1
|
Colley ME, Esselman AB, Scott CF, Spraggins JM. High-Specificity Imaging Mass Spectrometry. Annu Rev Anal Chem (Palo Alto Calif) 2024. [PMID: 38594938 DOI: 10.1146/annurev-anchem-083023-024546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Imaging mass spectrometry (IMS) enables highly multiplexed, untargeted tissue mapping for a broad range of molecular classes, facilitating in situ biological discovery. Yet, challenges persist in molecular specificity, which is the ability to discern one molecule from another, and spatial specificity, which is the ability to link untargeted imaging data to specific tissue features. Instrumental developments have dramatically improved IMS spatial resolution, allowing molecular observations to be more readily associated with distinct tissue features across spatial scales, ranging from larger anatomical regions to single cells. High-performance mass analyzers and systems integrating ion mobility technologies are also becoming more prevalent, further improving molecular coverage and the ability to discern chemical identity. This review provides an overview of recent advancements in high-specificity IMS that are providing critical biological context to untargeted molecular imaging, enabling integrated analyses, and addressing advanced biomedical research applications.
Collapse
Affiliation(s)
- Madeline E Colley
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison B Esselman
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Claire F Scott
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffrey M Spraggins
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- 5Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
2
|
Klein D, Rivera ES, Caprioli RM, Spraggins JM. Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer. Anal Chem 2024; 96:5065-5070. [PMID: 38517028 PMCID: PMC10993197 DOI: 10.1021/acs.analchem.3c05252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
In this work, we demonstrate rapid, high spatial, and high spectral resolution imaging of intact proteins by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on a hybrid quadrupole-reflectron time-of-flight (qTOF) mass spectrometer equipped with trapped ion mobility spectrometry (TIMS). Historically, untargeted MALDI IMS of proteins has been performed on TOF mass spectrometers. While advances in TOF instrumentation have enabled rapid, high spatial resolution IMS of intact proteins, TOF mass spectrometers generate relatively low-resolution mass spectra with limited mass accuracy. Conversely, the implementation of MALDI sources on high-resolving power Fourier transform (FT) mass spectrometers has allowed IMS experiments to be conducted with high spectral resolution with the caveat of increasingly long data acquisition times. As illustrated here, qTOF mass spectrometers enable protein imaging with the combined advantages of TOF and FT mass spectrometers. Protein isotope distributions were resolved for both a protein standard mixture and proteins detected from a whole-body mouse pup tissue section. Rapid (∼10 pixels/s) 10 μm lateral spatial resolution IMS was performed on a rat brain tissue section while maintaining isotopic spectral resolution. Lastly, proof-of-concept MALDI-TIMS data was acquired from a protein mixture to demonstrate the ability to differentiate charge states by ion mobility. These experiments highlight the advantages of qTOF and timsTOF platforms for resolving and interpreting complex protein spectra generated from tissue by IMS.
Collapse
Affiliation(s)
- Dustin
R. Klein
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Emilio S. Rivera
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Richard M. Caprioli
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
| |
Collapse
|
3
|
Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2024:10.1038/s41556-024-01384-0. [PMID: 38429479 DOI: 10.1038/s41556-024-01384-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
| |
Collapse
|
4
|
Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Adrien Maria Vierdag WM, Volkmann N, Wählby C, Wang SS, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ArXiv 2024:arXiv:2401.13022v4. [PMID: 38351940 PMCID: PMC10862930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges, and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
Collapse
Affiliation(s)
- Nikki Bialy
- Morgridge Institute for Research, Madison, USA
| | | | | | | | | | | | | | | | | | | | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Imaging Platform, Cambridge, USA
| | - Kevin Eliceiri
- Morgridge Institute for Research, Madison, USA
- University of Wisconsin-Madison, Madison, USA
| | | | | | | | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | - Michael Halter
- National Institute of Standards and Technology, Gaithersburg, USA
| | | | | | | | - Alex Laude
- Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lundberg
- Stanford University, Palo Alto, USA
- SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, USA
| | - Leonel Malacrida
- Institut Pasteur de Montevideo, & Universidad de la República, Montevideo, Uruguay
| | - Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany
| | - Glyn Nelson
- Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Anne L Plant
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | | | | | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, USA
| | | | | | | | | | - Ziv Yaniv
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | |
Collapse
|
5
|
Good CJ, Butrico CE, Colley ME, Gibson-Corley KN, Cassat JE, Spraggins JM, Caprioli RM. In situ lipidomics of Staphylococcus aureus osteomyelitis using imaging mass spectrometry. bioRxiv 2023:2023.12.01.569690. [PMID: 38077019 PMCID: PMC10705574 DOI: 10.1101/2023.12.01.569690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Osteomyelitis occurs when Staphylococcus aureus invades the bone microenvironment, resulting in a bone marrow abscess with a spatially defined architecture of cells and biomolecules. Imaging mass spectrometry and microscopy are invaluable tools that can be employed to interrogate the lipidome of S. aureus-infected murine femurs to reveal metabolic and signaling consequences of infection. Here, nearly 250 lipids were spatially mapped to healthy and infection-associated morphological features throughout the femur, establishing composition profiles for tissue types. Ether lipids and arachidonoyl lipids were significantly altered between cells and tissue structures in abscesses, suggesting their roles in abscess formation and inflammatory signaling. Sterols, triglycerides, bis(monoacylglycero)phosphates, and gangliosides possessed ring-like distributions throughout the abscess, indicating dysregulated lipid metabolism in a subpopulation of leukocytes that cannot be discerned with traditional microscopy. These data provide chemical insight into the signaling function and metabolism of cells in the fibrotic border of abscesses, likely characteristic of lipid-laden macrophages.
Collapse
Affiliation(s)
- Christopher J. Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Casey E. Butrico
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madeline E. Colley
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Katherine N. Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E. Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Medicine, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
| |
Collapse
|
6
|
Djambazova KV, van Ardenne JM, Spraggins JM. Advances in Imaging Mass Spectrometry for Biomedical and Clinical Research. Trends Analyt Chem 2023; 169:117344. [PMID: 38045023 PMCID: PMC10688507 DOI: 10.1016/j.trac.2023.117344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Imaging mass spectrometry (IMS) allows for the untargeted mapping of biomolecules directly from tissue sections. This technology is increasingly integrated into biomedical and clinical research environments to supplement traditional microscopy and provide molecular context for tissue imaging. IMS has widespread clinical applicability in the fields of oncology, dermatology, microbiology, and others. This review summarizes the two most widely employed IMS technologies, matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI), and covers technological advancements, including efforts to increase spatial resolution, specificity, and throughput. We also highlight recent biomedical applications of IMS, primarily focusing on disease diagnosis, classification, and subtyping.
Collapse
Affiliation(s)
- Katerina V. Djambazova
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jacqueline M. van Ardenne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| |
Collapse
|
7
|
Pi H, Sun R, McBride JR, Kruse ARS, Gibson-Corley KN, Krystofiak ES, Nicholson MR, Spraggins JM, Zhou Q, Skaar EP. Clostridioides difficile ferrosome organelles combat nutritional immunity. Nature 2023; 623:1009-1016. [PMID: 37968387 PMCID: PMC10822667 DOI: 10.1038/s41586-023-06719-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/05/2023] [Indexed: 11/17/2023]
Abstract
Iron is indispensable for almost all forms of life but toxic at elevated levels1-4. To survive within their hosts, bacterial pathogens have evolved iron uptake, storage and detoxification strategies to maintain iron homeostasis1,5,6. Recent studies showed that three Gram-negative environmental anaerobes produce iron-containing ferrosome granules7,8. However, it remains unclear whether ferrosomes are generated exclusively by Gram-negative bacteria. The Gram-positive bacterium Clostridioides difficile is the leading cause of nosocomial and antibiotic-associated infections in the USA9. Here we report that C. difficile undergoes an intracellular iron biomineralization process and stores iron in membrane-bound ferrosome organelles containing non-crystalline iron phosphate biominerals. We found that a membrane protein (FezA) and a P1B6-ATPase transporter (FezB), repressed by both iron and the ferric uptake regulator Fur, are required for ferrosome formation and play an important role in iron homeostasis during transition from iron deficiency to excess. Additionally, ferrosomes are often localized adjacent to cellular membranes as shown by cryo-electron tomography. Furthermore, using two mouse models of C. difficile infection, we demonstrated that the ferrosome system is activated in the inflamed gut to combat calprotectin-mediated iron sequestration and is important for bacterial colonization and survival during C. difficile infection.
Collapse
Affiliation(s)
- Hualiang Pi
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Rong Sun
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James R McBride
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN, USA
| | - Angela R S Kruse
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan S Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Maribeth R Nicholson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiangjun Zhou
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN, USA.
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
8
|
Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2023; 25:1089-1100. [PMID: 37468756 PMCID: PMC10681365 DOI: 10.1038/s41556-023-01194-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the production phase: the generation of reference spatial maps of functional tissue units across many organs from diverse populations and the creation of mapping tools and infrastructure to advance biomedical research.
Collapse
Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
| |
Collapse
|
9
|
Quardokus EM, Saunders DC, McDonough E, Hickey JW, Werlein C, Surrette C, Rajbhandari P, Casals AM, Tian H, Lowery L, Neumann EK, Björklund F, Neelakantan TV, Croteau J, Wiblin AE, Fisher J, Livengood AJ, Dowell KG, Silverstein JC, Spraggins JM, Pryhuber GS, Deutsch G, Ginty F, Nolan GP, Melov S, Jonigk D, Caldwell MA, Vlachos IS, Muller W, Gehlenborg N, Stockwell BR, Lundberg E, Snyder MP, Germain RN, Camarillo JM, Kelleher NL, Börner K, Radtke AJ. Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. Nat Methods 2023; 20:1174-1178. [PMID: 37468619 PMCID: PMC10406602 DOI: 10.1038/s41592-023-01846-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/14/2023] [Indexed: 07/21/2023]
Abstract
Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.
Collapse
Affiliation(s)
- Ellen M Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Diane C Saunders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Diabetes Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Anna Martinez Casals
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hua Tian
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | | | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Frida Björklund
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Josh Croteau
- Department of Business Development, BioLegend Inc., San Diego, CA, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam PLC, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Inc., Danvers, MA, USA
| | - April J Livengood
- Department of Protein and Cell Analysis, Thermo Fisher Scientific, Carlsbad, CA, USA
| | | | - Jonathan C Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Gloria S Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Gail Deutsch
- Department of Pathology, University of Washington Medical Center, Seattle, WA, USA
| | | | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute of Pathology, RWTH University of Aachen, Aachen, Germany
| | - Michael A Caldwell
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Ioannis S Vlachos
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Werner Muller
- Miltenyi Biotec B.V. and Co. KG, Bergisch Gladbach, Germany
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Emma Lundberg
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald N Germain
- Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Inotiv, Nashville, TN, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Andrea J Radtke
- Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA.
| |
Collapse
|
10
|
Jain Y, Godwin LL, Ju Y, Sood N, Quardokus EM, Bueckle A, Longacre T, Horning A, Lin Y, Esplin ED, Hickey JW, Snyder MP, Patterson NH, Spraggins JM, Börner K. Segmentation of human functional tissue units in support of a Human Reference Atlas. Commun Biol 2023; 6:717. [PMID: 37468557 PMCID: PMC10356924 DOI: 10.1038/s42003-023-04848-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/17/2023] [Indexed: 07/21/2023] Open
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to compile a Human Reference Atlas (HRA) for the healthy adult body at the cellular level. Functional tissue units (FTUs), relevant for HRA construction, are of pathobiological significance. Manual segmentation of FTUs does not scale; highly accurate and performant, open-source machine-learning algorithms are needed. We designed and hosted a Kaggle competition that focused on development of such algorithms and 1200 teams from 60 countries participated. We present the competition outcomes and an expanded analysis of the winning algorithms on additional kidney and colon tissue data, and conduct a pilot study to understand spatial location and density of FTUs across the kidney. The top algorithm from the competition, Tom, outperforms other algorithms in the expanded study, while using fewer computational resources. Tom was added to the HuBMAP infrastructure to run kidney FTU segmentation at scale-showcasing the value of Kaggle competitions for advancing research.
Collapse
Affiliation(s)
- Yashvardhan Jain
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
| | - Leah L Godwin
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA
| | - Yingnan Ju
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA
| | - Naveksha Sood
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA
| | - Ellen M Quardokus
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA
| | - Andreas Bueckle
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA
| | - Teri Longacre
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aaron Horning
- Thermo Fisher Scientific, South San Francisco, CA, 94080, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Edward D Esplin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - John W Hickey
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
| |
Collapse
|
11
|
Marshall CR, Farrow MA, Djambazova KV, Spraggins JM. Untangling Alzheimer's disease with spatial multi-omics: a brief review. Front Aging Neurosci 2023; 15:1150512. [PMID: 37533766 PMCID: PMC10390637 DOI: 10.3389/fnagi.2023.1150512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of neurological dementia, specified by extracellular β-amyloid plaque deposition, neurofibrillary tangles, and cognitive impairment. AD-associated pathologies like cerebral amyloid angiopathy (CAA) are also affiliated with cognitive impairment and have overlapping molecular drivers, including amyloid buildup. Discerning the complexity of these neurological disorders remains a significant challenge, and the spatiomolecular relationships between pathogenic features of AD and AD-associated pathologies remain poorly understood. This review highlights recent developments in spatial omics, including profiling and molecular imaging methods, and how they are applied to AD. These emerging technologies aim to characterize the relationship between how specific cell types and tissue features are organized in combination with mapping molecular distributions to provide a systems biology view of the tissue microenvironment around these neuropathologies. As spatial omics methods achieve greater resolution and improved molecular coverage, they are enabling deeper characterization of the molecular drivers of AD, leading to new possibilities for the prediction, diagnosis, and mitigation of this debilitating disease.
Collapse
Affiliation(s)
- Cody R. Marshall
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Melissa A. Farrow
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Jeffrey M. Spraggins
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| |
Collapse
|
12
|
Unsihuay D, Phipps WS, Paulovich AG, Chapman JR, Ducret A, Eberlin LS, Spraggins JM, Goodwin RJ. Tissue Mass Spectrometry: How Solid Is Our Future? Clin Chem 2023; 69:676-683. [PMID: 37293883 PMCID: PMC10732568 DOI: 10.1093/clinchem/hvad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/01/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Daisy Unsihuay
- Clinical Chemistry Fellow, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Clinical Chemistry Fellow, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - William S. Phipps
- Assistant Professor, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Amanda G. Paulovich
- Professor and Aven Foundation Endowed Chair, Translational Science and Therapeutics, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Director, CLIA Targeted Proteomic Laboratory, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Director, Clinical Research Proteomics Platform, Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
- Professor, Department of Medicine / Division of Oncology, University of Washington School of Medicine, Seattle, WA, United States
| | - Jessica R. Chapman
- Assistant Attending Mass Spectrometrist, Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Axel Ducret
- Project Leader, Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Livia S. Eberlin
- Associate Professor, Department of Surgery, Baylor College of Medicine, Houston, TX, United States
| | - Jeffrey M Spraggins
- Assistant Professor, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
- Assistant Professor, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
- Assistant Professor, Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Richard J.A. Goodwin
- Senior Director, Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Cambridge, United Kingdom
- Professor, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
13
|
Esselman AB, Patterson NH, Migas LG, Dufresne M, Djambazova KV, Colley ME, Van de Plas R, Spraggins JM. Microscopy-Directed Imaging Mass Spectrometry for Rapid High Spatial Resolution Molecular Imaging of Glomeruli. J Am Soc Mass Spectrom 2023. [PMID: 37319264 DOI: 10.1021/jasms.3c00033] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The glomerulus is a multicellular functional tissue unit (FTU) of the nephron that is responsible for blood filtration. Each glomerulus contains multiple substructures and cell types that are crucial for their function. To understand normal aging and disease in kidneys, methods for high spatial resolution molecular imaging within these FTUs across whole slide images is required. Here we demonstrate a workflow using microscopy-driven selected sampling to enable 5 μm pixel size matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) of all glomeruli within whole slide human kidney tissues. Such high spatial resolution imaging entails large numbers of pixels, increasing the data acquisition times. Automating FTU-specific tissue sampling enables high-resolution analysis of critical tissue structures, while concurrently maintaining throughput. Glomeruli were automatically segmented using coregistered autofluorescence microscopy data, and these segmentations were translated into MALDI IMS measurement regions. This allowed high-throughput acquisition of 268 glomeruli from a single whole slide human kidney tissue section. Unsupervised machine learning methods were used to discover molecular profiles of glomerular subregions and differentiate between healthy and diseased glomeruli. Average spectra for each glomerulus were analyzed using Uniform Manifold Approximation and Projection (UMAP) and k-means clustering, yielding 7 distinct groups of differentiated healthy and diseased glomeruli. Pixel-wise k-means clustering was applied to all glomeruli, showing unique molecular profiles localized to subregions within each glomerulus. Automated microscopy-driven, FTU-targeted acquisition for high spatial resolution molecular imaging maintains high-throughput and enables rapid assessment of whole slide images at cellular resolution and identification of tissue features associated with normal aging and disease.
Collapse
Affiliation(s)
- Allison B Esselman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Lukasz G Migas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 Delft, The Netherlands
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Madeline E Colley
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 Delft, The Netherlands
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|
14
|
Sharman K, Patterson NH, Migas LG, Neumann EK, Allen J, Gibson-Corley KN, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. MALDI IMS-Derived Molecular Contour Maps: Augmenting Histology Whole-Slide Images. J Am Soc Mass Spectrom 2023; 34:905-912. [PMID: 37061946 PMCID: PMC10787559 DOI: 10.1021/jasms.2c00370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Imaging mass spectrometry (IMS) provides untargeted, highly multiplexed maps of molecular distributions in tissue. Ion images are routinely presented as heatmaps and can be overlaid onto complementary microscopy images that provide greater context. However, heatmaps use transparency blending to visualize both images, obscuring subtle quantitative differences and distribution gradients. Here, we developed a contour mapping approach that combines information from IMS ion intensity distributions with that of stained microscopy. As a case study, we applied this approach to imaging data from Staphylococcus aureus-infected murine kidney. In a univariate, or single molecular species, use-case of the contour map representation of IMS data, certain lipids colocalizing with regions of infection were selected using Pearson's correlation coefficient. Contour maps of these lipids overlaid with stained microscopy showed enhanced visualization of lipid distributions and spatial gradients in and around the bacterial abscess as compared to traditional heatmaps. The full IMS data set comprising hundreds of individual ion images was then grouped into a smaller subset of representative patterns using non-negative matrix factorization (NMF). Contour maps of these multivariate NMF images revealed distinct molecular profiles of the major abscesses and surrounding immune response. This contour mapping workflow also enabled a molecular visualization of the transition zone at the host-pathogen interface, providing potential clues about the spatial molecular dynamics beyond what histological staining alone provides. In summary, we developed a new IMS-based contour mapping approach to augment classical stained microscopy images, providing an enhanced and more interpretable visualization of IMS-microscopy multimodal molecular imaging data sets.
Collapse
Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jamie Allen
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|
15
|
Lee HH, Tang Y, Bao S, Yang Q, Xu X, Schey KL, Spraggins JM, Huo Y, Landman BA. Unsupervised Registration Refinement for Generating Unbiased Eye Atlas. Proc SPIE Int Soc Opt Eng 2023; 12464:1246422. [PMID: 37465097 PMCID: PMC10353780 DOI: 10.1117/12.2653753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
With the confounding effects of demographics across large-scale imaging surveys, substantial variation is demonstrated with the volumetric structure of orbit and eye anthropometry. Such variability increases the level of difficulty to localize the anatomical features of the eye organs for populational analysis. To adapt the variability of eye organs with stable registration transfer, we propose an unbiased eye atlas template followed by a hierarchical coarse-to-fine approach to provide generalized eye organ context across populations. Furthermore, we retrieved volumetric scans from 1842 healthy patients for generating an eye atlas template with minimal biases. Briefly, we select 20 subject scans and use an iterative approach to generate an initial unbiased template. We then perform metric-based registration to the remaining samples with the unbiased template and generate coarse registered outputs. The coarse registered outputs are further leveraged to train a deep probabilistic network, which aims to refine the organ deformation in unsupervised setting. Computed tomography (CT) scans of 100 de-identified subjects are used to generate and evaluate the unbiased atlas template with the hierarchical pipeline. The refined registration shows the stable transfer of the eye organs, which were well-localized in the high-resolution (0.5 mm3) atlas space and demonstrated a significant improvement of 2.37% Dice for inverse label transfer performance. The subject-wise qualitative representations with surface rendering successfully demonstrate the transfer details of the organ context and showed the applicability of generalizing the morphological variation across patients.
Collapse
Affiliation(s)
- Ho Hin Lee
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Yucheng Tang
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Shunxing Bao
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Qi Yang
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Xin Xu
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA 37232
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Radiology and Radiological Science, Vanderbilt University Medical Center, Nashville, TN, USA 37235
| |
Collapse
|
16
|
Djambazova KV, Dufresne M, Migas LG, Kruse ARS, Van de Plas R, Caprioli RM, Spraggins JM. MALDI TIMS IMS of Disialoganglioside Isomers─GD1a and GD1b in Murine Brain Tissue. Anal Chem 2023; 95:1176-1183. [PMID: 36574465 DOI: 10.1021/acs.analchem.2c03939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gangliosides are acidic glycosphingolipids, containing ceramide moieties and oligosaccharide chains with one or more sialic acid residue(s) and are highly diverse isomeric structures with distinct biological roles. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables the untargeted spatial analysis of gangliosides, among other biomolecules, directly from tissue sections. Integrating trapped ion mobility spectrometry with MALDI IMS allows for the analysis of isomeric lipid structures in situ. Here, we demonstrate the gas-phase separation and identification of disialoganglioside isomers GD1a and GD1b that differ in the position of a sialic acid residue, in multiple samples, including a standard mixture of both isomers, a biological extract, and directly from thin tissue sections. The unique spatial distributions of GD1a/b (d36:1) and GD1a/b (d38:1) isomers were determined in rat hippocampus and spinal cord tissue sections, demonstrating the ability to structurally characterize and spatially map gangliosides based on both the carbohydrate chain and ceramide moieties.
Collapse
Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Angela R S Kruse
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States.,Department of Medicine, Vanderbilt University, 1161 21st Avenue S, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue S #3218, Nashville, Tennessee 37232, United States
| |
Collapse
|
17
|
Anderson DMG, Kotnala A, Messinger JD, Patterson NH, Spraggins JM, Curcio CA, Caprioli RM, Schey KL. High-Resolution Imaging Mass Spectrometry of Human Donor Eye: Photoreceptors Cells and Basal Laminar Deposit of Age-Related Macular Degeneration. Adv Exp Med Biol 2023; 1415:3-7. [PMID: 37440006 DOI: 10.1007/978-3-031-27681-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Pathologies of the retina are clinically visualized in vivo with OCT and ex vivo with immunohistochemistry. Although both techniques provide valuable information on prognosis and disease state, a comprehensive method for fully elucidating molecular constituents present in locations of interest is desirable. The purpose of this work was to use multimodal imaging technologies to localize the vast number of molecular species observed with matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) in aged and diseased retinal tissues. Herein, MALDI IMS was utilized to observe molecular species that reside in photoreceptor cells and also a basal laminar deposit from two human donor eyes. The molecular species observed to accumulate in these discrete regions can be further identified and studied to attempt to gain a greater understanding of biological processes occurring in debilitating eye diseases such as age-related macular degeneration (AMD).
Collapse
Affiliation(s)
- David M G Anderson
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ankita Kotnala
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey D Messinger
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathan Heath Patterson
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christine A Curcio
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| |
Collapse
|
18
|
Butrico CE, Eichelberger KR, Good CJ, Neumann EK, Spraggins JM, Cassat JE. 2349. Elucidating the Pathogenesis of Staphylococcus aureus During Hyperglycemic Osteomyelitis. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Staphylococcus aureus is a leading cause of antibiotic-resistant bacterial infections and can infect nearly every organ of the human body. One common manifestation of S. aureus disease is invasive bone infection, or osteomyelitis. Osteomyelitis is one of the most difficult to treat infections, often necessitating prolonged antibiotic treatment and surgical interventions. Hyperglycemia, or elevated blood glucose concentration, increases the risk for developing osteomyelitis. We hypothesized that S. aureus adapts specifically to the altered host environment during hyperglycemic osteomyelitis, thereby contributing to the increased infection severity.
Methods
To model hyperglycemic osteomyelitis, we treated mice with streptozotocin prior to infection with S. aureus in a post-traumatic osteomyelitis model. We analyzed bacterial burdens in homogenized tissues and bone parameters with microcomputed tomography. To identify changes in the spatial molecular architecture of infected, hyperglycemic femurs, we utilized imaging mass spectrometry. Finally, to obtain a comprehensive understanding of S. aureus metabolic and virulence changes and identify genes essential for staphylococcal growth in vivo in hyperglycemic mice, we performed a transposon sequencing experiment.
Results
We discovered that hyperglycemic mice sustained increased bacterial burdens within infected femurs and greater dissemination to other organs. We also found that hyperglycemic infected mice experienced increased rates of bone destruction and loss of trabecular bone volume, suggesting that hyperglycemia exacerbates infection-associated bone loss. Finally, we identified 71 genes as uniquely essential for S. aureus growth during hyperglycemic infection compared to euglycemic infection.
Conclusion
Hyperglycemia results in increased osteomyelitis infection severity. Multiple S. aureus genes involved in metabolism with roles in bacterial fitness in acidic environments were uniquely essential for bacterial fitness during comorbid infection. By identifying genes contributing to S. aureus survival during hyperglycemic osteomyelitis, we have the potential to inform targeted therapeutic development for treatment of exacerbated infections in patients with comorbid hyperglycemia.
Disclosures
All Authors: No reported disclosures.
Collapse
Affiliation(s)
| | | | | | | | | | - James E Cassat
- Vanderbilt University and Vanderbilt University Medical Center , Nashville, Tennessee
| |
Collapse
|
19
|
Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL. Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. Sci Adv 2022; 8:eabp9929. [PMID: 35947651 PMCID: PMC9365283 DOI: 10.1126/sciadv.abp9929] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/24/2022] [Indexed: 05/25/2023]
Abstract
Imaging of proteoforms in human tissues is hindered by low molecular specificity and limited proteome coverage. Here, we introduce proteoform imaging mass spectrometry (PiMS), which increases the size limit for proteoform detection and identification by fourfold compared to reported methods and reveals tissue localization of proteoforms at <80-μm spatial resolution. PiMS advances proteoform imaging by combining ambient nanospray desorption electrospray ionization with ion detection using individual ion mass spectrometry. We demonstrate highly multiplexed proteoform imaging of human kidney, annotating 169 of 400 proteoforms of <70 kDa using top-down MS and a database lookup of ~1000 kidney candidate proteoforms, including dozens of key enzymes in primary metabolism. PiMS images reveal distinct spatial localizations of proteoforms to both anatomical structures and cellular neighborhoods in the vasculature, medulla, and cortex regions of the human kidney. The benefits of PiMS are poised to increase proteome coverage for label-free protein imaging of tissues.
Collapse
Affiliation(s)
- Pei Su
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - John P. McGee
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Kenneth R. Durbin
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Michael A. R. Hollas
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Jamie L. Allen
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Bryon S. Drown
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | - Joseph B. Greer
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Bryan P. Early
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T. Fellers
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Departments of Chemistry and Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Jeannie M. Camarillo
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Jared O. Kafader
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Neil L. Kelleher
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
20
|
Perry WJ, Grunenwald CM, Van de Plas R, Witten JC, Martin DR, Apte SS, Cassat JE, Pettersson GB, Caprioli RM, Skaar EP, Spraggins JM. Visualizing Staphylococcus aureus pathogenic membrane modification within the host infection environment by multimodal imaging mass spectrometry. Cell Chem Biol 2022; 29:1209-1217.e4. [PMID: 35654040 PMCID: PMC9308753 DOI: 10.1016/j.chembiol.2022.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/10/2021] [Accepted: 05/11/2022] [Indexed: 11/30/2022]
Abstract
Bacterial pathogens have evolved virulence factors to colonize, replicate, and disseminate within the vertebrate host. Although there is an expanding body of literature describing how bacterial pathogens regulate their virulence repertoire in response to environmental signals, it is challenging to directly visualize virulence response within the host tissue microenvironment. Multimodal imaging approaches enable visualization of host-pathogen molecular interactions. Here we demonstrate multimodal integration of high spatial resolution imaging mass spectrometry and microscopy to visualize Staphylococcus aureus envelope modifications within infected murine and human tissues. Data-driven image fusion of fluorescent bacterial reporters and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance imaging mass spectrometry uncovered S. aureus lysyl-phosphatidylglycerol lipids, localizing to select bacterial communities within infected tissue. Absence of lysyl-phosphatidylglycerols is associated with decreased pathogenicity during vertebrate colonization as these lipids provide protection against the innate immune system. The presence of distinct staphylococcal lysyl-phosphatidylglycerol distributions within murine and human infections suggests a heterogeneous, spatially oriented microbial response to host defenses.
Collapse
Affiliation(s)
- William J Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA
| | - Caroline M Grunenwald
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Delft Center for Systems and Control, Delft University of Technology - TU Delft, Delft, the Netherlands; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
| | - James C Witten
- Department of Thoracic and Cardiovascular Surgery, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Daniel R Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - James E Cassat
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gösta B Pettersson
- Department of Thoracic and Cardiovascular Surgery, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37212, USA; Department of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
| |
Collapse
|
21
|
Sharman K, Patterson NH, Weiss A, Neumann EK, Guiberson ER, Ryan DJ, Gutierrez DB, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. J Proteome Res 2022; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.
Collapse
Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States,Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Elizabeth K. Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Emma R. Guiberson
- Mass Spectrometry Research Center and Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J. Ryan
- Pfizer Inc., Chesterfield, Missouri 63017, United States
| | - Danielle B. Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Department of Chemistry, and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States,Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States,Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M. Caprioli
- Mass Spectrometry Research Center and Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry and Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|
22
|
Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics 2022; 21:100254. [PMID: 35654359 PMCID: PMC9256833 DOI: 10.1016/j.mcpro.2022.100254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
Collapse
Affiliation(s)
- Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
| | - Thomas P Conrads
- Inova Women's Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marc Vidal
- Department of Genetics, Harvard University, Cambridge, Massachusetts, USA
| | - Christine Vogel
- New York University Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - David R Walt
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Wyss Institute at Harvard University, Boston, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
| |
Collapse
|
23
|
Lee HH, Tang Y, Xu K, Bao S, Fogo AB, Harris R, de Caestecker MP, Heinrich M, Spraggins JM, Huo Y, Landman BA. Multi-contrast computed tomography healthy kidney atlas. Comput Biol Med 2022; 146:105555. [DOI: 10.1016/j.compbiomed.2022.105555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022]
|
24
|
Weiss A, Murdoch CC, Edmonds KA, Jordan MR, Monteith AJ, Perera YR, Rodríguez Nassif AM, Petoletti AM, Beavers WN, Munneke MJ, Drury SL, Krystofiak ES, Thalluri K, Wu H, Kruse ARS, DiMarchi RD, Caprioli RM, Spraggins JM, Chazin WJ, Giedroc DP, Skaar EP. Zn-regulated GTPase metalloprotein activator 1 modulates vertebrate zinc homeostasis. Cell 2022; 185:2148-2163.e27. [PMID: 35584702 DOI: 10.1016/j.cell.2022.04.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/07/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Zinc (Zn) is an essential micronutrient and cofactor for up to 10% of proteins in living organisms. During Zn limitation, specialized enzymes called metallochaperones are predicted to allocate Zn to specific metalloproteins. This function has been putatively assigned to G3E GTPase COG0523 proteins, yet no Zn metallochaperone has been experimentally identified in any organism. Here, we functionally characterize a family of COG0523 proteins that is conserved across vertebrates. We identify Zn metalloprotease methionine aminopeptidase 1 (METAP1) as a COG0523 client, leading to the redesignation of this group of COG0523 proteins as the Zn-regulated GTPase metalloprotein activator (ZNG1) family. Using biochemical, structural, genetic, and pharmacological approaches across evolutionarily divergent models, including zebrafish and mice, we demonstrate a critical role for ZNG1 proteins in regulating cellular Zn homeostasis. Collectively, these data reveal the existence of a family of Zn metallochaperones and assign ZNG1 an important role for intracellular Zn trafficking.
Collapse
Affiliation(s)
- Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Caitlin C Murdoch
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Andrew J Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yasiru R Perera
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Aslin M Rodríguez Nassif
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Amber M Petoletti
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew J Munneke
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sydney L Drury
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Evan S Krystofiak
- Cell Imaging Shared Resource, Vanderbilt University, Nashville, TN 37232, USA
| | - Kishore Thalluri
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Angela R S Kruse
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Richard M Caprioli
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | - Jeffrey M Spraggins
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| |
Collapse
|
25
|
Guiberson ER, Good CJ, Wexler AG, Skaar EP, Spraggins JM, Caprioli RM. Multimodal Imaging Mass Spectrometry of Murine Gastrointestinal Tract with Retained Luminal Content. J Am Soc Mass Spectrom 2022; 33:1073-1076. [PMID: 35545232 PMCID: PMC9264265 DOI: 10.1021/jasms.1c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The gastrointestinal tract, including luminal content, harbors a complex mixture of microorganisms, host dietary content, and immune factors. Existing imaging approaches remove luminal content and only visualize small regions of the GI tract. Here, we demonstrate a workflow for multimodal imaging using matrix-assisted laser desorption/ionization imaging mass spectrometry, autofluorescence, and bright field microscopy for mapping intestinal tissue and luminal content. Results comparing tissue and luminal content in control murine tissue show both unique molecular and elemental distributions and abundances using multimodal protein, lipid, and elemental imaging. For instance, lipid PC(42:1) is 2× higher intensity in luminal content than tissue, while PC(32:0) is 80× higher intensity in tissue. Additionally, some ions such as the protein at m/z 3443 and the element manganese are only detected in luminal content, while the protein at m/z 8564 was only detected in tissue and phosphorus had 2× higher abundance in tissue. These data highlight the robust molecular information that can be gained from the gastrointestinal tract with the inclusion of luminal content.
Collapse
Affiliation(s)
- Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Christopher J Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Aaron G Wexler
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37203g, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37203, United States
| |
Collapse
|
26
|
Manz T, Gold I, Patterson NH, McCallum C, Keller MS, Herr BW, Börner K, Spraggins JM, Gehlenborg N. Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web. Nat Methods 2022; 19:515-516. [PMID: 35545714 PMCID: PMC9637380 DOI: 10.1038/s41592-022-01482-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Ilan Gold
- Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Richardson LT, Neumann EK, Caprioli RM, Spraggins JM, Solouki T. Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments. Anal Chem 2022; 94:5504-5513. [PMID: 35344335 PMCID: PMC10124143 DOI: 10.1021/acs.analchem.1c03715] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Because of their diverse functionalities in cells, lipids are of primary importance when characterizing molecular profiles of physiological and disease states. Imaging mass spectrometry (IMS) provides the spatial distributions of lipid populations in tissues. Referenced Kendrick mass defect (RKMD) analysis is an effective mass spectrometry (MS) data analysis tool for classification and annotation of lipids. Herein, we extend the capabilities of RKMD analysis and demonstrate an integrated method for lipid annotation and chemical structure-based filtering for IMS datasets. Annotation of lipid features with lipid molecular class, radyl carbon chain length, and degree of unsaturation allows image reconstruction and visualization based on each structural characteristic. We show a proof-of-concept application of the method to a computationally generated IMS dataset and validate that the RKMD method is highly specific for lipid components in the presence of confounding background ions. Moreover, we demonstrate an application of the RKMD-based annotation and filtering to matrix-assisted laser desorption/ionization (MALDI) IMS lipidomic data from human kidney tissue analysis.
Collapse
Affiliation(s)
- Luke T Richardson
- Department of Chemistry and Biochemistry, Baylor University, 101 Bagby Avenue, Waco, Texas 76706, United States
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Department of Cell and Development Biology, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, 101 Bagby Avenue, Waco, Texas 76706, United States
| |
Collapse
|
28
|
Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022; 19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
Collapse
Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Rebecca T Beuschel
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, MA, USA
| | | | - Julia Hatler
- Antibody Development Department, Bio-Techne, Minneapolis, MN, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA
| | - Josh Croteau
- Department of Applications Science, BioLegend, San Diego, CA, USA
| | | | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - R Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| |
Collapse
|
29
|
Abstract
Bone and bone marrow are vital to mammalian structure, movement, and immunity. These tissues are also commonly subjected to molecular alterations giving rise to debilitating diseases like rheumatoid arthritis and osteomyelitis. Technologies such as matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) facilitate the discovery of spatially resolved chemical information in biological tissue samples to help elucidate the complex molecular processes underlying pathology. Traditionally, preparation of osseous tissue for MALDI IMS has been difficult due to its mineralized composition and heterogeneous morphology, and compensation for these challenges with decalcification and fixation protocols can remove or delocalize molecular species. Here, sample preparation methods were advanced to enable multimodal MALDI IMS of undecalcified, fresh-frozen murine femurs, allowing the distribution of endogenous lipids to be linked to tissue structures and cell types. Adhesive-bound bone sections were mounted onto conductive glass slides with microscopy-compatible glue and freeze-dried to minimize artificial bone marrow damage. High spatial resolution (10 μm) MALDI IMS was employed to characterize lipid distributions, and use of complementary microscopy modalities aided tissue and cell assignments. For example, various phosphatidylcholines localize to the bone marrow, adipose tissue, marrow adipose tissue, and muscle. Further, sphingomyelin(42:1) was abundant in megakaryocytes, whereas sphingomyelin(42:2) was diminished in this cell type. These data reflect the vast molecular and cellular heterogeneity indicative of the bone marrow and the soft tissue surrounding the femur. Multimodal MALDI IMS has the potential to advance bone-related biomedical research by offering deep molecular coverage with spatial relevance in a preserved native bone microenvironment.
Collapse
Affiliation(s)
- Christopher J Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Casey E Butrico
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - James E Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
30
|
Kruse ARS, Spraggins JM. Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. Front Physiol 2022; 13:837773. [PMID: 35222094 PMCID: PMC8874197 DOI: 10.3389/fphys.2022.837773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
The kidney functions through the coordination of approximately one million multifunctional nephrons in 3-dimensional space. Molecular understanding of the kidney has relied on transcriptomic, proteomic, and metabolomic analyses of kidney homogenate, but these approaches do not resolve cellular identity and spatial context. Mass spectrometry analysis of isolated cells retains cellular identity but not information regarding its cellular neighborhood and extracellular matrix. Spatially targeted mass spectrometry is uniquely suited to molecularly characterize kidney tissue while retaining in situ cellular context. This review summarizes advances in methodology and technology for spatially targeted mass spectrometry analysis of kidney tissue. Profiling technologies such as laser capture microdissection (LCM) coupled to liquid chromatography tandem mass spectrometry provide deep molecular coverage of specific tissue regions, while imaging technologies such as matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) molecularly profile regularly spaced tissue regions with greater spatial resolution. These technologies individually have furthered our understanding of heterogeneity in nephron regions such as glomeruli and proximal tubules, and their combination is expected to profoundly expand our knowledge of the kidney in health and disease.
Collapse
Affiliation(s)
- Angela R. S. Kruse
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Jeffrey M. Spraggins,
| |
Collapse
|
31
|
Lee HH, Tang Y, Bao S, Yang Q, Xu X, Fogo AB, Harris R, de Caestecker MP, Spraggins JM, Heinrich M, Huo Y, Landman BA. Supervised Deep Generation of High-Resolution Arterial Phase Computed Tomography Kidney Substructure Atlas. Proc SPIE Int Soc Opt Eng 2022; 12032:120322S. [PMID: 36303577 PMCID: PMC9605120 DOI: 10.1117/12.2608290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) provides an opportunity to contextualize findings across cellular to organ systems levels. Constructing an atlas target is the primary endpoint for generalizing anatomical information across scales and populations. An initial target of HuBMAP is the kidney organ and arterial phase contrast-enhanced computed tomography (CT) provides distinctive appearance and anatomical context on the internal substructure of kidney organs such as renal context, medulla, and pelvicalyceal system. With the confounding effects of demographics and morphological characteristics of the kidney across large-scale imaging surveys, substantial variation is demonstrated with the internal substructure morphometry and the intensity contrast due to the variance of imaging protocols. Such variability increases the level of difficulty to localize the anatomical features of the kidney substructure in a well-defined spatial reference for clinical analysis. In order to stabilize the localization of kidney substructures in the context of this variability, we propose a high-resolution CT kidney substructure atlas template. Briefly, we introduce a deep learning preprocessing technique to extract the volumetric interest of the abdominal regions and further perform a deep supervised registration pipeline to stably adapt the anatomical context of the kidney internal substructure. To generate and evaluate the atlas template, arterial phase CT scans of 500 control subjects are de-identified and registered to the atlas template with a complete end-to-end pipeline. With stable registration to the abdominal wall and kidney organs, the internal substructure of both left and right kidneys are substantially localized in the high-resolution atlas space. The atlas average template successfully demonstrated the contextual details of the internal structure and was applicable to generalize the morphological variation of internal substructure across patients.
Collapse
Affiliation(s)
- Ho Hin Lee
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Yucheng Tang
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA 37212
| | - Shunxing Bao
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Qi Yang
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Xin Xu
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Agnes B Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA 37232
- Departments of Medicine and Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA 37232
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Raymond Harris
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Mark P de Caestecker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA 37232
| | - Mattias Heinrich
- Institute of Medical Informatics, University of Luebeck, Germany
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA 37212
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA 37212
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA 37212
- Institute of Medical Informatics, University of Luebeck, Germany
| |
Collapse
|
32
|
Neumann EK, Patterson NH, Rivera ES, Allen JL, Brewer M, deCaestecker MP, Caprioli RM, Fogo AB, Spraggins JM. Highly multiplexed immunofluorescence of the human kidney using co-detection by indexing. Kidney Int 2022; 101:137-143. [PMID: 34619231 PMCID: PMC8741652 DOI: 10.1016/j.kint.2021.08.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 01/03/2023]
Abstract
The human kidney is composed of many cell types that vary in their abundance and distribution from normal to diseased organ. As these cell types perform unique and essential functions, it is important to confidently label each within a single tissue to accurately assess tissue architecture and microenvironments. Towards this goal, we demonstrate the use of co-detection by indexing (CODEX) multiplexed immunofluorescence for visualizing 23 antigens within the human kidney. Using CODEX, many of the major cell types and substructures, such as collecting ducts, glomeruli, and thick ascending limb, were visualized within a single tissue section. Of these antibodies, 19 were conjugated in-house, demonstrating the flexibility and utility of this approach for studying the human kidney using custom and commercially available antibodies. We performed a pilot study that compared both fresh frozen and formalin-fixed paraffin-embedded healthy non-neoplastic and diabetic nephropathy kidney tissues. The largest cellular differences between the two groups was observed in cells labeled with aquaporin 1, cytokeratin 7, and α-smooth muscle actin. Thus, our data show the power of CODEX multiplexed immunofluorescence for surveying the cellular diversity of the human kidney and the potential for applications within pathology, histology, and building anatomical atlases.
Collapse
Affiliation(s)
- Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Nathan Heath Patterson
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Jamie L. Allen
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Maya Brewer
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Mark P. deCaestecker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232.,Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37232
| | - Agnes B. Fogo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA 37232.,Departments of Medicine and Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA 37232
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232.,Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37232,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA 37232
| |
Collapse
|
33
|
Fincher JA, Djambazova KV, Klein DR, Dufresne M, Migas LG, Van de Plas R, Caprioli RM, Spraggins JM. Molecular Mapping of Neutral Lipids Using Silicon Nanopost Arrays and TIMS Imaging Mass Spectrometry. J Am Soc Mass Spectrom 2021; 32:2519-2527. [PMID: 34435768 DOI: 10.1021/jasms.1c00159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate the utility of combining silicon nanopost arrays (NAPA) and trapped ion mobility imaging mass spectrometry (TIMS IMS) for high spatial resolution and specificity mapping of neutral lipid classes in tissue. Ionization of neutral lipid species such as triglycerides (TGs), cholestryl esters (CEs), and hexosylceramides (HexCers) from biological tissues has remained a challenge for imaging applications. NAPA, a matrix-free laser desorption ionization substrate, provides enhanced ionization efficiency for the above-mentioned neutral lipid species, providing complementary lipid coverage to matrix-assisted laser desorption ionization (MALDI). The combination of NAPA and TIMS IMS enables imaging of neutral lipid species at 20 μm spatial resolution while also increasing molecular coverage greater than 2-fold using gas-phase ion mobility separations. This is a significant improvement with respect to sensitivity, specificity, and spatial resolution compared to previously reported imaging studies using NAPA alone. Improved specificity for neutral lipid analysis using TIMS IMS was shown using rat kidney tissue to separate TGs, CEs, HexCers, and phospholipids into distinct ion mobility trendlines. Further, this technology allowed for the separation of isomeric species, including mobility resolved isomers of Cer(d42:2) (m/z 686.585) with distinct spatial localizations measured in rat kidney tissue section.
Collapse
Affiliation(s)
- Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 442 Robinson Research Building, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Cell & Developmental Biology, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
| |
Collapse
|
34
|
McMillen JC, Gutierrez DB, Judd AM, Spraggins JM, Caprioli RM. Enhancement of Tryptic Peptide Signals from Tissue Sections Using MALDI IMS Postionization (MALDI-2). J Am Soc Mass Spectrom 2021; 32:2583-2591. [PMID: 34515472 DOI: 10.1021/jasms.1c00213] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, unlabeled mapping of analytes from tissue sections. However, further work is needed to improve the sensitivity and depth of coverage for protein and peptide IMS. We demonstrate signal enhancement of proteolytic peptides from thin tissue sections of human kidney by conventional MALDI (MALDI-1) augmented using a second ionizing laser (termed MALDI-2). Proteins were digested in situ using trypsin prior to IMS analysis. For tentative identification of peptides and proteins, a tissue homogenate from the same organ used for IMS was analyzed by LC-MS/MS, and data are available via ProteomeXchange with identifier PXD023877. These identified proteins were then digested in silico to generate a database of theoretical peptides to then match to MALDI IMS data sets. Peptides were tentatively identified by matching the MALDI peak list to the database peptide list based on mass accuracy (5 ppm mass error). This resulted in 1337 ± 96 (n = 3) peptides and 2076 ± 362 (n = 3) unique peptides matched to IMS peaks from MALDI-1 and MALDI-2, respectively. Protein identifications requiring two or more peptides per protein resulted in 276 ± 20 proteins with MALDI-1 and 401 ± 60 with MALDI-2. These results demonstrate that MALDI-2 provides enhanced sensitivity for the spatial mapping of tryptic peptides and significantly increases the number of proteins identified in IMS experiments.
Collapse
Affiliation(s)
- Josiah C McMillen
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Audra M Judd
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue S #3218, Nashville, Tennessee 37205, United States
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 1161 21st Avenue S, Nashville, Tennessee 37232, United States
| |
Collapse
|
35
|
Neumann EK, Patterson NH, Allen JL, Migas LG, Yang H, Brewer M, Anderson DM, Harvey J, Gutierrez DB, Harris RC, deCaestecker MP, Fogo AB, Van de Plas R, Caprioli RM, Spraggins JM. Protocol for multimodal analysis of human kidney tissue by imaging mass spectrometry and CODEX multiplexed immunofluorescence. STAR Protoc 2021; 2:100747. [PMID: 34430920 PMCID: PMC8371244 DOI: 10.1016/j.xpro.2021.100747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Here, we describe the preservation and preparation of human kidney tissue for interrogation by histopathology, imaging mass spectrometry, and multiplexed immunofluorescence. Custom image registration and integration techniques are used to create cellular and molecular atlases of this organ system. Through careful optimization, we ensure high-quality and reproducible datasets suitable for cross-patient comparisons that are essential to understanding human health and disease. Moreover, each of these steps can be adapted to other organ systems or diseases, enabling additional atlas efforts.
Collapse
Affiliation(s)
- Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Nathan Heath Patterson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jamie L. Allen
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Lukasz G. Migas
- Delft Center for Systems and Control (DCSC), Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Haichun Yang
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maya Brewer
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David M. Anderson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jennifer Harvey
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Danielle B. Gutierrez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Raymond C. Harris
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark P. deCaestecker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Agnes B. Fogo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Departments of Medicine and Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Raf Van de Plas
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Delft Center for Systems and Control (DCSC), Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| |
Collapse
|
36
|
Dufresne M, Fincher JA, Patterson NH, Schey KL, Norris JL, Caprioli RM, Spraggins JM. α-Cyano-4-hydroxycinnamic Acid and Tri-Potassium Citrate Salt Pre-Coated Silicon Nanopost Array Provides Enhanced Lipid Detection for High Spatial Resolution MALDI Imaging Mass Spectrometry. Anal Chem 2021; 93:12243-12249. [PMID: 34449196 DOI: 10.1021/acs.analchem.1c01560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have developed a pre-coated substrate for matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) that enables high spatial resolution mapping of both phospholipids and neutral lipid classes in positive ion mode as metal cation adducts. The MALDI substrates are constructed by depositing a layer of α-cyano-4-hydroxycinnamic acid (CHCA) and potassium salts onto silicon nanopost arrays (NAPA) prior to tissue mounting. The matrix/salt pre-coated NAPA substrate significantly enhances all detected lipid signals allowing lipids to be detected at lower laser energies than bare NAPA. The improved sensitivity at lower laser energy enabled ion images to be generated at 10 μm spatial resolution from rat retinal tissue. Optimization of matrix pre-coated NAPA consisted of testing lithium, sodium, and potassium salts along with various matrices to investigate the increased sensitivity toward lipids for MALDI IMS experiments. It was determined that pre-coating NAPA with CHCA and potassium salts before thaw-mounting of tissue resulted in a signal intensity increase of at least 5.8 ± 0.1-fold for phospholipids and 2.0 ± 0.1-fold for neutral lipids compared to bare NAPA. Pre-coating NAPA with matrix and salt also reduced the necessary laser power to achieve desorption/ionization by ∼35%. This reduced the effective diameter of the ablation area from 13 ± 2 μm down to 8 ± 1 μm, enabling high spatial resolution MALDI IMS. Using pre-coated NAPA with CHCA and potassium salts offers a MALDI IMS substrate with broad molecular coverage of lipids in a single polarity that eliminates the need for extensive sample preparation after sectioning.
Collapse
Affiliation(s)
- Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Kevin L Schey
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|
37
|
Tideman LEM, Migas LG, Djambazova KV, Patterson NH, Caprioli RM, Spraggins JM, Van de Plas R. Automated biomarker candidate discovery in imaging mass spectrometry data through spatially localized Shapley additive explanations. Anal Chim Acta 2021; 1177:338522. [PMID: 34482894 PMCID: PMC10124144 DOI: 10.1016/j.aca.2021.338522] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/04/2021] [Accepted: 04/11/2021] [Indexed: 01/09/2023]
Abstract
The search for molecular species that are differentially expressed between biological states is an important step towards discovering promising biomarker candidates. In imaging mass spectrometry (IMS), performing this search manually is often impractical due to the large size and high-dimensionality of IMS datasets. Instead, we propose an interpretable machine learning workflow that automatically identifies biomarker candidates by their mass-to-charge ratios, and that quantitatively estimates their relevance to recognizing a given biological class using Shapley additive explanations (SHAP). The task of biomarker candidate discovery is translated into a feature ranking problem: given a classification model that assigns pixels to different biological classes on the basis of their mass spectra, the molecular species that the model uses as features are ranked in descending order of relative predictive importance such that the top-ranking features have a higher likelihood of being useful biomarkers. Besides providing the user with an experiment-wide measure of a molecular species' biomarker potential, our workflow delivers spatially localized explanations of the classification model's decision-making process in the form of a novel representation called SHAP maps. SHAP maps deliver insight into the spatial specificity of biomarker candidates by highlighting in which regions of the tissue sample each feature provides discriminative information and in which regions it does not. SHAP maps also enable one to determine whether the relationship between a biomarker candidate and a biological state of interest is correlative or anticorrelative. Our automated approach to estimating a molecular species' potential for characterizing a user-provided biological class, combined with the untargeted and multiplexed nature of IMS, allows for the rapid screening of thousands of molecular species and the obtention of a broader biomarker candidate shortlist than would be possible through targeted manual assessment. Our biomarker candidate discovery workflow is demonstrated on mouse-pup and rat kidney case studies.
Collapse
Affiliation(s)
- Leonoor E M Tideman
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
| |
Collapse
|
38
|
Wexler AG, Guiberson ER, Beavers WN, Shupe JA, Washington MK, Lacy DB, Caprioli RM, Spraggins JM, Skaar EP. Clostridioides difficile infection induces a rapid influx of bile acids into the gut during colonization of the host. Cell Rep 2021; 36:109683. [PMID: 34496241 PMCID: PMC8445666 DOI: 10.1016/j.celrep.2021.109683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/05/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Clostridioides difficile is the leading cause of nosocomial intestinal infections in the United States. Ingested C. difficile spores encounter host bile acids and other cues that are necessary for germinating into toxin-producing vegetative cells. While gut microbiota disruption (often by antibiotics) is a prerequisite for C. difficile infection (CDI), the mechanisms C. difficile employs for colonization remain unclear. Here, we pioneered the application of imaging mass spectrometry to study how enteric infection changes gut metabolites. We find that CDI induces an influx of bile acids into the gut within 24 h of the host ingesting spores. In response, the host reduces bile acid biosynthesis gene expression. These bile acids drive C. difficile outgrowth, as mice receiving the bile acid sequestrant cholestyramine display delayed colonization and reduced germination. Our findings indicate that C. difficile may facilitate germination upon infection and suggest that altering flux through bile acid pathways can modulate C. difficile outgrowth in CDI-prone patients.
Collapse
Affiliation(s)
- Aaron G Wexler
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Shupe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - D Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; The Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Vanderbilt University, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
39
|
Manzo T, Prentice BM, Anderson KG, Raman A, Schalck A, Codreanu GS, Nava Lauson CB, Tiberti S, Raimondi A, Jones MA, Reyzer M, Bates BM, Spraggins JM, Patterson NH, McLean JA, Rai K, Tacchetti C, Tucci S, Wargo JA, Rodighiero S, Clise-Dwyer K, Sherrod SD, Kim M, Navin NE, Caprioli RM, Greenberg PD, Draetta G, Nezi L. Accumulation of long-chain fatty acids in the tumor microenvironment drives dysfunction in intrapancreatic CD8+ T cells. J Exp Med 2021; 217:151833. [PMID: 32491160 PMCID: PMC7398173 DOI: 10.1084/jem.20191920] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/14/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
CD8+ T cells are master effectors of antitumor immunity, and their presence at tumor sites correlates with favorable outcomes. However, metabolic constraints imposed by the tumor microenvironment (TME) can dampen their ability to control tumor progression. We describe lipid accumulation in the TME areas of pancreatic ductal adenocarcinoma (PDA) populated by CD8+ T cells infiltrating both murine and human tumors. In this lipid-rich but otherwise nutrient-poor TME, access to using lipid metabolism becomes particularly valuable for sustaining cell functions. Here, we found that intrapancreatic CD8+ T cells progressively accumulate specific long-chain fatty acids (LCFAs), which, rather than provide a fuel source, impair their mitochondrial function and trigger major transcriptional reprogramming of pathways involved in lipid metabolism, with the subsequent reduction of fatty acid catabolism. In particular, intrapancreatic CD8+ T cells specifically exhibit down-regulation of the very-long-chain acyl-CoA dehydrogenase (VLCAD) enzyme, which exacerbates accumulation of LCFAs and very-long-chain fatty acids (VLCFAs) that mediate lipotoxicity. Metabolic reprogramming of tumor-specific T cells through enforced expression of ACADVL enabled enhanced intratumoral T cell survival and persistence in an engineered mouse model of PDA, overcoming one of the major hurdles to immunotherapy for PDA.
Collapse
Affiliation(s)
- Teresa Manzo
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boone M Prentice
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Kristin G Anderson
- Clinical Research Division and Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA.,Departments of Medicine/Oncology and Immunology, University of Washington School of Medicine, Seattle, WA
| | - Ayush Raman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Aislyn Schalck
- Department of Genetics and Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Carina B Nava Lauson
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy
| | - Silvia Tiberti
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy
| | - Andrea Raimondi
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, San Raffaele Vita-Salute University, Milano, Italy
| | - Marissa A Jones
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Michelle Reyzer
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Breanna M Bates
- Clinical Research Division and Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA.,Departments of Medicine/Oncology and Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jeffrey M Spraggins
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Nathan H Patterson
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - John A McLean
- Center for Innovative Technology, Vanderbilt University, Nashville, TN
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carlo Tacchetti
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, San Raffaele Vita-Salute University, Milano, Italy
| | - Sara Tucci
- Laboratory of Clinical Biochemistry and Metabolism Center for Pediatrics and Adolescent Medicine, University of Freiburg, Freiburg, Germany
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Simona Rodighiero
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stacy D Sherrod
- Center for Innovative Technology, Vanderbilt University, Nashville, TN
| | - Michael Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nicholas E Navin
- Department of Genetics and Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Richard M Caprioli
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Philip D Greenberg
- Clinical Research Division and Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA.,Departments of Medicine/Oncology and Immunology, University of Washington School of Medicine, Seattle, WA
| | - Giulio Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luigi Nezi
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
40
|
Lee HH, Tang Y, Xu K, Bao S, Fogo AB, Harris R, de Caestecker MP, Heinrich M, Spraggins JM, Huo Y, Landman BA. Construction of a Multi-Phase Contrast Computed Tomography Kidney Atlas. Proc SPIE Int Soc Opt Eng 2021; 11596. [PMID: 34354322 DOI: 10.1117/12.2580561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) seeks to create a molecular atlas at the cellular level of the human body to spur interdisciplinary innovations across spatial and temporal scales. While the preponderance of effort is allocated towards cellular and molecular scale mapping, differentiating and contextualizing findings within tissues, organs and systems are essential for the HuBMAP efforts. The kidney is an initial organ target of HuBMAP, and constructing a framework (or atlas) for integrating information across scales is needed for visualizing and integrating information. However, there is no abdominal atlas currently available in the public domain. Substantial variation in healthy kidneys exists with sex, body size, and imaging protocols. With the integration of clinical archives for secondary research use, we are able to build atlases based on a diverse population and clinically relevant protocols. In this study, we created a computed tomography (CT) phase-specific atlas for the abdomen, which is optimized for the kidney organ. A two-stage registration pipeline was used by registering extracted abdominal volume of interest from body part regression, to a high-resolution CT. Affine and non-rigid registration were performed to all scans hierarchically. To generate and evaluate the atlas, multiphase CT scans of 500 control subjects (age: 15 - 50, 250 males, 250 females) are registered to the atlas target through the complete pipeline. The abdominal body and kidney registration are shown to be stable with the variance map computed from the result average template. Both left and right kidneys are substantially localized in the high-resolution target space, which successfully demonstrated the sharp details of its anatomical characteristics across each phase. We illustrated the applicability of the atlas template for integrating across normal kidney variation from 64 cm3 to 302 cm3.
Collapse
Affiliation(s)
- Ho Hin Lee
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Yucheng Tang
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Kaiwen Xu
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Shunxing Bao
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Agnes B Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA 37232.,Departments of Medicine and Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA 37232
| | - Raymond Harris
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Mark P de Caestecker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Mattias Heinrich
- Institute of Medical Informatics, University of Luebeck, Germany
| | | | - Yuankai Huo
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA 37212
| | - Bennett A Landman
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA 37212.,Radiology, Vanderbilt University Medical Center, Nashville, TN, USA 37235
| |
Collapse
|
41
|
Guiberson ER, Weiss A, Ryan DJ, Monteith AJ, Sharman K, Gutierrez DB, Perry WJ, Caprioli RM, Skaar EP, Spraggins JM. Spatially Targeted Proteomics of the Host-Pathogen Interface during Staphylococcal Abscess Formation. ACS Infect Dis 2021; 7:101-113. [PMID: 33270421 DOI: 10.1021/acsinfecdis.0c00647] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Staphylococcus aureus is a common cause of invasive and life-threatening infections that are often multidrug resistant. To develop novel treatment approaches, a detailed understanding of the complex host-pathogen interactions during infection is essential. This is particularly true for the molecular processes that govern the formation of tissue abscesses, as these heterogeneous structures are important contributors to staphylococcal pathogenicity. To fully characterize the developmental process leading to mature abscesses, temporal and spatial analytical approaches are required. Spatially targeted proteomic technologies such as micro-liquid extraction surface analysis offer insight into complex biological systems including detection of bacterial proteins and their abundance in the host environment. By analyzing the proteomic constituents of different abscess regions across the course of infection, we defined the immune response and bacterial contribution to abscess development through spatial and temporal proteomic assessment. The information gathered was mapped to biochemical pathways to characterize the metabolic processes and immune strategies employed by the host. These data provide insights into the physiological state of bacteria within abscesses and elucidate pathogenic processes at the host-pathogen interface.
Collapse
Affiliation(s)
- Emma R. Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, United States
| | - Daniel J. Ryan
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Andrew J. Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, United States
| | - Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Danielle B. Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - William J. Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, United States
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| |
Collapse
|
42
|
Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM. Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. J Am Soc Mass Spectrom 2020; 31:2401-2415. [PMID: 32886506 PMCID: PMC9278956 DOI: 10.1021/jasms.0c00232] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Imaging mass spectrometry has become a mature molecular mapping technology that is used for molecular discovery in many medical and biological systems. While powerful by itself, imaging mass spectrometry can be complemented by the addition of other orthogonal, chemically informative imaging technologies to maximize the information gained from a single experiment and enable deeper understanding of biological processes. Within this review, we describe MALDI, SIMS, and DESI imaging mass spectrometric technologies and how these have been integrated with other analytical modalities such as microscopy, transcriptomics, spectroscopy, and electrochemistry in a field termed multimodal imaging. We explore the future of this field and discuss forthcoming developments that will bring new insights to help unravel the molecular complexities of biological systems, from single cells to functional tissue structures and organs.
Collapse
Affiliation(s)
- Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| |
Collapse
|
43
|
Anderson DMG, Messinger JD, Patterson NH, Rivera ES, Kotnala A, Spraggins JM, Caprioli RM, Curcio CA, Schey KL. Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:2426-2436. [PMID: 32628476 PMCID: PMC8161663 DOI: 10.1021/jasms.0c00119] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The human retina provides vision at light levels ranging from starlight to sunlight. Its supporting tissues regulate plasma-delivered lipophilic essentials for vision, including retinoids. The macula is an anatomic specialization for high-acuity and color vision that is also vulnerable to prevalent blinding diseases. The retina's exquisite architecture comprises numerous cell types that are aligned horizontally, yielding structurally distinct cell, synaptic, and vascular layers that are visible in histology and in diagnostic clinical imaging. MALDI imaging mass spectrometry (IMS) is now capable of uniting low micrometer spatial resolution with high levels of chemical specificity. In this study, a multimodal imaging approach fortified with accurate multi-image registration was used to localize lipids in human retina tissue at laminar, cellular, and subcellular levels. Multimodal imaging results indicate differences in distributions and abundances of lipid species across and within single cell types. Of note are distinct localizations of signals within specific layers of the macula. For example, phosphatidylethanolamine and phosphatidylinositol lipids were localized to central RPE cells, whereas specific plasmalogen lipids were localized to cells of the perifoveal RPE and Henle fiber layer. Subcellular compartments of photoreceptors were distinguished by PE(20:0_22:5) in the outer nuclear layer, PE(18:0_22:6) in outer and inner segments, and cardiolipin CL(70:5) in the mitochondria-rich inner segments. Several lipids, differing by a single double bond, have markedly different distributions between the central fovea and the ganglion cell and inner nuclear layers. A lipid atlas, initiated in this study, can serve as a reference database for future examination of diseased tissues.
Collapse
Affiliation(s)
- David M G Anderson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jeffrey D Messinger
- Department of Ophthalmology and Visual Science, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Nathan H Patterson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Emilio S Rivera
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Ankita Kotnala
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department of Ophthalmology and Visual Science, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Richard M Caprioli
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Christine A Curcio
- Department of Ophthalmology and Visual Science, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Kevin L Schey
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| |
Collapse
|
44
|
Rivera ES, Djambazova KV, Neumann EK, Caprioli RM, Spraggins JM. Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. J Mass Spectrom 2020; 55:e4614. [PMID: 32955134 PMCID: PMC8211109 DOI: 10.1002/jms.4614] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 05/02/2023]
Abstract
Imaging mass spectrometry (IMS) technologies are capable of mapping a wide array of biomolecules in diverse cellular and tissue environments. IMS has emerged as an essential tool for providing spatially targeted molecular information due to its high sensitivity, wide molecular coverage, and chemical specificity. One of the major challenges for mapping the complex cellular milieu is the presence of many isomers and isobars in these samples. This challenge is traditionally addressed using orthogonal liquid chromatography (LC)-based analysis, though, common approaches such as chromatography and electrophoresis are not able to be performed at timescales that are compatible with most imaging applications. Ion mobility offers rapid, gas-phase separations that are readily integrated with IMS workflows in order to provide additional data dimensionality that can improve signal-to-noise, dynamic range, and specificity. Here, we highlight recent examples of ion mobility coupled to IMS and highlight their importance to the field.
Collapse
Key Words
- IMS
- desorption electrospray ionization, DESI
- drift tube ion mobility spectrometry, DTIMS
- high-field asymmetric waveform ion mobility, FAIMS
- imaging mass spectrometry
- infrared matrix-assisted laser desorption electrospray ionization, IR-MALDESI
- ion mobility
- laser ablation electrospray ionization, LAESI
- lipids
- liquid extraction surface analysis, LESA
- liquid microjunction, (LMJ)
- matrix-assisted laser desorption electrospray ionization, MALDI
- metabolites
- proteins
- tissue analysis
- trapped ion mobility spectrometry, TIMS
- travelling wave ion mobility spectrometry, TWIMS
Collapse
Affiliation(s)
- Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| |
Collapse
|
45
|
McMillen JC, Fincher JA, Klein DR, Spraggins JM, Caprioli RM. Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. J Mass Spectrom 2020; 55:e4663. [PMID: 33241625 DOI: 10.26434/chemrxiv.12494705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/14/2020] [Indexed: 05/18/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, untargeted detection of many hundreds of analytes from tissue. Recently, laser postionization (MALDI-2) has been developed for increased ion yield and sensitivity for lipid IMS. However, the dependence of MALDI-2 performance on the various lipid classes is largely unknown. To understand the effect of the applied matrix on MALDI-2 analysis of lipids, samples including an equimolar lipid standard mixture, various tissue homogenates, and intact rat kidney tissue sections were analyzed using the following matrices: α-cyano-4-hydroxycinnamic acid, 2',5'-dihydroxyacetophenone, 2',5'-dihydroxybenzoic acid (DHB), and norharmane (NOR). Lipid signal enhancement of protonated species using MALDI-2 technology varied based on the matrix used. Although signal improvements were observed for all matrices, the most dramatic effects using MALDI-2 were observed using NOR and DHB. For lipid standards analyzed by MALDI-2, NOR provided the broadest coverage, enabling the detection of all 13 protonated standards, including nonpolar lipids, whereas DHB gave less coverage but gave the highest signal increase for those lipids recorded. With respect to tissue homogenates and rat kidney tissue, mass spectra were compared and showed that the number and intensity of neutral lipids tentatively identified with MALDI-2 using NOR increased significantly (e.g., fivefold intensity increase for triacylglycerol). In the cases of DHB with MALDI-2, the number of protonated lipids identified from tissue homogenates doubled with 152 on average compared with 76 with MALDI alone. High spatial resolution imaging (~20 μm) of rat kidney tissue showed similar results using DHB with 125 lipids tentatively identified from MALDI-2 spectra versus just 72 using standard MALDI. From the four matrices tested, NOR provided the greatest increase in sensitivity for neutral lipids (triacylglycerol, diacylglycerol, monoacylglycerol, and cholesterol ester), and DHB provided the highest overall number of lipids detected using MALDI-2 technology.
Collapse
Affiliation(s)
- Josiah C McMillen
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
| | - Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
- Department of Pharmacology, Vanderbilt University
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, 37232, USA
| |
Collapse
|
46
|
McMillen JC, Fincher JA, Klein DR, Spraggins JM, Caprioli RM. Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. J Mass Spectrom 2020; 55:e4663. [PMID: 33241625 PMCID: PMC8099046 DOI: 10.1002/jms.4663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/14/2020] [Indexed: 05/04/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, untargeted detection of many hundreds of analytes from tissue. Recently, laser postionization (MALDI-2) has been developed for increased ion yield and sensitivity for lipid IMS. However, the dependence of MALDI-2 performance on the various lipid classes is largely unknown. To understand the effect of the applied matrix on MALDI-2 analysis of lipids, samples including an equimolar lipid standard mixture, various tissue homogenates, and intact rat kidney tissue sections were analyzed using the following matrices: α-cyano-4-hydroxycinnamic acid, 2',5'-dihydroxyacetophenone, 2',5'-dihydroxybenzoic acid (DHB), and norharmane (NOR). Lipid signal enhancement of protonated species using MALDI-2 technology varied based on the matrix used. Although signal improvements were observed for all matrices, the most dramatic effects using MALDI-2 were observed using NOR and DHB. For lipid standards analyzed by MALDI-2, NOR provided the broadest coverage, enabling the detection of all 13 protonated standards, including nonpolar lipids, whereas DHB gave less coverage but gave the highest signal increase for those lipids recorded. With respect to tissue homogenates and rat kidney tissue, mass spectra were compared and showed that the number and intensity of neutral lipids tentatively identified with MALDI-2 using NOR increased significantly (e.g., fivefold intensity increase for triacylglycerol). In the cases of DHB with MALDI-2, the number of protonated lipids identified from tissue homogenates doubled with 152 on average compared with 76 with MALDI alone. High spatial resolution imaging (~20 μm) of rat kidney tissue showed similar results using DHB with 125 lipids tentatively identified from MALDI-2 spectra versus just 72 using standard MALDI. From the four matrices tested, NOR provided the greatest increase in sensitivity for neutral lipids (triacylglycerol, diacylglycerol, monoacylglycerol, and cholesterol ester), and DHB provided the highest overall number of lipids detected using MALDI-2 technology.
Collapse
Affiliation(s)
- Josiah C. McMillen
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jarod A. Fincher
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Dustin R. Klein
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jeffrey M. Spraggins
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Pharmacology, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| |
Collapse
|
47
|
Limbrick EM, Graf M, Derewacz DK, Nguyen F, Spraggins JM, Wieland M, Ynigez-Gutierrez AE, Reisman BJ, Zinshteyn B, McCulloch KM, Iverson TM, Green R, Wilson DN, Bachmann BO. Bifunctional Nitrone-Conjugated Secondary Metabolite Targeting the Ribosome. J Am Chem Soc 2020; 142:18369-18377. [PMID: 32709196 DOI: 10.1021/jacs.0c04675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Many microorganisms possess the capacity for producing multiple antibiotic secondary metabolites. In a few notable cases, combinations of secondary metabolites produced by the same organism are used in important combination therapies for treatment of drug-resistant bacterial infections. However, examples of conjoined roles of bioactive metabolites produced by the same organism remain uncommon. During our genetic functional analysis of oxidase-encoding genes in the everninomicin producer Micromonospora carbonacea var. aurantiaca, we discovered previously uncharacterized antibiotics everninomicin N and O, comprised of an everninomicin fragment conjugated to the macrolide rosamicin via a rare nitrone moiety. These metabolites were determined to be hydrolysis products of everninomicin P, a nitrone-linked conjugate likely the result of nonenzymatic condensation of the rosamicin aldehyde and the octasaccharide everninomicin F, possessing a hydroxylamino sugar moiety. Rosamicin binds the erythromycin macrolide binding site approximately 60 Å from the orthosomycin binding site of everninomicins. However, while individual ribosomal binding sites for each functional half of everninomicin P are too distant for bidentate binding, ligand displacement studies demonstrated that everninomicin P competes with rosamicin for ribosomal binding. Chemical protection studies and structural analysis of everninomicin P revealed that everninomicin P occupies both the macrolide- and orthosomycin-binding sites on the 70S ribosome. Moreover, resistance mutations within each binding site were overcome by the inhibition of the opposite functional antibiotic moiety binding site. These data together demonstrate a strategy for coupling orthogonal antibiotic pharmacophores, a surprising tolerance for substantial covalent modification of each antibiotic, and a potential beneficial strategy to combat antibiotic resistance.
Collapse
Affiliation(s)
- Emilianne M Limbrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael Graf
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Dagmara K Derewacz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Fabian Nguyen
- Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Maximiliane Wieland
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | | | - Benjamin J Reisman
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States
| | - Kathryn M McCulloch
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - T M Iverson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Center for Structural Biology, Nashville, Tennessee 37232, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Daniel N Wilson
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37205, United States
| |
Collapse
|
48
|
Neumann EK, Migas LG, Allen JL, Caprioli RM, Van de Plas R, Spraggins JM. Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Mass Spectrometry. Anal Chem 2020. [PMID: 32668145 DOI: 10.26434/chemrxiv.12118644.v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Low molecular weight metabolites are essential for defining the molecular phenotypes of cells. However, spatial metabolomics tools often lack the sensitivity, specify, and spatial resolution to provide comprehensive descriptions of these species in tissue. MALDI imaging mass spectrometry (IMS) of low molecular weight ions is particularly challenging as MALDI matrix clusters are often nominally isobaric with multiple metabolite ions, requiring high resolving power instrumentation or derivatization to circumvent this issue. An alternative to this is to perform ion mobility separation before ion detection, enabling the visualization of metabolites without the interference of matrix ions. Additional difficulties surrounding low weight metabolite visualization include high resolution imaging, while maintaining sufficient ion numbers for broad and representative analysis of the tissue chemical complement. Here, we use MALDI timsTOF IMS to image low molecular weight metabolites at higher spatial resolution than most metabolite MALDI IMS experiments (20 μm) while maintaining broad coverage within the human kidney. We demonstrate that trapped ion mobility spectrometry (TIMS) can resolve matrix peaks from metabolite signal and separate both isobaric and isomeric metabolites with different distributions within the kidney. The added ion mobility data dimension dramatically increased the peak capacity for spatial metabolomics experiments. Through this improved sensitivity, we have found >40 low molecular weight metabolites in human kidney tissue, such as argininic acid, acetylcarnitine, and choline that localize to the cortex, medulla, and renal pelvis, respectively. Future work will involve further exploring metabolomic profiles of human kidneys as a function of age, sex, and race.
Collapse
Affiliation(s)
- Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, Building 34, 2628 CD Delft, The Netherlands
| | - Jamie L Allen
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Raf Van de Plas
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, Building 34, 2628 CD Delft, The Netherlands
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| |
Collapse
|
49
|
Djambazova KV, Klein DR, Migas LG, Neumann EK, Rivera ES, Van de Plas R, Caprioli RM, Spraggins JM. Resolving the Complexity of Spatial Lipidomics Using MALDI TIMS Imaging Mass Spectrometry. Anal Chem 2020; 92:13290-13297. [PMID: 32808523 DOI: 10.26434/chemrxiv.12331652.v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows for direct mapping of biomolecules in tissues. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here, we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) mass spectrometer with trapped ion mobility spectrometry (TIMS) enables a >250% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn backbone isomers, acyl chain isomers, and double-bond position and stereoisomers, is demonstrated. As a proof of concept, in situ separation and imaging of lipid isomers with distinct spatial distributions were performed using tissue sections from a whole-body mouse pup.
Collapse
Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Emilio S Rivera
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| |
Collapse
|
50
|
Prentice BM, Ryan DJ, Grove KJ, Cornett DS, Caprioli RM, Spraggins JM. Dynamic Range Expansion by Gas-Phase Ion Fractionation and Enrichment for Imaging Mass Spectrometry. Anal Chem 2020; 92:13092-13100. [PMID: 32845133 PMCID: PMC8340028 DOI: 10.1021/acs.analchem.0c02121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the analysis of biological tissue by imaging mass spectrometry (IMS), the limit of detection and dynamic range are of paramount importance in obtaining experimental results that provide insight into underlying biological processes. Many important biomolecules are present in the tissue milieu in low concentrations and in complex mixtures with other compounds of widely ranging abundances, challenging the limits of analytical technologies. In many IMS experiments, the ion signal can be dominated by a few highly abundant ion species. On trap-based instrument platforms that accumulate ions prior to mass analysis, these high abundance ions can diminish the detection and dynamic range of lower abundance ions. Herein, we describe two strategies for combating these challenges during IMS experiments on a hybrid QhFT-ICR MS. In one iteration, the mass resolving capabilities of a quadrupole mass filter are used to selectively enrich ions of interest via a technique previously termed continuous accumulation of selected ions. Second, we have introduced a supplemental dipolar AC waveform to the quadrupole mass filter of a commercial QhFT-ICR mass spectrometer to perform selected ion ejection prior to the ion accumulation region. This setup allows the selective ejection of the most abundant ion species prior to ion accumulation, thereby greatly improving the molecular depth with which IMS can probe tissue samples. The gain in sensitivity of both of these approaches roughly scales with the number of accumulated laser shots up to the charge capacity of the ion accumulation cell. The efficiencies of these two strategies are described here by performing lipid imaging mass spectrometry analyses of a rat brain.
Collapse
Affiliation(s)
- Boone M Prentice
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Daniel J Ryan
- ExxonMobil Research and Engineering Company, Annandale, New Jersey 08801, United States
| | - Kerri J Grove
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Pharmacology and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|