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Chappel JR, Kirkwood-Donelson KI, Reif DM, Baker ES. From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome. Anal Bioanal Chem 2024; 416:2189-2202. [PMID: 37875675 PMCID: PMC10954412 DOI: 10.1007/s00216-023-04991-2] [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: 08/30/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023]
Abstract
The goal of lipidomic studies is to provide a broad characterization of cellular lipids present and changing in a sample of interest. Recent lipidomic research has significantly contributed to revealing the multifaceted roles that lipids play in fundamental cellular processes, including signaling, energy storage, and structural support. Furthermore, these findings have shed light on how lipids dynamically respond to various perturbations. Continued advancement in analytical techniques has also led to improved abilities to detect and identify novel lipid species, resulting in increasingly large datasets. Statistical analysis of these datasets can be challenging not only because of their vast size, but also because of the highly correlated data structure that exists due to many lipids belonging to the same metabolic or regulatory pathways. Interpretation of these lipidomic datasets is also hindered by a lack of current biological knowledge for the individual lipids. These limitations can therefore make lipidomic data analysis a daunting task. To address these difficulties and shed light on opportunities and also weaknesses in current tools, we have assembled this review. Here, we illustrate common statistical approaches for finding patterns in lipidomic datasets, including univariate hypothesis testing, unsupervised clustering, supervised classification modeling, and deep learning approaches. We then describe various bioinformatic tools often used to biologically contextualize results of interest. Overall, this review provides a framework for guiding lipidomic data analysis to promote a greater assessment of lipidomic results, while understanding potential advantages and weaknesses along the way.
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Affiliation(s)
- Jessie R Chappel
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27606, USA
| | - Kaylie I Kirkwood-Donelson
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - David M Reif
- Predictive Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA.
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA.
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Steven RT, Burton A, Taylor AJ, Robinson KN, Dexter A, Nikula CJ, Bunch J. Evaluation of Inlet Temperature with Three Sprayer Designs for Desorption Electrospray Ionization Mass Spectrometry Tissue Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:224-233. [PMID: 38181191 DOI: 10.1021/jasms.3c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Mass spectrometry imaging (MSI) allows for the spatially resolved detection of endogenous and exogenous molecules and atoms in biological samples, typically prepared as thin tissue sections. Desorption electrospray ionization (DESI) is one of the most commonly utilized MSI modalities in preclinical research. DESI ion source technology is still rapidly evolving, with new sprayer designs and heated inlet capillaries having recently been incorporated in commercially available systems. In this study, three iterations of DESI sprayer designs are evaluated: (1) the first, and until recently only, commercially available Waters sprayer; (2) a developmental desorption electro-flow focusing ionization (DEFFI)-type sprayer; and (3) a prototype of the newly released Waters commercial sprayer. A heated inlet capillary is also employed, allowing for controlled inlet temperatures up to 500 °C. These three sprayers are evaluated by comparative tissue imaging analyses of murine testes across this temperature range. Single ion intensity versus temperature trends are evaluated as exemplar cases for putatively identified species of interest, such as lactate and glutamine. A range of trends are observed, where intensities follow either increasing, decreasing, bell-shaped, or other trends with temperature. Data for all sprayers show approximately similar trends for the ions studied, with the commercial prototype sprayer (sprayer version 3) matching or outperforming the other sprayers for the ions investigated. Finally, the mass spectra acquired using sprayer version 3 are evaluated by uniform manifold approximation and projection (UMAP) and k-means clustering. This approach is shown to provide valuable insight that is complementary to the presented univariate evaluation for reviewing the parameter space in this study. Full spectral temperature optimization data are provided as supporting data to enable other researchers to design experiments that are optimal for specific ions.
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Affiliation(s)
- Rory T Steven
- National Physical Laboratory Teddington TW11 0LW, U.K
| | - Amy Burton
- National Physical Laboratory Teddington TW11 0LW, U.K
| | - Adam J Taylor
- National Physical Laboratory Teddington TW11 0LW, U.K
| | | | - Alex Dexter
- National Physical Laboratory Teddington TW11 0LW, U.K
| | | | - Josephine Bunch
- National Physical Laboratory Teddington TW11 0LW, U.K
- Imperial College London, Department of Metabolism, Digestion and Reproduction, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, U.K
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Lee S, Verkhoturov DS, Eller MJ, Verkhoturov SV, Shaw MA, Gwon K, Kim Y, Lucien F, Malhi H, Revzin A, Schweikert EA. Nanoprojectile Secondary Ion Mass Spectrometry Enables Multiplexed Analysis of Individual Hepatic Extracellular Vesicles. ACS NANO 2023; 17:23584-23594. [PMID: 38033295 PMCID: PMC10985841 DOI: 10.1021/acsnano.3c06604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Extracellular vesicles (EVs) are nanoscale lipid bilayer particles secreted by cells. EVs may carry markers of the tissue of origin and its disease state, which makes them incredibly promising for disease diagnosis and surveillance. While the armamentarium of EV analysis technologies is rapidly expanding, there remains a strong need for multiparametric analysis with single EV resolution. Nanoprojectile (NP) secondary ion mass spectrometry (NP-SIMS) relies on bombarding a substrate of interest with individual gold NPs resolved in time and space. Each projectile creates an impact crater of 10-20 nm in diameter while molecules emitted from each impact are mass analyzed and recorded as individual mass spectra. We demonstrate the utility of NP-SIMS for statistical analysis of single EVs derived from normal liver cells (hepatocytes) and liver cancer cells. EVs were captured on antibody (Ab)-functionalized gold substrate and then labeled with Abs carrying lanthanide (Ln) MS tags (Ab@Ln). These tags targeted four markers selected for identifying all EVs, and specific to hepatocytes or liver cancer. NP-SIMS was used to detect Ab@Ln-tags colocalized on the same EV and to construct scatter plots of surface marker expression for thousands of EVs with the capability of categorizing individual EVs. Additionally, NP-SIMS revealed information about the chemical nanoenvironment where targeted moieties colocalized. Our approach allowed analysis of population heterogeneity with single EV resolution and distinguishing between hepatocyte and liver cancer EVs based on surface marker expression. NP-SIMS holds considerable promise for multiplexed analysis of single EVs and may become a valuable tool for identifying and validating EV biomarkers of cancer and other diseases.
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Affiliation(s)
- Seonhwa Lee
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Michael J. Eller
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | | | - Michael A. Shaw
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | - Kihak Gwon
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yohan Kim
- Departments of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fabrice Lucien
- Departments of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | - Emile A. Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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Lee S, Verkhoturov DS, Eller MJ, Verkhoturov SV, Shaw MA, Gwon K, Kim Y, Lucien F, Malhi H, Revzin A, Schweikert EA. Nanoprojectile Secondary Ion Mass Spectrometry Enables Multiplexed Analysis of Individual Hepatic Extracellular Vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554053. [PMID: 37662200 PMCID: PMC10473594 DOI: 10.1101/2023.08.21.554053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Extracellular vesicles (EVs) are nanoscale lipid bilayer particles secreted by cells. EVs may carry markers of the tissue of origin and its disease state which makes them incredibly promising for disease diagnosis and surveillance. While the armamentarium of EV analysis technologies is rapidly expanding, there remains a strong need for multiparametric analysis with single EV resolution. Nanoprojectile (NP) secondary ion mass spectrometry (NP-SIMS) relies on bombarding a substrate of interest with individual gold NPs resolved in time and space. Each projectile creates an impact crater of 10-20 nm in diameter while molecules emitted from each impact are mass analyzed and recorded as individual mass spectra. We demonstrate the utility of NP-SIMS for analysis of single EVs derived from normal liver cells (hepatocytes) and liver cancer cells. EVs were captured on antibody (Ab)-functionalized gold substrate then labeled with Abs carrying lanthanide (Ln) MS tags (Ab@Ln). These tags targeted four markers selected for identifying all EVs, and specific to hepatocytes or liver cancer. NP-SIMS was used to detect Ab@Ln-tags co-localized on the same EV and to construct scatter plots of surface marker expression for thousands of EVs with the capability of categorizing individual EVs. Additionally, NP-SIMS revealed information about the chemical nano-environment where targeted moieties co-localized. Our approach allowed analysis of population heterogeneity with single EV resolution and distinguishing between hepatocyte and liver cancer EVs based on surface marker expression. NP-SIMS holds considerable promise for multiplexed analysis of single EVs and may become a valuable tool for identifying and validating EV biomarkers of cancer and other diseases.
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