-4_4] [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] [Indexed: 06/14/2023]
Abstract
Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.
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Affiliation(s)
- Laith Z Samarah
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Akos Vertes
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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9
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Abstract
Bacillus subtilis is a soil bacterium that can form biofilms, which are communities of cells encased by an extracellular matrix. In these complex communities, cells perform numerous metabolic processes and undergo differentiation into functionally distinct phenotypes as a survival strategy. Because biofilms are often studied in bulk, it remains unclear how metabolite production spatially correlates with B. subtilis phenotypes within biofilm structures. In many cases, we still do not know where these biological processes are occurring in the biofilm. Here, we developed a method to analyze the localization of molecules within sagittal thin sections of B. subtilis biofilms using high-resolution mass spectrometry imaging. We correlated the organization of specific molecules to the localization of well-studied B. subtilis phenotypic reporters determined by confocal laser scanning fluorescence microscopy within analogous biofilm thin sections. The correlations between these two data sets suggest the role of surfactin as a signal for extracellular matrix gene expression in the biofilm periphery and the role of bacillibactin as an iron-scavenging molecule. Taken together, this method will help us generate hypotheses to discover relationships between metabolites and phenotypic cell states in B. subtilis and other biofilm-forming bacteria. IMPORTANCE Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered. Here, we used multimodal imaging to analyze B. subtilis biofilm processes at the metabolic and gene expression levels in biofilm sagittal thin sections. Often, imaging techniques analyze only the top of the surface of the biofilm and miss the multifaceted interactions that occur deep within the biofilm. Our analysis of the sagittal planes of B. subtilis biofilms revealed the distributions of metabolic processes throughout the depths of these structures and allowed us to draw correlations between metabolites and phenotypically important subpopulations of B. subtilis cells. This technique provides a platform to generate hypotheses about the role of specific molecules and their relationships to B. subtilis subpopulations of cells.
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Birer-Williams CMC, Chu RK, Anderton CR, Wright ES. SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions. mSystems 2021; 6:e0090221. [PMID: 34427520 PMCID: PMC8422993 DOI: 10.1128/msystems.00902-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 11/20/2022] Open
Abstract
Communication within the microbiome occurs through an immense diversity of small molecules. Capturing these microbial interactions is a significant challenge due to the complexity of the exometabolome and its sensitivity to environmental stimuli. Traditional methods for acquiring exometabolomic data from interacting microorganisms are limited by their low throughput or lack of sampling depth. To address this challenge, we introduce subtapping (short for substrate tapping), a technique for tapping into extracellular metabolites that are being transferred through the growth substrate during coculture. High-throughput subtapping is made possible by a new coculturing platform, named SubTap, that we engineered to resemble a 96-well plate. The three-dimensional (3D) printed SubTap platform captures the exometabolome in an agar compartment that connects physically separated growth chambers, which permits cell growth without competition for space. We show how SubTap facilitates replicable and quick detection of exometabolites via direct infusion mass spectrometry analysis. Using bacterial isolates from the soil, we apply SubTap to characterize the effects of growth medium, growth duration, and mixed versus unmixed coculturing on the exometabolome. Finally, we demonstrate SubTap's versatility by interrogating microbial interactions in multicultures with up to four strains. IMPORTANCE Improvements in experimental techniques and instrumentation have led to the discovery that the microbiome plays an essential role in human and environmental health. Nevertheless, there remain major impediments to conducting large-scale interrogations of the microbiome in a high-throughput manner, particularly in the field of exometabolomics. Existing methods to coculture microorganisms and interrogate their interactions are labor-intensive and low throughput. This inspired us to develop a solution for coculturing that was (i) open source, (ii) inexpensive, (iii) scalable, (iv) customizable, and (v) compatible with existing mass spectrometry instrumentation. Here, we present SubTap-a 3D printed coculturing platform that permits tapping directly into the growth substrate between physically separated, but interconnected, growth compartments. SubTap allows multiculture (with up to four distinct growth compartments) in spatially mixed or unmixed configurations and enables repeatable results with mass spectrometry, as shown by our validation with known compounds and cultures of one to four organisms.
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Affiliation(s)
- Caroline M. C. Birer-Williams
- Biomolécules et Biotechnologies Végétales (BBV) EA 2106, Université de Tours, Tours, France
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Erik S. Wright
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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11
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Expanding Molecular Coverage in Mass Spectrometry Imaging of Microbial Systems Using Metal-Assisted Laser Desorption/Ionization. Microbiol Spectr 2021; 9:e0052021. [PMID: 34287059 PMCID: PMC8552643 DOI: 10.1128/spectrum.00520-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mass spectrometry imaging (MSI) is becoming an increasingly popular analytical technique to investigate microbial systems. However, differences in the ionization efficiencies of distinct MSI methods lead to biases in terms of what types and classes of molecules can be detected. Here, we sought to increase the molecular coverage of microbial colonies by employing metal-assisted laser desorption/ionization (MetA-LDI) MSI, and we compared our results to more commonly utilized matrix-assisted laser desorption/ionization MALDI MSI. We found substantial (∼67%) overlap in the molecules detected in our analysis of Bacillus subtilis colony biofilms using both methods, but each ionization technique did lead to the identification of a unique subset of molecular species. MetA-LDI MSI tended to identify more small molecules and neutral lipids, whereas MALDI MSI more readily detected other lipids and surfactin species. Putative annotations were made using METASPACE, Metlin, and the BsubCyc database. These annotations were then confirmed from analyses of replicate bacterial colonies using liquid extraction surface analysis tandem mass spectrometry. Additionally, we analyzed B. subtilis biofilms in a polymer-based emulated soil micromodel using MetA-LDI MSI to better understand bacterial processes and metabolism in a native, soil-like environment. We were able to detect different molecular signatures within the micropore regions of the micromodel. We also show that MetA-LDI MSI can be used to analyze microbial biofilms from electrically insulating material. Overall, this study expands the molecular universe of microbial metabolism that can be visualized by MSI. IMPORTANCE Matrix-assisted laser desorption/ionization mass spectrometry imaging is becoming an important technique to investigate molecular processes within microbial colonies and microbiomes under different environmental conditions. However, this method is limited in terms of the types and classes of molecules that can be detected. In this study, we utilized metal-assisted laser desorption/ionization mass spectrometry imaging, which expanded the range of molecules that could be imaged from microbial samples. One advantage of this technique is that the addition of a metal helps facilitate ionization from electrically nonconductive substrates, which allows for the investigation of biofilms grown in polymer-based devices, like soil-emulating micromodels.
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Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
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Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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13
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Daley SK, Cordell GA. Natural Products, the Fourth Industrial Revolution, and the Quintuple Helix. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211003029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The profound interconnectedness of the sciences and technologies embodied in the Fourth Industrial Revolution is discussed in terms of the global role of natural products, and how that interplays with the development of sustainable and climate-conscious practices of cyberecoethnopharmacolomics within the Quintuple Helix for the promotion of a healthier planet and society.
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Affiliation(s)
| | - Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
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14
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Zhan L, Huang X, Xue J, Liu H, Xiong C, Wang J, Nie Z. MALDI-TOF/TOF tandem mass spectrometry imaging reveals non-uniform distribution of disaccharide isomers in plant tissues. Food Chem 2020; 338:127984. [PMID: 33092001 DOI: 10.1016/j.foodchem.2020.127984] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/20/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique for investigating the biomolecular locations within tissues. However, the isomeric compounds are rarely distinguished due to inability of MSI to differentiate isomers in the probing area. Coupling tandem mass spectrometry with MSI can facilitate differentiating isomeric compounds. Here MALDI-TOF/TOF tandem mass spectrometry imaging approach was applied to probing the spatial distributions of isomeric disaccharides in plant tissues. First, MS/MS imaging analysis of disaccharide-matrix droplet spots demonstrated the feasibility of distinguishing isomeric species in tissues, by measuring the relative intensity of specific fragments. Then, tandem MS imaging of disaccharides in onion bulb tissues indicated that sucrose and other unknown non-sucrose disaccharides exhibit heterogeneous locations throughout the tissues. This method enables us to image disaccharide isomers differentially in biological tissues, and to discover new saccharide species in plant. This work also emphasizes the necessity of considering isobaric compounds when interpreting MSI results.
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Affiliation(s)
- Lingpeng Zhan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xi Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jinjuan Xue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jiyun Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; National Center for Mass Spectrometry in Beijing, Beijing 100190, China.
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15
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Chen B, Vavrek M, Gundersdorf R, Zhong W, Cancilla MT. Combining MALDI mass spectrometry imaging and droplet-base surface sampling analysis for tissue distribution, metabolite profiling, and relative quantification of cyclic peptide melanotan II. Anal Chim Acta 2020; 1125:279-287. [PMID: 32674774 DOI: 10.1016/j.aca.2020.05.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/30/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
Peptides have become a fast-growing segment of the pharmaceutical industry over the past few decades. It is essential to develop cutting edge analytical techniques to support the discovery and development of peptide therapeutics, especially to examine their absorption, distribution, metabolism and excretion (ADME) properties. Herein, we utilized two label-free mass spectrometry (MS) based techniques to investigate representative challenges in developing therapeutic peptides, such as tissue distribution, metabolic stability and clearance. A tool proof-of-concept cyclic peptide, melanotan II, was used in this study. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), which is a well-developed label-free imaging technique, was used to map the detailed molecular distribution of melanotan II and its metabolites. Droplet-based liquid microjunction surface sampling liquid chromatography-high resolution mass spectrometry (LMJ-SSP-LC-HRMS) was used in combination with MALDI-MSI to rapidly profile molecular information and provide structural insights on drug and metabolites. Using both techniques in parallel allowed a more comprehensive and complementary data set than using either technique independently. We envision MALDI-MSI and droplet-based LMJ-SSP-LC-HRMS, which can be used in combination or as standalone techniques, to become valuable tools for assessing the in vivo fate of peptide therapeutics in support of drug discovery and development.
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Affiliation(s)
- Bingming Chen
- Department of Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA.
| | - Marissa Vavrek
- Department of Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Richard Gundersdorf
- Department of Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Wendy Zhong
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Mark T Cancilla
- Department of Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA.
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16
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Flint LE, Hamm G, Ready JD, Ling S, Duckett CJ, Cross NA, Cole LM, Smith DP, Goodwin RJA, Clench MR. Characterization of an Aggregated Three-Dimensional Cell Culture Model by Multimodal Mass Spectrometry Imaging. Anal Chem 2020; 92:12538-12547. [PMID: 32786495 PMCID: PMC7497704 DOI: 10.1021/acs.analchem.0c02389] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Mass
spectrometry imaging (MSI) is an established analytical tool
capable of defining and understanding complex tissues by determining
the spatial distribution of biological molecules. Three-dimensional
(3D) cell culture models mimic the pathophysiological environment
of in vivo tumors and are rapidly emerging as a valuable
research tool. Here, multimodal MSI techniques were employed to characterize
a novel aggregated 3D lung adenocarcinoma model, developed by the
group to mimic the in vivo tissue. Regions of tumor
heterogeneity and the hypoxic microenvironment were observed based
on the spatial distribution of a variety of endogenous molecules.
Desorption electrospray ionization (DESI)-MSI defined regions of a
hypoxic core and a proliferative outer layer from metabolite distribution.
Targeted metabolites (e.g., lactate, glutamine, and citrate) were
mapped to pathways of glycolysis and the TCA cycle demonstrating tumor
metabolic behavior. The first application of imaging mass cytometry
(IMC) with 3D cell culture enabled single-cell phenotyping at 1 μm
spatial resolution. Protein markers of proliferation (Ki-67) and hypoxia (glucose transporter 1) defined metabolic
signaling in the aggregoid model, which complemented the metabolite
data. Laser ablation inductively coupled plasma (LA-ICP)-MSI analysis
localized endogenous elements including magnesium and copper, further
differentiating the hypoxia gradient and validating the protein expression.
Obtaining a large amount of molecular information on a complementary
nature enabled an in-depth understanding of the biological processes
within the novel tumor model. Combining powerful imaging techniques
to characterize the aggregated 3D culture highlighted a future methodology
with potential applications in cancer research and drug development.
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Affiliation(s)
- Lucy E Flint
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Gregory Hamm
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 0WG, United Kingdom
| | - Joseph D Ready
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Stephanie Ling
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 0WG, United Kingdom
| | - Catherine J Duckett
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Neil A Cross
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Laura M Cole
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - David P Smith
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Richard J A Goodwin
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 0WG, United Kingdom.,Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
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17
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Recent advances of ambient mass spectrometry imaging for biological tissues: A review. Anal Chim Acta 2020; 1117:74-88. [DOI: 10.1016/j.aca.2020.01.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/30/2022]
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18
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Zink KE, Tarnowski DA, Mandel MJ, Sanchez LM. Optimization of a minimal sample preparation protocol for imaging mass spectrometry of unsectioned juvenile invertebrates. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4458. [PMID: 31693273 PMCID: PMC7145758 DOI: 10.1002/jms.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/02/2019] [Accepted: 10/17/2019] [Indexed: 05/03/2023]
Abstract
Tissue sections have long been the subject matter for the application of imaging mass spectrometry, but recently the technique has been adapted for many other purposes including bacterial colonies and 3D cell culture. Here, we present a simple preparation method for unsectioned invertebrate tissue without the need for fixing, embedding, or slicing. The protocol was used to successfully prepare a Hawaiian bobtail squid hatchling for analysis, and the resulting data detected ions that correspond to compounds present in the host only during its symbiotic colonization by Vibrio fischeri.
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Affiliation(s)
- Katherine E Zink
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612
| | - Denise A Tarnowski
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI 53706
- Department of Microbiology & Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior Street, Chicago, IL 60611
| | - Mark J Mandel
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI 53706
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612
- Corresponding author: Phone: 312-996-0842
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19
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Veličković D, Chu RK, Myers GL, Ahkami AH, Anderton CR. An approach for visualizing the spatial metabolome of an entire plant root system inspired by the Swiss-rolling technique. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4363. [PMID: 31018010 DOI: 10.1002/jms.4363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 05/11/2023]
Abstract
The spatial configuration and morphology of roots are commonly monitored for a better understanding of plant health and development. However, this approach provides minimal details about the biochemistry regulating the observable traits. Therefore, the ability to metabolically map the entire root structure would be of major value. Here, we developed a sample preparation approach that enables imaging of the entire root within a restricted space (width of microscope slide), which was influenced by the Swiss-rolling technique. We were able to image and confidently identify molecules along the entire root structure from rolled-root tissue sections using multiple spatially resolved mass spectrometry approaches.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Gabriel L Myers
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
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20
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Veličković D, Zhang G, Bezbradica D, Bhattacharjee A, Paša-Tolić L, Sharma K, Alexandrov T, Anderton CR. Response Surface Methodology As a New Approach for Finding Optimal MALDI Matrix Spraying Parameters for Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:508-516. [PMID: 32126772 PMCID: PMC7293970 DOI: 10.1021/jasms.9b00074] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Automated spraying devices have become ubiquitous in laboratories employing matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), in part because they permit control of a number of matrix application parameters that can easily be reproduced for intra- and interlaboratory studies. Determining the optimal parameters for MALDI matrix application, such as temperature, flow rate, spraying velocity, number of spraying cycles, and solvent composition for matrix application, is critical for obtaining high-quality MALDI-MSI data. However, there are no established approaches for optimizing these multiple parameters simultaneously. Instead optimization is performed iteratively (i.e., one parameter at a time), which is time-consuming and can lead to overall nonoptimal settings. In this report, we demonstrate the use a novel experimental design and the response surface methodology to optimize five parameters of MALDI matrix application using a robotic sprayer. Thirty-two combinations of MALDI matrix spraying conditions were tested, which allowed us to elucidate relationships between each of the application parameters as determined by MALDI-MS (specifically, using a 15 T Fourier transform ion cyclotron resonance mass spectrometer). As such, we were able to determine the optimal automated spraying parameters that minimized signal delocalization and enabled high MALDI sensitivity. We envision this optimization strategy can be utilized for other matrix application approaches and MALDI-MSI analyses of other molecular classes and tissue types.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Guanshi Zhang
- Center for Renal Precision Medicine, University of Texas Health-San Antonio, San Antonio, Texas 78284, United States
| | - Dejan Bezbradica
- Department of Biochemical Engineering and Biotechnology, Faculty of Technology and Metallurgy, University of Belgrade, Belgrade 11000, Serbia
| | - Arunima Bhattacharjee
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health-San Antonio, San Antonio, Texas 78284, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Center for Renal Precision Medicine, University of Texas Health-San Antonio, San Antonio, Texas 78284, United States
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21
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Spraker JE, Luu GT, Sanchez LM. Imaging mass spectrometry for natural products discovery: a review of ionization methods. Nat Prod Rep 2020; 37:150-162. [PMID: 31364647 PMCID: PMC6992513 DOI: 10.1039/c9np00038k] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Covering: 2009-2019 Over the last decade, methods in imaging mass spectrometry (IMS) have progressively improved and diversified toward a variety of applications in natural products research. Because IMS allows for the spatial mapping of the production and distribution of biologically active molecules in situ, it facilitates phenotype and organelle driven discovery efforts. As practitioners of IMS for natural products discovery, we find one of the most important aspects of these experiments is the sample preparation and compatibility with different ionization sources that are available to a given researcher. As such, we have focused this mini review to cover types of ionization sources that have been used in natural products discovery applications and provided concrete examples of use for natural products discovery while discussing the advantages and limitations of each method. We aim for this article to serve as a resource to guide the broader natural product community interested in IMS toward the application/method that would best serve their natural product discovery needs given the sample and analyte(s) of interest. This mini review has been limited to applications using natural products and thus is not exhaustive of all possible ionization methods which have only been applied to image other types of samples such as mammalian tissues. Additionally, we briefly review how IMS has been coupled with other imaging platforms, such as microscopy, to enhance information outputs as well as offer our future perspectives on the incorporation of IMS in natural products discovery.
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Affiliation(s)
- Joseph E Spraker
- Hexagon Bio, 1505 Adams Drive, Suite A, Menlo Park, CA 94025, USA
| | - Gordon T Luu
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA,
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA,
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22
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Bowman AP, Blakney GT, Hendrickson CL, Ellis SR, Heeren RMA, Smith DF. Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS. Anal Chem 2020; 92:3133-3142. [PMID: 31955581 PMCID: PMC7031845 DOI: 10.1021/acs.analchem.9b04768] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Detailed characterization
of complex biological surfaces by matrix-assisted
laser desorption/ionization (MALDI) mass spectrometry imaging (MSI)
requires instrumentation that is capable of high mass resolving power,
mass accuracy, and dynamic range. Fourier transform ion cyclotron
resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral
performance for MALDI MSI experiments, and often reveals molecular
features that are unresolved on lower performance instrumentation.
Higher magnetic field strength improves all performance characteristics
of FT-ICR; mass resolving power improves linearly, while mass accuracy
and dynamic range improve quadratically with magnetic field strength.
Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving
power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below
100 ppb, and dynamic range per pixel over 500:1 were obtained from
the direct analysis of biological tissue sections. Molecular features
with m/z differences as small as
1.79 mDa were resolved and identified with high mass accuracy. These
features allow for the separation and identification of lipids to
the underlying structures of tissues. The unique molecular detail,
accuracy, sensitivity, and dynamic range combined in a 21T MALDI FT-ICR
MSI experiment enable researchers to visualize molecular structures
in complex tissues that have remained hidden until now. The instrument
described allows for future innovative, such as high-end studies to
unravel the complexity of biological, geological, and engineered organic
material surfaces with an unsurpassed detail.
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Affiliation(s)
- Andrew P Bowman
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Greg T Blakney
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States.,Department of Chemistry and Biochemistry , Florida State University , 95 Chieftain Way , Tallahassee , Florida 32306 , United States
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Donald F Smith
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States
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23
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Veličkovic D, Liao HL, Vilgalys R, Chu RK, Anderton CR. Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization. JOURNAL OF NATURAL PRODUCTS 2019; 82:1382-1386. [PMID: 31009217 DOI: 10.1021/acs.jnatprod.8b01050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Root alkaloids remain highly unexplored in ectomycorrhizae development studies. By employing ultrahigh mass resolution mass spectrometry imaging techniques, we showed substantial relocation and transformation of piperidine alkaloids in pine root tips in response to Suillus mycorrhization. We imaged, in the time frame of ectomycorrhizae formation, a completely different alkaloid profile in Pinus strobus, where basidiospores of Suillus spraguei induce morphogenesis of symbiotic tissues, than in Pinus taeda, where such interaction fails to induce morphogenesis. On the basis of spatial colocalization studies, we proposed some alternative routes for biosynthesis of these alkaloids that supplement existing literature data.
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Affiliation(s)
- Dušan Veličkovic
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Hui-Ling Liao
- Biology Department , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
- North Florida Research and Education Center , University of Florida , 155 Research Road , Quincy , Florida 32351 , United States
| | - Rytas Vilgalys
- Biology Department , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
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24
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Castellanos A, Ramirez CE, Michalkova V, Nouzova M, Noriega FG, Francisco FL. Three Dimensional Secondary Ion Mass Spectrometry Imaging (3D-SIMS) of Aedes aegypti ovarian follicles. JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY 2019; 34:874-883. [PMID: 31680712 PMCID: PMC6824543 DOI: 10.1039/c8ja00425k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The mobilization of nutrient reserves into the ovaries of Aedes aegypti mosquitoes after sugar-feeding plays a vital role in the female's reproductive maturation. In the present work, three-dimensional secondary ion mass spectrometry imaging (3D-SIMS) was used to generate ultrahigh spatial resolution (~1 μm) chemical maps and study the composition and spatial distribution of lipids at the single ovarian follicle level (~100 μm in size). 3D-Mass Spectrometry Imaging (3D-MSI) allowed the identification of cellular types in the follicle (oocyte, nurse and follicular cells) using endogenous markers, and revealed that most of the triacyglycerides (TGs) were compartmentalized in the oocyte region. By comparing follicles from water-fed and sugar-fed females (n=2), 3D-MSI-Time of Flight-SIMS showed that TGs were more abundant in ovarian follicles of sugar-fed females; despite relative sample reproducibility per feeding condition, more biological replicates will better support the trends observed. While the current 3D-MSI-TOF-SIMS does not permit MS/MS analysis of the lipid species, complementary LC-MS/MS analysis of the ovarian follicles aided tentative lipid assignments of the SIMS data. The combination of these MS approaches is giving us a first glimpse of the distribution of functionally relevant ovarian lipid molecules at the cellular level. These new tools can be used to investigate the roles of different lipids on follicle fitness and overall mosquito reproductive output.
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Affiliation(s)
- Anthony Castellanos
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Cesar E. Ramirez
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Veronika Michalkova
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
| | - Marcela Nouzova
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
- Institute of Parasitology, Biology Centre CAS, Ceske, Budejovice, Czech Republic; and
| | - Fernando G. Noriega
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Fernández-Lima Francisco
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
- Corresponding author: Francisco A. Fernández-Lima, Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St AHC4-233, Miami, FL 33199, USA;
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25
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Stopka SA, Samarah LZ, Shaw JB, Liyu AV, Veličković D, Agtuca BJ, Kukolj C, Koppenaal DW, Stacey G, Paša-Tolić L, Anderton CR, Vertes A. Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution Using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry. Anal Chem 2019; 91:5028-5035. [PMID: 30821434 DOI: 10.1021/acs.analchem.8b05084] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS) is an indispensable analytical tool to capture the array of metabolites within complex biological systems. However, conventional MS-based metabolomic workflows require extensive sample processing and separation resulting in limited throughput and potential alteration of the native molecular states in these systems. Ambient ionization methods, capable of sampling directly from tissues, circumvent some of these issues but require high-performance MS to resolve the molecular complexity within these samples. Here, we demonstrate a unique combination of laser ablation electrospray ionization (LAESI) coupled with a 21 tesla Fourier transform ion cyclotron resonance (21T-FTICR) for direct MS analysis and imaging applications. This analytical platform provides isotopic fine structure information directly from biological tissues, enabling the rapid assignment of molecular formulas and delivering a higher degree of confidence for molecular identification.
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Affiliation(s)
- Sylwia A Stopka
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Laith Z Samarah
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Caroline Kukolj
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Akos Vertes
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
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26
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Nagy G, Veličković D, Chu RK, Carrell AA, Weston DJ, Ibrahim YM, Anderton CR, Smith RD. Towards resolving the spatial metabolome with unambiguous molecular annotations in complex biological systems by coupling mass spectrometry imaging with structures for lossless ion manipulations. Chem Commun (Camb) 2019; 55:306-309. [PMID: 30534702 PMCID: PMC6537888 DOI: 10.1039/c8cc07482h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We demonstrate the coupling of liquid extraction surface analysis (LESA) to structures for lossless ion manipulations in conjunction with serpentine ultralong path with extending routing (SLIM SUPER) ion mobility-mass spectrometry (IM-MS) for the unambiguous annotation of important isomeric glycoforms in carbon-fixing communities.
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Affiliation(s)
- Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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