1
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Freiberg JA, Reyes Ruiz VM, Gimza BD, Murdoch CC, Green ER, Curry JM, Cassat JE, Skaar EP. Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus. Nat Commun 2024; 15:6734. [PMID: 39112491 PMCID: PMC11306626 DOI: 10.1038/s41467-024-51144-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Staphylococcus aureus is responsible for a substantial number of invasive infections globally each year. These infections are problematic because they are frequently recalcitrant to antibiotic treatment. Antibiotic tolerance, the ability of bacteria to persist despite normally lethal doses of antibiotics, contributes to antibiotic treatment failure in S. aureus infections. To understand how antibiotic tolerance is induced, S. aureus biofilms exposed to multiple anti-staphylococcal antibiotics are examined using both quantitative proteomics and transposon sequencing. These screens indicate that arginine metabolism is involved in antibiotic tolerance within a biofilm and support the hypothesis that depletion of arginine within S. aureus communities can induce antibiotic tolerance. Consistent with this hypothesis, inactivation of argH, the final gene in the arginine synthesis pathway, induces antibiotic tolerance. Arginine restriction induces antibiotic tolerance via inhibition of protein synthesis. In murine skin and bone infection models, an argH mutant has enhanced ability to survive antibiotic treatment with vancomycin, highlighting the relationship between arginine metabolism and antibiotic tolerance during S. aureus infection. Uncovering this link between arginine metabolism and antibiotic tolerance has the potential to open new therapeutic avenues targeting previously recalcitrant S. aureus infections.
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Affiliation(s)
- Jeffrey A Freiberg
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Valeria M Reyes Ruiz
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brittney D Gimza
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caitlin C Murdoch
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Erin R Green
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Jacob M Curry
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James E Cassat
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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2
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Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L. Spatial top-down proteomics for the functional characterization of human kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580062. [PMID: 38405958 PMCID: PMC10888776 DOI: 10.1101/2024.02.13.580062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.
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Affiliation(s)
- Kevin J. Zemaitis
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - James M. Fulcher
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Rashmi Kumar
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - David J. Degnan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Logan A. Lewis
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Yen-Chen Liao
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Marija Veličković
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Sarah M. Williams
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lisa M. Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
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3
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Chandrasekharan G, Unnikrishnan M. High throughput methods to study protein-protein interactions during host-pathogen interactions. Eur J Cell Biol 2024; 103:151393. [PMID: 38306772 DOI: 10.1016/j.ejcb.2024.151393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
The ability of a pathogen to survive and cause an infection is often determined by specific interactions between the host and pathogen proteins. Such interactions can be both intra- and extracellular and may define the outcome of an infection. There are a range of innovative biochemical, biophysical and bioinformatic techniques currently available to identify protein-protein interactions (PPI) between the host and the pathogen. However, the complexity and the diversity of host-pathogen PPIs has led to the development of several high throughput (HT) techniques that enable the study of multiple interactions at once and/or screen multiple samples at the same time, in an unbiased manner. We review here the major HT laboratory-based technologies employed for host-bacterial interaction studies.
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Affiliation(s)
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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4
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Ma Y, Shi W, Dong Y, Sun Y, Jin Q. Spatial Multi-Omics in Alzheimer's Disease: A Multi-Dimensional Approach to Understanding Pathology and Progression. Curr Issues Mol Biol 2024; 46:4968-4990. [PMID: 38785566 PMCID: PMC11119029 DOI: 10.3390/cimb46050298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Alzheimer's Disease (AD) presents a complex neuropathological landscape characterized by hallmark amyloid plaques and neurofibrillary tangles, leading to progressive cognitive decline. Despite extensive research, the molecular intricacies contributing to AD pathogenesis are inadequately understood. While single-cell omics technology holds great promise for application in AD, particularly in deciphering the understanding of different cell types and analyzing rare cell types and transcriptomic expression changes, it is unable to provide spatial distribution information, which is crucial for understanding the pathological processes of AD. In contrast, spatial multi-omics research emerges as a promising and comprehensive approach to analyzing tissue cells, potentially better suited for addressing these issues in AD. This article focuses on the latest advancements in spatial multi-omics technology and compares various techniques. Additionally, we provide an overview of current spatial omics-based research results in AD. These technologies play a crucial role in facilitating new discoveries and advancing translational AD research in the future. Despite challenges such as balancing resolution, increasing throughput, and data analysis, the application of spatial multi-omics holds immense potential in revolutionizing our understanding of human disease processes and identifying new biomarkers and therapeutic targets, thereby potentially contributing to the advancement of AD research.
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Affiliation(s)
| | | | | | | | - Qiguan Jin
- College of Physical Education, Yangzhou University, Yangzhou 225127, China; (Y.M.); (W.S.); (Y.D.); (Y.S.)
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5
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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] [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.
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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
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6
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Abstract
Imaging mass spectrometry is a well-established technology that can easily and succinctly communicate the spatial localization of molecules within samples. This review communicates the recent advances in the field, with a specific focus on matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) applied on tissues. The general sample preparation strategies for different analyte classes are explored, including special considerations for sample types (fresh frozen or formalin-fixed,) strategies for various analytes (lipids, metabolites, proteins, peptides, and glycans) and how multimodal imaging strategies can leverage the strengths of each approach is mentioned. This work explores appropriate experimental design approaches and standardization of processes needed for successful studies, as well as the various data analysis platforms available to analyze data and their strengths. The review concludes with applications of imaging mass spectrometry in various fields, with a focus on medical research, and some examples from plant biology and microbe metabolism are mentioned, to illustrate the breadth and depth of MALDI IMS.
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Affiliation(s)
- Jessica L Moore
- Department of Proteomics, Discovery Life Sciences, Huntsville, Alabama 35806, United States
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, Connecticut 06520, United States
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7
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Gosline SJC, Veličković M, Pino JC, Day LZ, Attah IK, Swensen AC, Danna V, Posso C, Rodland KD, Chen J, Matthews CE, Campbell-Thompson M, Laskin J, Burnum-Johnson K, Zhu Y, Piehowski PD. Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence. Mol Cell Proteomics 2023; 22:100592. [PMID: 37328065 PMCID: PMC10460696 DOI: 10.1016/j.mcpro.2023.100592] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/24/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023] Open
Abstract
The need for a clinically accessible method with the ability to match protein activity within heterogeneous tissues is currently unmet by existing technologies. Our proteomics sample preparation platform, named microPOTS (Microdroplet Processing in One pot for Trace Samples), can be used to measure relative protein abundance in micron-scale samples alongside the spatial location of each measurement, thereby tying biologically interesting proteins and pathways to distinct regions. However, given the smaller pixel/voxel number and amount of tissue measured, standard mass spectrometric analysis pipelines have proven inadequate. Here we describe how existing computational approaches can be adapted to focus on the specific biological questions asked in spatial proteomics experiments. We apply this approach to present an unbiased characterization of the human islet microenvironment comprising the entire complex array of cell types involved while maintaining spatial information and the degree of the islet's sphere of influence. We identify specific functional activity unique to the pancreatic islet cells and demonstrate how far their signature can be detected in the adjacent tissue. Our results show that we can distinguish pancreatic islet cells from the neighboring exocrine tissue environment, recapitulate known biological functions of islet cells, and identify a spatial gradient in the expression of RNA processing proteins within the islet microenvironment.
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Affiliation(s)
- Sara J C Gosline
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | | | - James C Pino
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Le Z Day
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Isaac K Attah
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Adam C Swensen
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Vincent Danna
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Camilo Posso
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Karin D Rodland
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Clayton E Matthews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Ying Zhu
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Paul D Piehowski
- Pacific Northwest National Laboratories, Richland, Washington, USA.
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8
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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] [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.
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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
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9
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun 2023; 14:4013. [PMID: 37419873 PMCID: PMC10329015 DOI: 10.1038/s41467-023-39616-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA, USA
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Darci Phillips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Samuel M Naik
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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10
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King ME, Lin M, Spradlin M, Eberlin LS. Advances and Emerging Medical Applications of Direct Mass Spectrometry Technologies for Tissue Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:1-25. [PMID: 36944233 DOI: 10.1146/annurev-anchem-061020-015544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Offering superb speed, chemical specificity, and analytical sensitivity, direct mass spectrometry (MS) technologies are highly amenable for the molecular analysis of complex tissues to aid in disease characterization and help identify new diagnostic, prognostic, and predictive markers. By enabling detection of clinically actionable molecular profiles from tissues and cells, direct MS technologies have the potential to guide treatment decisions and transform sample analysis within clinical workflows. In this review, we highlight recent health-related developments and applications of direct MS technologies that exhibit tangible potential to accelerate clinical research and disease diagnosis, including oncological and neurodegenerative diseases and microbial infections. We focus primarily on applications that employ direct MS technologies for tissue analysis, including MS imaging technologies to map spatial distributions of molecules in situ as well as handheld devices for rapid in vivo and ex vivo tissue analysis.
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Affiliation(s)
- Mary E King
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA;
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA;
| | - Monica Lin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA;
| | - Meredith Spradlin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA;
| | - Livia S Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA;
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11
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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 2023; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
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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, Vanderbilt University, Nashville, Tennessee 37235, United States
- 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, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, 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
| | - 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, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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12
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Yang M, Unsihuay D, Hu H, Meke FN, Qu Z, Zhang ZY, Laskin J. Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. Anal Chem 2023; 95:5214-5222. [PMID: 36917636 PMCID: PMC11330692 DOI: 10.1021/acs.analchem.2c04795] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for label-free mapping of the spatial distribution of proteins in biological tissues. We have previously demonstrated imaging of individual proteoforms in biological tissues using nanospray desorption electrospray ionization (nano-DESI), an ambient liquid extraction-based MSI technique. Nano-DESI MSI generates multiply charged protein ions, which is advantageous for their identification using top-down proteomics analysis. In this study, we demonstrate proteoform mapping in biological tissues with a spatial resolution down to 7 μm using nano-DESI MSI. A substantial decrease in protein signals observed in high-spatial-resolution MSI makes these experiments challenging. We have enhanced the sensitivity of nano-DESI MSI experiments by optimizing the design of the capillary-based probe and the thickness of the tissue section. In addition, we demonstrate that oversampling may be used to further improve spatial resolution at little or no expense to sensitivity. These developments represent a new step in MSI-based spatial proteomics, which complements targeted imaging modalities widely used for studying biological systems.
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Affiliation(s)
- Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisy Unsihuay
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Hang Hu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Frederick Nguele Meke
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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13
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Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
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Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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14
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Imaging Mass Spectrometry Reveals Complex Lipid Distributions Across Staphylococcus aureus Biofilm Layers. J Mass Spectrom Adv Clin Lab 2022; 26:36-46. [PMID: 36388058 PMCID: PMC9641601 DOI: 10.1016/j.jmsacl.2022.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Although Staphylococcus aureus is the leading cause of biofilm-related infections, the lipidomic distributions within these biofilms is poorly understood. Here, lipidomic mapping of S. aureus biofilm cross-sections was performed to investigate heterogeneity between horizontal biofilm layers. Methods S. aureus biofilms were grown statically, embedded in a mixture of carboxymethylcellulose/gelatin, and prepared for downstream matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS). Trapped ion mobility spectrometry (TIMS) was also applied prior to mass analysis. Results Implementation of TIMS led to a ∼ threefold increase in the number of lipid species detected. Washing biofilm samples with ammonium formate (150 mM) increased signal intensity for some bacterial lipids by as much as tenfold, with minimal disruption of the biofilm structure. MALDI TIMS IMS revealed that most lipids localize primarily to a single biofilm layer, and species from the same lipid class such as cardiolipins CL(57:0) - CL(66:0) display starkly different localizations, exhibiting between 1.5 and 6.3-fold intensity differences between layers (n = 3, p < 0.03). No horizontal layers were observed within biofilms grown anaerobically, and lipids were distributed homogenously. Conclusions High spatial resolution analysis of S. aureus biofilm cross-sections by MALDI TIMS IMS revealed stark lipidomic heterogeneity between horizontal S. aureus biofilm layers demonstrating that each layer was molecularly distinct. Finally, this workflow uncovered an absence of layers in biofilms grown under anaerobic conditions, possibly indicating that oxygen contributes to the observed heterogeneity under aerobic conditions. Future applications of this workflow to study spatially localized molecular responses to antimicrobials could provide new therapeutic strategies.
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15
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Kwon Y, Piehowski PD, Zhao R, Sontag RL, Moore RJ, Burnum-Johnson KE, Smith RD, Qian WJ, Kelly RT, Zhu Y. Hanging drop sample preparation improves sensitivity of spatial proteomics. LAB ON A CHIP 2022; 22:2869-2877. [PMID: 35838077 PMCID: PMC9320080 DOI: 10.1039/d2lc00384h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Spatial proteomics holds great promise for revealing tissue heterogeneity in both physiological and pathological conditions. However, one significant limitation of most spatial proteomics workflows is the requirement of large sample amounts that blurs cell-type-specific or microstructure-specific information. In this study, we developed an improved sample preparation approach for spatial proteomics and integrated it with our previously-established laser capture microdissection (LCM) and microfluidics sample processing platform. Specifically, we developed a hanging drop (HD) method to improve the sample recovery by positioning a nanowell chip upside-down during protein extraction and tryptic digestion steps. Compared with the commonly-used sitting-drop method, the HD method keeps the tissue pixel away from the container surface, and thus improves the accessibility of the extraction/digestion buffer to the tissue sample. The HD method can increase the MS signal by 7 fold, leading to a 66% increase in the number of identified proteins. An average of 721, 1489, and 2521 proteins can be quantitatively profiled from laser-dissected 10 μm-thick mouse liver tissue pixels with areas of 0.0025, 0.01, and 0.04 mm2, respectively. The improved system was further validated in the study of cell-type-specific proteomes of mouse uterine tissues.
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Affiliation(s)
- Yumi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Paul D Piehowski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Ryan L Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
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16
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Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J. Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. Angew Chem Int Ed Engl 2022; 61:e202200721. [PMID: 35446460 PMCID: PMC9276647 DOI: 10.1002/anie.202200721] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 01/28/2023]
Abstract
Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform‐specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano‐DESI MSI) for the proteoform‐selective imaging of biological tissues. Nano‐DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof‐of‐concept experiments demonstrate that nano‐DESI MSI combined with on‐tissue top‐down proteomics is ideally suited for the proteoform‐selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain.
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Affiliation(s)
- Manxi Yang
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
| | - Hang Hu
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
| | - Pei Su
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Paul M. Thomas
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Jeannie M. Camarillo
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Joseph B. Greer
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Bryan P. Early
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Ryan T. Fellers
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Julia Laskin
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
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17
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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: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [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.
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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.
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18
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Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J. Proteoform‐Selective Imaging of Tissues Using Mass Spectrometry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manxi Yang
- Purdue University Department of Chemistry chemistry 560 Oval Dr. 47906 West Lafayette UNITED STATES
| | - Hang Hu
- Purdue University Chemistry UNITED STATES
| | - Pei Su
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Paul M. Thomas
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | | | - Joseph B. Greer
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Bryan P. Early
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Ryan T. Fellers
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Neil L. Kelleher
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Julia Laskin
- Purdue University Department of Chemistry 560 Oval Dr. 47907 West Lafayette UNITED STATES
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19
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Zheng Q, Guo Z, Chen Y. Capillary array electrophoresis imaging of biochemicals in tissue sections. Talanta 2022; 240:123183. [PMID: 34996017 DOI: 10.1016/j.talanta.2021.123183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/21/2021] [Accepted: 12/25/2021] [Indexed: 10/19/2022]
Abstract
It is of great significance to reveal the molecular distribution images in biological tissues, which has led to the bloom of mass spectrometry imaging. Unfortunately, its application is encountering the resistance of high technical barriers and equipment cost, as well as the inability to image substances that cannot be desorbed or ionized, or cannot be separated by their mass-to-charge ratios. Herein presented is a complementary and cost-effective method called capillary array electrophoresis (CAE) imaging. To have the information of molecules and their spatial location, a gridding cutter was fabricated to orderly dissect a tissue section into a leakproof array of micro wells enclosed by the grid-blade arrays. After in situ extraction and fluorophore-labeling of analytes, the samples in the wells were directly subjected to CAE-LIF (laser-induced fluorescence), and the molecular distribution images were depicted with the separated peaks. The practicability was demonstrated by CAE imaging of rat brain tissue sections with amino acid neurotransmitters (e.g., glutamine, 4-aminobutyric acid, alanine, glutamic acid and aspartic acid) as targets. The resultant images showed the global differences of molecular distributions, with a spatial resolution of 1000 μm that was presently determined by the well width but ultimately by the bore size of capillary (down to 10-50 μm). CAE imaging can hence be promising for its low cost, low technical barriers and abundant mechanisms to separate the charged and non-charged, chiral and non-chiral substances.
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Affiliation(s)
- Qingfeng Zheng
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenpeng Guo
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yi Chen
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Huaiyin Institute of Technology, Huaian, 223001, China; Beijing National Laboratory for Molecular Science, Beijing, 100190, China.
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20
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Rankin‐Turner S, Reynolds JC, Turner MA, Heaney LM. Applications of ambient ionization mass spectrometry in 2021: An annual review. ANALYTICAL SCIENCE ADVANCES 2022; 3:67-89. [PMID: 38715637 PMCID: PMC10989594 DOI: 10.1002/ansa.202100067] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/17/2022] [Accepted: 02/27/2022] [Indexed: 06/26/2024]
Abstract
Ambient ionization mass spectrometry (AIMS) has revolutionized the field of analytical chemistry, enabling the rapid, direct analysis of samples in their native state. Since the inception of AIMS almost 20 years ago, the analytical community has driven the further development of this suite of techniques, motivated by the plentiful advantages offered in addition to traditional mass spectrometry. Workflows can be simplified through the elimination of sample preparation, analysis times can be significantly reduced and analysis remote from the traditional laboratory space has become a real possibility. As such, the interest in AIMS has rapidly spread through analytical communities worldwide, and AIMS techniques are increasingly being integrated with standard laboratory operations. This annual review covers applications of AIMS techniques throughout 2021, with a specific focus on AIMS applications in a number of key fields of research including disease diagnostics, forensics and security, food safety testing and environmental sciences. While some new techniques are introduced, the focus in AIMS research is increasingly shifting from the development of novel techniques toward efforts to improve existing AIMS techniques, particularly in terms of reproducibility, quantification and ease-of-use.
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Affiliation(s)
- Stephanie Rankin‐Turner
- W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - James C. Reynolds
- Department of ChemistryLoughborough UniversityLoughboroughLeicestershireUK
| | - Matthew A. Turner
- Department of ChemistryLoughborough UniversityLoughboroughLeicestershireUK
| | - Liam M. Heaney
- School of SportExercise and Health SciencesLoughborough UniversityLoughboroughLeicestershireUK
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21
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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] [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.
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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,
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22
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Sisley EK, Hale OJ, Styles IB, Cooper HJ. Native Ambient Mass Spectrometry Imaging of Ligand-Bound and Metal-Bound Proteins in Rat Brain. J Am Chem Soc 2022; 144:2120-2128. [DOI: 10.1021/jacs.1c10032] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Emma K. Sisley
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Oliver J. Hale
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Iain B. Styles
- School of Computer Science, University of Birmingham, Birmingham, B15 2TT, U.K
- The Alan Turing Institute, London, NW1 2DB, U.K
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, B15 2TT, U.K
- University of Nottingham, Midlands, NG7 2RD, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, U.K
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23
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24
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Monteith AJ, Miller JM, Maxwell CN, Chazin WJ, Skaar EP. Neutrophil extracellular traps enhance macrophage killing of bacterial pathogens. SCIENCE ADVANCES 2021; 7:eabj2101. [PMID: 34516771 PMCID: PMC8442908 DOI: 10.1126/sciadv.abj2101] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/20/2021] [Indexed: 05/16/2023]
Abstract
Neutrophils and macrophages are critical to the innate immune response, but cooperative mechanisms used by these cells to combat extracellular pathogens are not well understood. This study reveals that S100A9-deficient neutrophils produce higher levels of mitochondrial superoxide in response to Staphylococcus aureus and, as a result, form neutrophil extracellular traps (suicidal NETosis). Increased suicidal NETosis does not improve neutrophil killing of S. aureus in isolation but augments macrophage killing. NET formation enhances antibacterial activity by increasing phagocytosis by macrophages and by transferring neutrophil-specific antimicrobial peptides to them. Similar results were observed in response to other phylogenetically distinct bacterial pathogens including Streptococcus pneumoniae and Pseudomonas aeruginosa, implicating this as an immune defense mechanism that broadly enhances antibacterial activity. These results demonstrate that achieving maximal bactericidal activity through NET formation requires macrophages and that accelerated and more robust suicidal NETosis makes neutrophils adept at increasing antibacterial activity, especially when A9 deficient.
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Affiliation(s)
- Andrew J. Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeanette M. Miller
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - C. Noel Maxwell
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Walter J. Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, 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
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25
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Mao Y, Wang X, Huang P, Tian R. Spatial proteomics for understanding the tissue microenvironment. Analyst 2021; 146:3777-3798. [PMID: 34042124 DOI: 10.1039/d1an00472g] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human body comprises rich populations of cells, which are arranged into tissues and organs with diverse functionalities. These cells exhibit a broad spectrum of phenotypes and are often organized as a heterogeneous but sophisticatedly regulated ecosystem - tissue microenvironment, inside which every cell interacts with and is reciprocally influenced by its surroundings through its life span. Therefore, it is critical to comprehensively explore the cellular machinery and biological processes in the tissue microenvironment, which is best exemplified by the tumor microenvironment (TME). The past decade has seen increasing advances in the field of spatial proteomics, the main purpose of which is to characterize the abundance and spatial distribution of proteins and their post-translational modifications in the microenvironment of diseased tissues. Herein, we outline the achievements and remaining challenges of mass spectrometry-based tissue spatial proteomics. Exciting technology developments along with important biomedical applications of spatial proteomics are highlighted. In detail, we focus on high-quality resources built by scalpel macrodissection-based region-resolved proteomics, method development of sensitive sample preparation for laser microdissection-based spatial proteomics, and antibody recognition-based multiplexed tissue imaging. In the end, critical issues and potential future directions for spatial proteomics are also discussed.
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Affiliation(s)
- Yiheng Mao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China. and Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Wang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China and Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Peiwu Huang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
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26
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Cantrell LS, Schey KL. Proteomic characterization of the human lens and Cataractogenesis. Expert Rev Proteomics 2021; 18:119-135. [PMID: 33849365 DOI: 10.1080/14789450.2021.1913062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION The goal of this review is to highlight the triumphs and frontiers in measurement of the lens proteome as it relates to onset of age-related nuclear cataract. As global life expectancy increases, so too does the frequency of age-related nuclear cataracts. Molecular therapeutics do not exist for delay or relief of cataract onset in humans. Since lens fiber cells are incapable of protein synthesis after initial maturation, age-related changes in proteome composition and post-translational modification accumulation can be measured with various techniques. Several of these modifications have been associated with cataract onset. AREAS COVERED We discuss the impact of long-lived proteins on the lens proteome and lens homeostasis as well as proteomic techniques that may be used to measure proteomes at various levels of proteomic specificity and spatial resolution. EXPERT OPINION There is clear evidence that several proteome modifications are correlated with cataract formation. Past studies should be enhanced with cutting-edge, spatially resolved mass spectrometry techniques to enhance the specificity and sensitivity of modification detection as it relates to cataract formation.
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Affiliation(s)
- Lee S Cantrell
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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27
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Veis DJ, Cassat JE. Infectious Osteomyelitis: Marrying Bone Biology and Microbiology to Shed New Light on a Persistent Clinical Challenge. J Bone Miner Res 2021; 36:636-643. [PMID: 33740314 DOI: 10.1002/jbmr.4279] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/01/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
Infections of bone occur in a variety of clinical settings, ranging from spontaneous isolated infections arising from presumed hematogenous spread to those associated with skin and soft tissue wounds or medical implants. The majority are caused by the ubiquitous bacterium Staphyloccocus (S.) aureus, which can exist as a commensal organism on human skin as well as an invasive pathogen, but a multitude of other microbes are also capable of establishing bone infections. While studies of clinical isolates and small animal models have advanced our understanding of the role of various pathogen and host factors in infectious osteomyelitis (iOM), many questions remain unaddressed. Thus, there are many opportunities to elucidate host-pathogen interactions that may be leveraged toward treatment or prevention of this troublesome problem. Herein, we combine perspectives from bone biology and microbiology and suggest that interdisciplinary approaches will bring new insights to the field. © 2021 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Deborah J Veis
- Division of Bone and Mineral Diseases, Departments of Medicine and Pathology, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, USA.,Shriners Hospitals for Children, St. Louis, MO, USA
| | - James E Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville,, TN, USA.,Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Institute for Infection, Immunology and Inflammation (VI4), Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, TN, USA
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28
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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: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [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.
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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
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29
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Drake RR, Scott DA, Angel PM. Imaging Mass Spectrometry. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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30
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Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM. Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2401-2415. [PMID: 32886506 PMCID: PMC9278956 DOI: 10.1021/jasms.0c00232] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [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.
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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
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31
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Tuck M, Blanc L, Touti R, Patterson NH, Van Nuffel S, Villette S, Taveau JC, Römpp A, Brunelle A, Lecomte S, Desbenoit N. Multimodal Imaging Based on Vibrational Spectroscopies and Mass Spectrometry Imaging Applied to Biological Tissue: A Multiscale and Multiomics Review. Anal Chem 2020; 93:445-477. [PMID: 33253546 DOI: 10.1021/acs.analchem.0c04595] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tuck
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Landry Blanc
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Rita Touti
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-8575, United States
| | - Sebastiaan Van Nuffel
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sandrine Villette
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Jean-Christophe Taveau
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Andreas Römpp
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Alain Brunelle
- Laboratoire d'Archéologie Moléculaire et Structurale, LAMS UMR 8220, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Sophie Lecomte
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nicolas Desbenoit
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
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32
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Cintron-Diaz YL, Acanda de la Rocha AM, Castellanos A, Chambers JM, Fernandez-Lima F. Mapping chemotherapeutic drug distribution in cancer cell spheroids using 2D-TOF-SIMS and LESA-TIMS-MS. Analyst 2020; 145:7056-7062. [PMID: 32966375 DOI: 10.1039/c9an02245g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three-dimensional (3D) cancer cell cultures grown in the form of spheroids are effective models for the study of in vivo-like processes simulating cancer tumor pharmacological dynamics and morphology. In this study, we show the advantages of Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) combined with in situ Liquid Extraction Surface Analysis coupled to trapped Ion Mobility Spectrometry Mass Spectrometry (LESA-TIMS-TOF MS) for high spatial resolution mapping and quantitation of ABT-737, a chemotherapeutic drug, at the level of single human colon carcinoma cell spheroids (HCT 116 MCS). 2D-TOF-SIMS studies of consecutive sections (∼16 μm thick slices) showed that ABT-737 is homogenously distributed in the outer layers of the HCT 116 MCS. Complementary in situ LESA-TIMS-TOF MS/MS measurements confirmed the presence of the ABT-737 drug in the MCS slides by the observation of the molecular ion [M + H]+m/z and mobility, and the charateristic fragmentation pattern. LESA-TIMS-TOF MS allowed a quantitative assessment of the ABT-737 drug of the control MCS slice spiked with ABT-737 standard over the 0.4-4.1 ng range and MCS treated starting at 10 μM for 24 h. These experiments showcase an effective protocol for unambigous characterization and 3D mapping of chemotherapeutic drug distribution at the single MCS level.
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Affiliation(s)
- Yarixa L Cintron-Diaz
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, FL 33199, USA.
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33
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Blutke A, Sun N, Xu Z, Buck A, Harrison L, Schriever SC, Pfluger PT, Wiles D, Kunzke T, Huber K, Schlegel J, Aichler M, Feuchtinger A, Matiasek K, Hauck SM, Walch A. Light sheet fluorescence microscopy guided MALDI-imaging mass spectrometry of cleared tissue samples. Sci Rep 2020; 10:14461. [PMID: 32879402 PMCID: PMC7468256 DOI: 10.1038/s41598-020-71465-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 08/10/2020] [Indexed: 02/08/2023] Open
Abstract
Light sheet fluorescence microscopy (LSFM) of optically cleared biological samples represents a powerful tool to analyze the 3-dimensional morphology of tissues and organs. Multimodal combinations of LSFM with additional analyses of the identical sample help to limit the consumption of restricted specimen and reduce inter-sample variation. Here, we demonstrate the proof-of-concept that LSFM of cleared brain tissue samples can be combined with Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI) for detection and quantification of proteins. Samples of freshly dissected murine brain and of archived formalin-fixed paraffin-embedded (FFPE) human brain tissue were cleared (3DISCO). Tissue regions of interest were defined by LSFM and excised, (re)-embedded in paraffin, and sectioned. Mouse sections were coated with sinapinic acid matrix. Human brain sections were pre-digested with trypsin and coated with α-cyano-4-hydroxycinnamic acid matrix. Subsequently, sections were subjected to MALDI-time-of-flight (TOF)-MSI in mass ranges between 0.8 to 4 kDa (human tissue sections), or 2.5–25 kDa (mouse tissue sections) with a lateral resolution of 50 µm. Protein- and peptide-identities corresponding to acquired MALDI-MSI spectra were confirmed by parallel liquid chromatography tandem mass spectrometry (LC–MS/MS) analysis. The spatial abundance- and intensity-patterns of established marker proteins detected by MALDI-MSI were also confirmed by immunohistochemistry.
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Affiliation(s)
- Andreas Blutke
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Zhihao Xu
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Luke Harrison
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.,Division of Metabolic Diseases, Technische Universität München, 80333, Munich, Germany
| | - Sonja C Schriever
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Paul T Pfluger
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | | | - Thomas Kunzke
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Katharina Huber
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Jürgen Schlegel
- Institute for Pathology, Department of Neuropathology, Technische Universität München, 80333, Munich, Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany.
| | - Kaspar Matiasek
- Institute for Veterinary Pathology at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Stefanie M Hauck
- Research Unit for Protein Science, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
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34
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Wang Z, Ryan DJ, Schey KL. Localization of the lens intermediate filament switch by imaging mass spectrometry. Exp Eye Res 2020; 198:108134. [PMID: 32682822 PMCID: PMC7508834 DOI: 10.1016/j.exer.2020.108134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/07/2020] [Accepted: 06/29/2020] [Indexed: 01/18/2023]
Abstract
Imaging mass spectrometry (IMS) enables targeted and untargeted visualization of the spatial localization of molecules in tissues with great specificity. The lens is a unique tissue that contains fiber cells corresponding to various stages of differentiation that are packed in a highly spatial order. The application of IMS to lens tissue localizes molecular features that are spatially related to the fiber cell organization. Such spatially resolved molecular information assists our understanding of lens structure and physiology; however, protein IMS studies are typically limited to abundant, soluble, low molecular weight proteins. In this study, a method was developed for imaging low solubility cytoskeletal proteins in the lens; a tissue that is filled with high concentrations of soluble crystallins. Optimized tissue washes combined with on-tissue enzymatic digestion allowed successful imaging of peptides corresponding to known lens cytoskeletal proteins. The resulting peptide signals facilitated segmentation of the bovine lens into molecularly distinct regions. A sharp intermediate filament transition from vimentin to lens-specific beaded filament proteins was detected in the lens cortex. MALDI IMS also revealed the region where posttranslational myristoylation of filensin occurs and the results indicate that truncation and myristoylation of filensin starts soon after filensin expression increased in the inner cortex. From intermediate filament switch to filensin truncation and myristoylation, multiple remarkable changes occur in the narrow region of lens cortex. MALDI images delineated the boundaries of distinct lens regions that will guide further proteomic and interactomic studies.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Daniel J Ryan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
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35
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Roche B, Bumann D. Single-cell reporters for pathogen responses to antimicrobial host attacks. Curr Opin Microbiol 2020; 59:16-23. [PMID: 32810800 DOI: 10.1016/j.mib.2020.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/20/2020] [Accepted: 07/26/2020] [Indexed: 12/12/2022]
Abstract
Host-pathogen interactions are often heterogeneous involving individual encounters between host and pathogen cells with diverse molecular mechanisms, response networks, and diverging outcomes. Single-cell reporters can identify the various types of interactions and participating pathogen subsets, help to unravel underlying molecular mechanism, and determine individual outcomes and their impact on disease progression. In this review, we discuss reporters-based on fluorescent proteins. We present different types of reporters and their experimental advantages and challenges, and describe how different strategies can interrogate exposure to antimicrobial host mechanism, pathogen response, inflicted damage, and impact on pathogen fitness at the single-cell level. We find many gaps in available tools but also exciting avenues to address these issues.
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Affiliation(s)
- Béatrice Roche
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland.
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36
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Huo Y, Liu K, Lou X. Strong additive and synergistic effects of polyoxyethylene nonionic surfactant-assisted protein MALDI imaging mass spectrometry. Talanta 2020; 222:121524. [PMID: 33167234 DOI: 10.1016/j.talanta.2020.121524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
Protein MALDI imaging mass spectrometry (MALDI-IMS) holds a great promise to acquire spatial distribution information of proteins on biological tissue, but it suffers from the small number of proteins detected by direct MALDI-IMS detection. Ionic surfactants have been extensively used for protein extraction to improve the number of proteins detected in tissue samples by LC-MS analysis, but seldom by direct MALDI-IMS detection. Nonionic surfactants are milder than ionic surfactants and protein native structures are remained after extraction, which favors the spatial resolution of direct MALDI-IMS. However, nonionic surfactants are less effective than ionic surfactants. In this report, we utilized polyoxyethylene nonionic surfactants (PNS) to pre-incubate the tissue section, followed by the on-tissue trypsin digestion and then direct MALDI detection of in-situ formed peptides. For the first time, we observed that the additive effect of PNS and the synergistic effect of the mixed PNS in improving the number of peptides detected. Specifically, the peptides detected were 73.0-90.7% distinct when the different PNS (Tween 80 or Triton X-100 alone or their mixture) was used. Taking advantage of this additive effect, the 96 proteins including 12 transmembrane proteins were detected, corresponding to a ~10-fold improvement compared to MALDI-IMS without surfactant. When the mixed surfactants were used to replace Tween 80 and Triton X-100 alone, the optimized surfactant concentration decreased 20-100-fold and the number of peptides detected with m/z > 2500 Da was improved 15-fold. The additive and synergistic effects of PNS suggested that the interaction mode between each PNS and proteins is highly variable. Benefiting from the strong additive effect and diversity of PNS, further improvement of the number of proteins detected by MALDI-IMS is clearly feasible.
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Affiliation(s)
- Yumeng Huo
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Kehui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, 100048, China.
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37
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Sokolovskaya OM, Shelton AN, Taga ME. Sharing vitamins: Cobamides unveil microbial interactions. Science 2020; 369:369/6499/eaba0165. [PMID: 32631870 DOI: 10.1126/science.aba0165] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda N Shelton
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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Who's in control? Regulation of metabolism and pathogenesis in space and time. Curr Opin Microbiol 2020; 55:88-96. [PMID: 32532689 DOI: 10.1016/j.mib.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 02/07/2023]
Abstract
Bacterial pathogens need to sense and respond to their environments during infection to align cell metabolism and virulence factor production to survive and battle host defenses. Complex regulatory networks including ligand-binding transcription factors, two-component systems, RNA-binding proteins, and small non-coding regulatory RNAs adjust gene expression programs in response to changes in metabolic fluxes, environmental cues, and nutrient availability. Recent studies underlined that these different layers of regulation occur along varying spatial and temporal scales, leading to changes in cell behavior and heterogeneity among the bacterial community. This brief review will highlight current research emphasizing that cell metabolism and pathogenesis are inextricably intertwined in both Gram-positive and Gram-negative bacteria.
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Host nutrient milieu drives an essential role for aspartate biosynthesis during invasive Staphylococcus aureus infection. Proc Natl Acad Sci U S A 2020; 117:12394-12401. [PMID: 32414924 PMCID: PMC7275739 DOI: 10.1073/pnas.1922211117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus can infect a diverse array of host environments. The broad tissue tropism of S. aureus requires metabolic flexibility to utilize the variety of nutrient sources found within target organ systems. In this work, we conducted a systematic analysis of the central metabolic pathways required for S. aureus survival during bone infection, one of the most frequent sites of invasive staphylococcal disease. We show that S. aureus requires aspartate biosynthesis to survive during bone infection, despite possessing an aspartate transporter, due to inhibition of aspartate utilization by the amino acid glutamate. Our results reveal a crucial role for inflammation-associated shifts in the host nutrient milieu for determining the metabolic pathways utilized by S. aureus during invasive infection. The bacterial pathogen Staphylococcus aureus is capable of infecting a broad spectrum of host tissues, in part due to flexibility of metabolic programs. S. aureus, like all organisms, requires essential biosynthetic intermediates to synthesize macromolecules. We therefore sought to determine the metabolic pathways contributing to synthesis of essential precursors during invasive S. aureus infection. We focused specifically on staphylococcal infection of bone, one of the most common sites of invasive S. aureus infection and a unique environment characterized by dynamic substrate accessibility, infection-induced hypoxia, and a metabolic profile skewed toward aerobic glycolysis. Using a murine model of osteomyelitis, we examined survival of S. aureus mutants deficient in central metabolic pathways, including glycolysis, gluconeogenesis, the tricarboxylic acid (TCA) cycle, and amino acid synthesis/catabolism. Despite the high glycolytic demand of skeletal cells, we discovered that S. aureus requires glycolysis for survival in bone. Furthermore, the TCA cycle is dispensable for survival during osteomyelitis, and S. aureus instead has a critical need for anaplerosis. Bacterial synthesis of aspartate in particular is absolutely essential for staphylococcal survival in bone, despite the presence of an aspartate transporter, which we identified as GltT and confirmed biochemically. This dependence on endogenous aspartate synthesis derives from the presence of excess glutamate in infected tissue, which inhibits aspartate acquisition by S. aureus. Together, these data elucidate the metabolic pathways required for staphylococcal infection within bone and demonstrate that the host nutrient milieu can determine essentiality of bacterial nutrient biosynthesis pathways despite the presence of dedicated transporters.
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Sisley EK, Ujma J, Palmer M, Giles K, Fernandez-Lima FA, Cooper HJ. LESA Cyclic Ion Mobility Mass Spectrometry of Intact Proteins from Thin Tissue Sections. Anal Chem 2020; 92:6321-6326. [PMID: 32271006 PMCID: PMC7304663 DOI: 10.1021/acs.analchem.9b05169] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Liquid
extraction surface analysis (LESA) is an ambient surface
sampling technique that allows the analysis of intact proteins directly
from tissue samples via mass spectrometry. Integration of ion mobility
separation to LESA mass spectrometry workflows has shown significant
improvements in the signal-to-noise ratios of the resulting protein
mass spectra and hence the number of proteins detected. Here, we report
the use of a quadrupole–cyclic ion mobility–time-of-flight
mass spectrometer (Q-cIM-ToF) for the analysis of proteins from mouse
brain and rat kidney tissues sampled via LESA. Among other features,
the instrument allows multiple pass cyclic ion mobility separation,
with concomitant increase in resolving power. Single-pass experiments
enabled the detection of 30 proteins from mouse brain tissue, rising
to 44 when quadrupole isolation was employed. In the absence of ion
mobility separation, 21 proteins were detected in rat kidney tissue
including the abundant α- and β-globin chains from hemoglobin.
Single-pass cyclic ion mobility mass spectrometry enabled the detection
of 60 additional proteins. Multipass experiments of a narrow m/z range (m/z 870–920) resulted in the detection of 24 proteins (one pass),
37 proteins (two passes) and 54 proteins (three passes), thus demonstrating
the benefits of improved mobility resolving power.
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Affiliation(s)
| | - Jakub Ujma
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom
| | - Martin Palmer
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom
| | - Kevin Giles
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom
| | - Francisco A Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
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41
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Hale OJ, Cooper HJ. In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates. Biochem Soc Trans 2020; 48:317-326. [PMID: 32010951 PMCID: PMC7054757 DOI: 10.1042/bst20190793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
Abstract
Advances in sample preparation, ion sources and mass spectrometer technology have enabled the detection and characterisation of intact proteins. The challenges associated include an appropriately soft ionisation event, efficient transmission and detection of the often delicate macromolecules. Ambient ion sources, in particular, offer a wealth of strategies for analysis of proteins from solution environments, and directly from biological substrates. The last two decades have seen rapid development in this area. Innovations include liquid extraction surface analysis, desorption electrospray ionisation and nanospray desorption electrospray ionisation. Similarly, developments in native mass spectrometry allow protein-protein and protein-ligand complexes to be ionised and analysed. Identification and characterisation of these large ions involves a suite of hyphenated mass spectrometry techniques, often including the coupling of ion mobility spectrometry and fragmentation techniques. The latter include collision, electron and photon-induced methods, each with their own characteristics and benefits for intact protein identification. In this review, recent developments for in situ protein analysis are explored, with a focus on ion sources and tandem mass spectrometry techniques used for identification.
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Affiliation(s)
- Oliver J. Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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Lewis HM, Webb RP, Verbeck GF, Bunch J, de Jesus J, Costa C, Palitsin V, Swales J, Goodwin RJA, Sears P, Bailey MJ. Nanoextraction Coupled to Liquid Chromatography Mass Spectrometry Delivers Improved Spatially Resolved Analysis. Anal Chem 2019; 91:15411-15417. [PMID: 31747247 DOI: 10.1021/acs.analchem.9b02821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Direct analyte-probed nanoextraction (DAPNe) is a technique that allows extraction of drug and endogenous compounds from a discrete location on a tissue sample using a nano capillary filled with solvent. Samples can be extracted from spot diameters as low as 6 μm. Studies previously undertaken by our group have shown that the technique can provide good precision (5%) for analyzing drug molecules in 150 μm diameter areas of homogenized tissue, provided an internal standard is sprayed on to the tissue prior to analysis. However, without an isotopically labeled standard, the repeatability is poor, even after normalization to the spot area or matrix compounds. By application to tissue homogenates spiked with drug compounds, we can demonstrate that it is possible to significantly improve the repeatability of the technique by incorporating a liquid chromatography separation step. Liquid chromatography is a technique for separating compounds prior to mass spectrometry (LC-MS) which enables separation of isomeric compounds that cannot be discriminated using mass spectrometry alone, as well as reducing matrix interferences. Conventionally, LC-MS is carried out on bulk or homogenized samples, which means analysis is essentially an average of the sample and does not take into account discrete areas. This work opens a new opportunity for spatially resolved liquid chromatography mass spectrometry with precision better than 20%.
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Affiliation(s)
- Holly-May Lewis
- Advanced Technology Institute , University of Surrey , Guildford GU2 7XH , U.K
| | - Roger P Webb
- Ion Beam Centre , University of Surrey , Guildford GU2 7XH , U.K
| | | | | | - Janella de Jesus
- Department of Chemistry , University of Surrey , Guildford GU2 7XH , U.K
| | - Catia Costa
- Ion Beam Centre , University of Surrey , Guildford GU2 7XH , U.K
| | | | - John Swales
- Pathology Sciences , Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca , Cambridge CB2 0AA , United Kingdom
| | - Richard J A Goodwin
- Pathology Sciences , Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca , Cambridge CB2 0AA , United Kingdom
| | - Patrick Sears
- Department of Chemistry , University of Surrey , Guildford GU2 7XH , U.K
| | - Melanie J Bailey
- Department of Chemistry , University of Surrey , Guildford GU2 7XH , U.K
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Schey KL, Wang Z, Friedrich MG, Garland DL, Truscott RJW. Spatiotemporal changes in the human lens proteome: Critical insights into long-lived proteins. Prog Retin Eye Res 2019; 76:100802. [PMID: 31704338 DOI: 10.1016/j.preteyeres.2019.100802] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022]
Abstract
The ocular lens is a unique tissue that contains an age gradient of cells and proteins ranging from newly differentiated cells containing newly synthesized proteins to cells and proteins that are as old as the organism. Thus, the ocular lens is an excellent model for studying long-lived proteins (LLPs) and the effects of aging and post-translational modifications on protein structure and function. Given the architecture of the lens, with young fiber cells in the outer cortex and the oldest cells in the lens nucleus, spatially-resolved studies provide information on age-specific protein changes. In this review, experimental strategies and proteomic methods that have been used to examine age-related and cataract-specific changes to the human lens proteome are described. Measured spatio-temporal changes in the human lens proteome are summarized and reveal a highly consistent, time-dependent set of modifications observed in transparent human lenses. Such measurements have led to the discovery of cataract-specific modifications and the realization that many animal systems are unsuitable to study many of these modifications. Mechanisms of protein modifications such as deamidation, racemization, truncation, and protein-protein crosslinking are presented and the implications of such mechanisms for other long-lived proteins in other tissues are discussed in the context of age-related neurological diseases. A comprehensive understanding of LLP modifications will enhance our ability to develop new therapies for the delay, prevention or reversal of age-related diseases.
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Affiliation(s)
- Kevin L Schey
- Department of Biochemistry, Vanderbilt University, USA.
| | - Zhen Wang
- Department of Biochemistry, Vanderbilt University, USA
| | - Michael G Friedrich
- Illawarra Health and Medical Research Institute, University of Wollongong, Australia
| | | | - Roger J W Truscott
- Illawarra Health and Medical Research Institute, University of Wollongong, Australia
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