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Won Y, Jang B, Lee SH, Reyzer ML, Presentation KS, Kim H, Caldwell B, Zhang C, Lee HS, Lee C, Trinh VQ, Tan MCB, Kim K, Caprioli RM, Choi E. Oncogenic Fatty Acid Metabolism Rewires Energy Supply Chain in Gastric Carcinogenesis. Gastroenterology 2024; 166:772-786.e14. [PMID: 38272100 PMCID: PMC11040571 DOI: 10.1053/j.gastro.2024.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND & AIMS Gastric carcinogenesis develops within a sequential carcinogenic cascade from precancerous metaplasia to dysplasia and adenocarcinoma, and oncogenic gene activation can drive the process. Metabolic reprogramming is considered a key mechanism for cancer cell growth and proliferation. However, how metabolic changes contribute to the progression of metaplasia to dysplasia remains unclear. We have examined metabolic dynamics during gastric carcinogenesis using a novel mouse model that induces Kras activation in zymogen-secreting chief cells. METHODS We generated a Gif-rtTA;TetO-Cre;KrasG12D (GCK) mouse model that continuously induces active Kras expression in chief cells after doxycycline treatment. Histologic examination and imaging mass spectrometry were performed in the GCK mouse stomachs at 2 to 14 weeks after doxycycline treatment. Mouse and human gastric organoids were used for metabolic enzyme inhibitor treatment. The GCK mice were treated with a stearoyl- coenzyme A desaturase (SCD) inhibitor to inhibit the fatty acid desaturation. Tissue microarrays were used to assess the SCD expression in human gastrointestinal cancers. RESULTS The GCK mice developed metaplasia and high-grade dysplasia within 4 months. Metabolic reprogramming from glycolysis to fatty acid metabolism occurred during metaplasia progression to dysplasia. Altered fatty acid desaturation through SCD produces a novel eicosenoic acid, which fuels dysplastic cell hyperproliferation and survival. The SCD inhibitor killed both mouse and human dysplastic organoids and selectively targeted dysplastic cells in vivo. SCD was up-regulated during carcinogenesis in human gastrointestinal cancers. CONCLUSIONS Active Kras expression only in gastric chief cells drives the full spectrum of gastric carcinogenesis. Also, oncogenic metabolic rewiring is an essential adaptation for high-energy demand in dysplastic cells.
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Affiliation(s)
- Yoonkyung Won
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Bogun Jang
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Jeju National University College of Medicine and Jeju National University Hospital, Jeju, Republic of Korea
| | - Su-Hyung Lee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michelle L Reyzer
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee
| | - Kimberly S Presentation
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hyesung Kim
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Jeju National University College of Medicine, Jeju, Republic of Korea
| | - Brianna Caldwell
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Changqing Zhang
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hye Seung Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Cheol Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Vincent Q Trinh
- The Digital Histology and Advanced Pathology Research, The Institute for Research in Immunology and Cancer (IRIC) of the Université de Montréal, Montréal, Québec, Canada
| | - Marcus C B Tan
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kwangho Kim
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee
| | - Eunyoung Choi
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.
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Klein D, Rivera ES, Caprioli RM, Spraggins JM. Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer. Anal Chem 2024; 96:5065-5070. [PMID: 38517028 PMCID: PMC10993197 DOI: 10.1021/acs.analchem.3c05252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
In this work, we demonstrate rapid, high spatial, and high spectral resolution imaging of intact proteins by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on a hybrid quadrupole-reflectron time-of-flight (qTOF) mass spectrometer equipped with trapped ion mobility spectrometry (TIMS). Historically, untargeted MALDI IMS of proteins has been performed on TOF mass spectrometers. While advances in TOF instrumentation have enabled rapid, high spatial resolution IMS of intact proteins, TOF mass spectrometers generate relatively low-resolution mass spectra with limited mass accuracy. Conversely, the implementation of MALDI sources on high-resolving power Fourier transform (FT) mass spectrometers has allowed IMS experiments to be conducted with high spectral resolution with the caveat of increasingly long data acquisition times. As illustrated here, qTOF mass spectrometers enable protein imaging with the combined advantages of TOF and FT mass spectrometers. Protein isotope distributions were resolved for both a protein standard mixture and proteins detected from a whole-body mouse pup tissue section. Rapid (∼10 pixels/s) 10 μm lateral spatial resolution IMS was performed on a rat brain tissue section while maintaining isotopic spectral resolution. Lastly, proof-of-concept MALDI-TIMS data was acquired from a protein mixture to demonstrate the ability to differentiate charge states by ion mobility. These experiments highlight the advantages of qTOF and timsTOF platforms for resolving and interpreting complex protein spectra generated from tissue by IMS.
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Affiliation(s)
- Dustin
R. Klein
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Emilio S. Rivera
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Richard M. Caprioli
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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3
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Good CJ, Butrico CE, Colley ME, Gibson-Corley KN, Cassat JE, Spraggins JM, Caprioli RM. In situ lipidomics of Staphylococcus aureus osteomyelitis using imaging mass spectrometry. bioRxiv 2023:2023.12.01.569690. [PMID: 38077019 PMCID: PMC10705574 DOI: 10.1101/2023.12.01.569690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Osteomyelitis occurs when Staphylococcus aureus invades the bone microenvironment, resulting in a bone marrow abscess with a spatially defined architecture of cells and biomolecules. Imaging mass spectrometry and microscopy are invaluable tools that can be employed to interrogate the lipidome of S. aureus-infected murine femurs to reveal metabolic and signaling consequences of infection. Here, nearly 250 lipids were spatially mapped to healthy and infection-associated morphological features throughout the femur, establishing composition profiles for tissue types. Ether lipids and arachidonoyl lipids were significantly altered between cells and tissue structures in abscesses, suggesting their roles in abscess formation and inflammatory signaling. Sterols, triglycerides, bis(monoacylglycero)phosphates, and gangliosides possessed ring-like distributions throughout the abscess, indicating dysregulated lipid metabolism in a subpopulation of leukocytes that cannot be discerned with traditional microscopy. These data provide chemical insight into the signaling function and metabolism of cells in the fibrotic border of abscesses, likely characteristic of lipid-laden macrophages.
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Affiliation(s)
- Christopher J. Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Casey E. Butrico
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madeline E. Colley
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Katherine N. Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E. Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Medicine, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
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4
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Moore JL, Patterson NH, Norris JL, Caprioli RM. Prospective on Imaging Mass Spectrometry in Clinical Diagnostics. Mol Cell Proteomics 2023; 22:100576. [PMID: 37209813 PMCID: PMC10545939 DOI: 10.1016/j.mcpro.2023.100576] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Imaging mass spectrometry (IMS) is a molecular technology utilized for spatially driven research, providing molecular maps from tissue sections. This article reviews matrix-assisted laser desorption ionization (MALDI) IMS and its progress as a primary tool in the clinical laboratory. MALDI mass spectrometry has been used to classify bacteria and perform other bulk analyses for plate-based assays for many years. However, the clinical application of spatial data within a tissue biopsy for diagnoses and prognoses is still an emerging opportunity in molecular diagnostics. This work considers spatially driven mass spectrometry approaches for clinical diagnostics and addresses aspects of new imaging-based assays that include analyte selection, quality control/assurance metrics, data reproducibility, data classification, and data scoring. It is necessary to implement these tasks for the rigorous translation of IMS to the clinical laboratory; however, this requires detailed standardized protocols for introducing IMS into the clinical laboratory to deliver reliable and reproducible results that inform and guide patient care.
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Affiliation(s)
| | - Nathan Heath Patterson
- Frontier Diagnostics, Nashville, Tennessee, USA; Vanderbilt University Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeremy L Norris
- Frontier Diagnostics, Nashville, Tennessee, USA; Vanderbilt University Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M Caprioli
- Frontier Diagnostics, Nashville, Tennessee, USA; Vanderbilt University Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA; Departments of Biochemistry, Pharmacology, Chemistry, and Medicine, Vanderbilt University, Nashville, Tennessee, USA.
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5
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Sharman K, Patterson NH, Migas LG, Neumann EK, Allen J, Gibson-Corley KN, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. MALDI IMS-Derived Molecular Contour Maps: Augmenting Histology Whole-Slide Images. J Am Soc Mass Spectrom 2023; 34:905-912. [PMID: 37061946 PMCID: PMC10787559 DOI: 10.1021/jasms.2c00370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Imaging mass spectrometry (IMS) provides untargeted, highly multiplexed maps of molecular distributions in tissue. Ion images are routinely presented as heatmaps and can be overlaid onto complementary microscopy images that provide greater context. However, heatmaps use transparency blending to visualize both images, obscuring subtle quantitative differences and distribution gradients. Here, we developed a contour mapping approach that combines information from IMS ion intensity distributions with that of stained microscopy. As a case study, we applied this approach to imaging data from Staphylococcus aureus-infected murine kidney. In a univariate, or single molecular species, use-case of the contour map representation of IMS data, certain lipids colocalizing with regions of infection were selected using Pearson's correlation coefficient. Contour maps of these lipids overlaid with stained microscopy showed enhanced visualization of lipid distributions and spatial gradients in and around the bacterial abscess as compared to traditional heatmaps. The full IMS data set comprising hundreds of individual ion images was then grouped into a smaller subset of representative patterns using non-negative matrix factorization (NMF). Contour maps of these multivariate NMF images revealed distinct molecular profiles of the major abscesses and surrounding immune response. This contour mapping workflow also enabled a molecular visualization of the transition zone at the host-pathogen interface, providing potential clues about the spatial molecular dynamics beyond what histological staining alone provides. In summary, we developed a new IMS-based contour mapping approach to augment classical stained microscopy images, providing an enhanced and more interpretable visualization of IMS-microscopy multimodal molecular imaging data sets.
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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
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jamie Allen
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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6
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Djambazova KV, Dufresne M, Migas LG, Kruse ARS, Van de Plas R, Caprioli RM, Spraggins JM. MALDI TIMS IMS of Disialoganglioside Isomers─GD1a and GD1b in Murine Brain Tissue. Anal Chem 2023; 95:1176-1183. [PMID: 36574465 DOI: 10.1021/acs.analchem.2c03939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gangliosides are acidic glycosphingolipids, containing ceramide moieties and oligosaccharide chains with one or more sialic acid residue(s) and are highly diverse isomeric structures with distinct biological roles. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables the untargeted spatial analysis of gangliosides, among other biomolecules, directly from tissue sections. Integrating trapped ion mobility spectrometry with MALDI IMS allows for the analysis of isomeric lipid structures in situ. Here, we demonstrate the gas-phase separation and identification of disialoganglioside isomers GD1a and GD1b that differ in the position of a sialic acid residue, in multiple samples, including a standard mixture of both isomers, a biological extract, and directly from thin tissue sections. The unique spatial distributions of GD1a/b (d36:1) and GD1a/b (d38:1) isomers were determined in rat hippocampus and spinal cord tissue sections, demonstrating the ability to structurally characterize and spatially map gangliosides based on both the carbohydrate chain and ceramide moieties.
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Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Angela R S Kruse
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States.,Department of Medicine, Vanderbilt University, 1161 21st Avenue S, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue S #3218, Nashville, Tennessee 37232, United States
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7
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Anderson DMG, Kotnala A, Messinger JD, Patterson NH, Spraggins JM, Curcio CA, Caprioli RM, Schey KL. High-Resolution Imaging Mass Spectrometry of Human Donor Eye: Photoreceptors Cells and Basal Laminar Deposit of Age-Related Macular Degeneration. Adv Exp Med Biol 2023; 1415:3-7. [PMID: 37440006 DOI: 10.1007/978-3-031-27681-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Pathologies of the retina are clinically visualized in vivo with OCT and ex vivo with immunohistochemistry. Although both techniques provide valuable information on prognosis and disease state, a comprehensive method for fully elucidating molecular constituents present in locations of interest is desirable. The purpose of this work was to use multimodal imaging technologies to localize the vast number of molecular species observed with matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) in aged and diseased retinal tissues. Herein, MALDI IMS was utilized to observe molecular species that reside in photoreceptor cells and also a basal laminar deposit from two human donor eyes. The molecular species observed to accumulate in these discrete regions can be further identified and studied to attempt to gain a greater understanding of biological processes occurring in debilitating eye diseases such as age-related macular degeneration (AMD).
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Affiliation(s)
- David M G Anderson
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ankita Kotnala
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey D Messinger
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathan Heath Patterson
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christine A Curcio
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
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8
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Perry WJ, Grunenwald CM, Van de Plas R, Witten JC, Martin DR, Apte SS, Cassat JE, Pettersson GB, Caprioli RM, Skaar EP, Spraggins JM. Visualizing Staphylococcus aureus pathogenic membrane modification within the host infection environment by multimodal imaging mass spectrometry. Cell Chem Biol 2022; 29:1209-1217.e4. [PMID: 35654040 PMCID: PMC9308753 DOI: 10.1016/j.chembiol.2022.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/10/2021] [Accepted: 05/11/2022] [Indexed: 11/30/2022]
Abstract
Bacterial pathogens have evolved virulence factors to colonize, replicate, and disseminate within the vertebrate host. Although there is an expanding body of literature describing how bacterial pathogens regulate their virulence repertoire in response to environmental signals, it is challenging to directly visualize virulence response within the host tissue microenvironment. Multimodal imaging approaches enable visualization of host-pathogen molecular interactions. Here we demonstrate multimodal integration of high spatial resolution imaging mass spectrometry and microscopy to visualize Staphylococcus aureus envelope modifications within infected murine and human tissues. Data-driven image fusion of fluorescent bacterial reporters and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance imaging mass spectrometry uncovered S. aureus lysyl-phosphatidylglycerol lipids, localizing to select bacterial communities within infected tissue. Absence of lysyl-phosphatidylglycerols is associated with decreased pathogenicity during vertebrate colonization as these lipids provide protection against the innate immune system. The presence of distinct staphylococcal lysyl-phosphatidylglycerol distributions within murine and human infections suggests a heterogeneous, spatially oriented microbial response to host defenses.
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Affiliation(s)
- William J Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA
| | - Caroline M Grunenwald
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Delft Center for Systems and Control, Delft University of Technology - TU Delft, Delft, the Netherlands; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
| | - James C Witten
- Department of Thoracic and Cardiovascular Surgery, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Daniel R Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - James E Cassat
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gösta B Pettersson
- Department of Thoracic and Cardiovascular Surgery, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37212, USA; Department of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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9
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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 2022; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.
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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 and Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J. Ryan
- Pfizer Inc., Chesterfield, Missouri 63017, United States
| | - Danielle B. Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Department of Chemistry, and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States,Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States,Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M. Caprioli
- Mass Spectrometry Research Center and Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States,Department of Biochemistry and Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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10
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Weiss A, Murdoch CC, Edmonds KA, Jordan MR, Monteith AJ, Perera YR, Rodríguez Nassif AM, Petoletti AM, Beavers WN, Munneke MJ, Drury SL, Krystofiak ES, Thalluri K, Wu H, Kruse ARS, DiMarchi RD, Caprioli RM, Spraggins JM, Chazin WJ, Giedroc DP, Skaar EP. Zn-regulated GTPase metalloprotein activator 1 modulates vertebrate zinc homeostasis. Cell 2022; 185:2148-2163.e27. [PMID: 35584702 DOI: 10.1016/j.cell.2022.04.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/07/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Zinc (Zn) is an essential micronutrient and cofactor for up to 10% of proteins in living organisms. During Zn limitation, specialized enzymes called metallochaperones are predicted to allocate Zn to specific metalloproteins. This function has been putatively assigned to G3E GTPase COG0523 proteins, yet no Zn metallochaperone has been experimentally identified in any organism. Here, we functionally characterize a family of COG0523 proteins that is conserved across vertebrates. We identify Zn metalloprotease methionine aminopeptidase 1 (METAP1) as a COG0523 client, leading to the redesignation of this group of COG0523 proteins as the Zn-regulated GTPase metalloprotein activator (ZNG1) family. Using biochemical, structural, genetic, and pharmacological approaches across evolutionarily divergent models, including zebrafish and mice, we demonstrate a critical role for ZNG1 proteins in regulating cellular Zn homeostasis. Collectively, these data reveal the existence of a family of Zn metallochaperones and assign ZNG1 an important role for intracellular Zn trafficking.
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Affiliation(s)
- Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Caitlin C Murdoch
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Andrew J Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yasiru R Perera
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Aslin M Rodríguez Nassif
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Amber M Petoletti
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew J Munneke
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sydney L Drury
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Evan S Krystofiak
- Cell Imaging Shared Resource, Vanderbilt University, Nashville, TN 37232, USA
| | - Kishore Thalluri
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Angela R S Kruse
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Richard M Caprioli
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | - Jeffrey M Spraggins
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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11
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Guiberson ER, Good CJ, Wexler AG, Skaar EP, Spraggins JM, Caprioli RM. Multimodal Imaging Mass Spectrometry of Murine Gastrointestinal Tract with Retained Luminal Content. J Am Soc Mass Spectrom 2022; 33:1073-1076. [PMID: 35545232 PMCID: PMC9264265 DOI: 10.1021/jasms.1c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The gastrointestinal tract, including luminal content, harbors a complex mixture of microorganisms, host dietary content, and immune factors. Existing imaging approaches remove luminal content and only visualize small regions of the GI tract. Here, we demonstrate a workflow for multimodal imaging using matrix-assisted laser desorption/ionization imaging mass spectrometry, autofluorescence, and bright field microscopy for mapping intestinal tissue and luminal content. Results comparing tissue and luminal content in control murine tissue show both unique molecular and elemental distributions and abundances using multimodal protein, lipid, and elemental imaging. For instance, lipid PC(42:1) is 2× higher intensity in luminal content than tissue, while PC(32:0) is 80× higher intensity in tissue. Additionally, some ions such as the protein at m/z 3443 and the element manganese are only detected in luminal content, while the protein at m/z 8564 was only detected in tissue and phosphorus had 2× higher abundance in tissue. These data highlight the robust molecular information that can be gained from the gastrointestinal tract with the inclusion of luminal content.
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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
| | - Christopher J Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Aaron G Wexler
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37203, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37203, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37203g, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37203, United States
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12
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Gunawardana M, Remedios-Chan M, Sanchez D, Webster S, Castonguay AE, Webster P, Buser C, Moss JA, Trinh M, Beliveau M, Hendrix CW, Marzinke MA, Tuck M, Caprioli RM, Reyzer ML, Kuo J, Gallay PA, Baum MM. Fundamental aspects of long-acting tenofovir alafenamide delivery from subdermal implants for HIV prophylaxis. Sci Rep 2022; 12:8224. [PMID: 35581262 PMCID: PMC9114338 DOI: 10.1038/s41598-022-11020-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/15/2022] [Indexed: 01/04/2023] Open
Abstract
Global efforts aimed at preventing human immunodeficiency virus type one (HIV-1) infection in vulnerable populations appear to be stalling, limiting our ability to control the epidemic. Long-acting, controlled drug administration from subdermal implants holds significant potential by reducing the compliance burden associated with frequent dosing. We, and others, are exploring the development of complementary subdermal implant technologies delivering the potent prodrug, tenofovir alafenamide (TAF). The current report addresses knowledge gaps in the preclinical pharmacology of long-acting, subdermal TAF delivery using several mouse models. Systemic drug disposition during TAF implant dosing was explained by a multi-compartment pharmacokinetic (PK) model. Imaging mass spectrometry was employed to characterize the spatial distribution of TAF and its principal five metabolites in local tissues surrounding the implant. Humanized mouse studies determined the effective TAF dose for preventing vaginal and rectal HIV-1 acquisition. Our results represent an important step in the development of a safe and effective TAF implant for HIV-1 prevention.
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Affiliation(s)
- Manjula Gunawardana
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - Mariana Remedios-Chan
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - Debbie Sanchez
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - Simon Webster
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - Amalia E Castonguay
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - Paul Webster
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - Christopher Buser
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - John A Moss
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA
| | - MyMy Trinh
- Certara Integrated Drug Development, 2000 Peel Street, Suite 570, Montreal, QC, Canada
| | - Martin Beliveau
- Certara Integrated Drug Development, 2000 Peel Street, Suite 570, Montreal, QC, Canada
| | - Craig W Hendrix
- Department of Medicine, Johns Hopkins University, 600 N. Wolfe Street, Baltimore, MD, USA
| | - Mark A Marzinke
- Department of Medicine, Johns Hopkins University, 600 N. Wolfe Street, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University, 600 N. Wolfe Street/Carnegie 417, Baltimore, MD, USA
| | - Michael Tuck
- Department of Biochemistry, Vanderbilt University, 9160 MRB III, 465 21st Ave. South, Nashville, TN, USA
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 9160 MRB III, 465 21st Ave. South, Nashville, TN, USA
| | - Michelle L Reyzer
- Department of Biochemistry, Vanderbilt University, 9160 MRB III, 465 21st Ave. South, Nashville, TN, USA
| | - Joseph Kuo
- Department of Immunology & Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Philippe A Gallay
- Department of Immunology & Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Marc M Baum
- Department of Chemistry, Oak Crest Institute of Science, 128-132 W. Chestnut Ave., Monrovia, CA, USA.
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13
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Richardson LT, Neumann EK, Caprioli RM, Spraggins JM, Solouki T. Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments. Anal Chem 2022; 94:5504-5513. [PMID: 35344335 PMCID: PMC10124143 DOI: 10.1021/acs.analchem.1c03715] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Because of their diverse functionalities in cells, lipids are of primary importance when characterizing molecular profiles of physiological and disease states. Imaging mass spectrometry (IMS) provides the spatial distributions of lipid populations in tissues. Referenced Kendrick mass defect (RKMD) analysis is an effective mass spectrometry (MS) data analysis tool for classification and annotation of lipids. Herein, we extend the capabilities of RKMD analysis and demonstrate an integrated method for lipid annotation and chemical structure-based filtering for IMS datasets. Annotation of lipid features with lipid molecular class, radyl carbon chain length, and degree of unsaturation allows image reconstruction and visualization based on each structural characteristic. We show a proof-of-concept application of the method to a computationally generated IMS dataset and validate that the RKMD method is highly specific for lipid components in the presence of confounding background ions. Moreover, we demonstrate an application of the RKMD-based annotation and filtering to matrix-assisted laser desorption/ionization (MALDI) IMS lipidomic data from human kidney tissue analysis.
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Affiliation(s)
- Luke T Richardson
- Department of Chemistry and Biochemistry, Baylor University, 101 Bagby Avenue, Waco, Texas 76706, United States
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Department of Cell and Development Biology, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, 101 Bagby Avenue, Waco, Texas 76706, United States
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14
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Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022; 19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
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Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Rebecca T Beuschel
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, MA, USA
| | | | - Julia Hatler
- Antibody Development Department, Bio-Techne, Minneapolis, MN, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA
| | - Josh Croteau
- Department of Applications Science, BioLegend, San Diego, CA, USA
| | | | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - R Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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15
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Abstract
Bone and bone marrow are vital to mammalian structure, movement, and immunity. These tissues are also commonly subjected to molecular alterations giving rise to debilitating diseases like rheumatoid arthritis and osteomyelitis. Technologies such as matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) facilitate the discovery of spatially resolved chemical information in biological tissue samples to help elucidate the complex molecular processes underlying pathology. Traditionally, preparation of osseous tissue for MALDI IMS has been difficult due to its mineralized composition and heterogeneous morphology, and compensation for these challenges with decalcification and fixation protocols can remove or delocalize molecular species. Here, sample preparation methods were advanced to enable multimodal MALDI IMS of undecalcified, fresh-frozen murine femurs, allowing the distribution of endogenous lipids to be linked to tissue structures and cell types. Adhesive-bound bone sections were mounted onto conductive glass slides with microscopy-compatible glue and freeze-dried to minimize artificial bone marrow damage. High spatial resolution (10 μm) MALDI IMS was employed to characterize lipid distributions, and use of complementary microscopy modalities aided tissue and cell assignments. For example, various phosphatidylcholines localize to the bone marrow, adipose tissue, marrow adipose tissue, and muscle. Further, sphingomyelin(42:1) was abundant in megakaryocytes, whereas sphingomyelin(42:2) was diminished in this cell type. These data reflect the vast molecular and cellular heterogeneity indicative of the bone marrow and the soft tissue surrounding the femur. Multimodal MALDI IMS has the potential to advance bone-related biomedical research by offering deep molecular coverage with spatial relevance in a preserved native bone microenvironment.
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Affiliation(s)
- Christopher J Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Casey E Butrico
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - James E Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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16
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Neumann EK, Patterson NH, Rivera ES, Allen JL, Brewer M, deCaestecker MP, Caprioli RM, Fogo AB, Spraggins JM. Highly multiplexed immunofluorescence of the human kidney using co-detection by indexing. Kidney Int 2022; 101:137-143. [PMID: 34619231 PMCID: PMC8741652 DOI: 10.1016/j.kint.2021.08.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 01/03/2023]
Abstract
The human kidney is composed of many cell types that vary in their abundance and distribution from normal to diseased organ. As these cell types perform unique and essential functions, it is important to confidently label each within a single tissue to accurately assess tissue architecture and microenvironments. Towards this goal, we demonstrate the use of co-detection by indexing (CODEX) multiplexed immunofluorescence for visualizing 23 antigens within the human kidney. Using CODEX, many of the major cell types and substructures, such as collecting ducts, glomeruli, and thick ascending limb, were visualized within a single tissue section. Of these antibodies, 19 were conjugated in-house, demonstrating the flexibility and utility of this approach for studying the human kidney using custom and commercially available antibodies. We performed a pilot study that compared both fresh frozen and formalin-fixed paraffin-embedded healthy non-neoplastic and diabetic nephropathy kidney tissues. The largest cellular differences between the two groups was observed in cells labeled with aquaporin 1, cytokeratin 7, and α-smooth muscle actin. Thus, our data show the power of CODEX multiplexed immunofluorescence for surveying the cellular diversity of the human kidney and the potential for applications within pathology, histology, and building anatomical atlases.
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Affiliation(s)
- Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Nathan Heath Patterson
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Jamie L. Allen
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Maya Brewer
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Mark P. deCaestecker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232.,Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37232
| | - Agnes B. Fogo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA 37232.,Departments of Medicine and Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA 37232
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232.,Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37232,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA 37232
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17
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Fincher JA, Djambazova KV, Klein DR, Dufresne M, Migas LG, Van de Plas R, Caprioli RM, Spraggins JM. Molecular Mapping of Neutral Lipids Using Silicon Nanopost Arrays and TIMS Imaging Mass Spectrometry. J Am Soc Mass Spectrom 2021; 32:2519-2527. [PMID: 34435768 DOI: 10.1021/jasms.1c00159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate the utility of combining silicon nanopost arrays (NAPA) and trapped ion mobility imaging mass spectrometry (TIMS IMS) for high spatial resolution and specificity mapping of neutral lipid classes in tissue. Ionization of neutral lipid species such as triglycerides (TGs), cholestryl esters (CEs), and hexosylceramides (HexCers) from biological tissues has remained a challenge for imaging applications. NAPA, a matrix-free laser desorption ionization substrate, provides enhanced ionization efficiency for the above-mentioned neutral lipid species, providing complementary lipid coverage to matrix-assisted laser desorption ionization (MALDI). The combination of NAPA and TIMS IMS enables imaging of neutral lipid species at 20 μm spatial resolution while also increasing molecular coverage greater than 2-fold using gas-phase ion mobility separations. This is a significant improvement with respect to sensitivity, specificity, and spatial resolution compared to previously reported imaging studies using NAPA alone. Improved specificity for neutral lipid analysis using TIMS IMS was shown using rat kidney tissue to separate TGs, CEs, HexCers, and phospholipids into distinct ion mobility trendlines. Further, this technology allowed for the separation of isomeric species, including mobility resolved isomers of Cer(d42:2) (m/z 686.585) with distinct spatial localizations measured in rat kidney tissue section.
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Affiliation(s)
- Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 442 Robinson Research Building, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Cell & Developmental Biology, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
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18
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McMillen JC, Gutierrez DB, Judd AM, Spraggins JM, Caprioli RM. Enhancement of Tryptic Peptide Signals from Tissue Sections Using MALDI IMS Postionization (MALDI-2). J Am Soc Mass Spectrom 2021; 32:2583-2591. [PMID: 34515472 DOI: 10.1021/jasms.1c00213] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, unlabeled mapping of analytes from tissue sections. However, further work is needed to improve the sensitivity and depth of coverage for protein and peptide IMS. We demonstrate signal enhancement of proteolytic peptides from thin tissue sections of human kidney by conventional MALDI (MALDI-1) augmented using a second ionizing laser (termed MALDI-2). Proteins were digested in situ using trypsin prior to IMS analysis. For tentative identification of peptides and proteins, a tissue homogenate from the same organ used for IMS was analyzed by LC-MS/MS, and data are available via ProteomeXchange with identifier PXD023877. These identified proteins were then digested in silico to generate a database of theoretical peptides to then match to MALDI IMS data sets. Peptides were tentatively identified by matching the MALDI peak list to the database peptide list based on mass accuracy (5 ppm mass error). This resulted in 1337 ± 96 (n = 3) peptides and 2076 ± 362 (n = 3) unique peptides matched to IMS peaks from MALDI-1 and MALDI-2, respectively. Protein identifications requiring two or more peptides per protein resulted in 276 ± 20 proteins with MALDI-1 and 401 ± 60 with MALDI-2. These results demonstrate that MALDI-2 provides enhanced sensitivity for the spatial mapping of tryptic peptides and significantly increases the number of proteins identified in IMS experiments.
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Affiliation(s)
- Josiah C McMillen
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Audra M Judd
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue S #3218, Nashville, Tennessee 37205, United States
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 1161 21st Avenue S, Nashville, Tennessee 37232, United States
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19
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Neumann EK, Patterson NH, Allen JL, Migas LG, Yang H, Brewer M, Anderson DM, Harvey J, Gutierrez DB, Harris RC, deCaestecker MP, Fogo AB, Van de Plas R, Caprioli RM, Spraggins JM. Protocol for multimodal analysis of human kidney tissue by imaging mass spectrometry and CODEX multiplexed immunofluorescence. STAR Protoc 2021; 2:100747. [PMID: 34430920 PMCID: PMC8371244 DOI: 10.1016/j.xpro.2021.100747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Here, we describe the preservation and preparation of human kidney tissue for interrogation by histopathology, imaging mass spectrometry, and multiplexed immunofluorescence. Custom image registration and integration techniques are used to create cellular and molecular atlases of this organ system. Through careful optimization, we ensure high-quality and reproducible datasets suitable for cross-patient comparisons that are essential to understanding human health and disease. Moreover, each of these steps can be adapted to other organ systems or diseases, enabling additional atlas efforts.
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Affiliation(s)
- Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Nathan Heath Patterson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jamie L. Allen
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Lukasz G. Migas
- Delft Center for Systems and Control (DCSC), Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Haichun Yang
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maya Brewer
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David M. Anderson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jennifer Harvey
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Danielle B. Gutierrez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Raymond C. Harris
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark P. deCaestecker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Agnes B. Fogo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Departments of Medicine and Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Raf Van de Plas
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Delft Center for Systems and Control (DCSC), Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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20
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Dufresne M, Fincher JA, Patterson NH, Schey KL, Norris JL, Caprioli RM, Spraggins JM. α-Cyano-4-hydroxycinnamic Acid and Tri-Potassium Citrate Salt Pre-Coated Silicon Nanopost Array Provides Enhanced Lipid Detection for High Spatial Resolution MALDI Imaging Mass Spectrometry. Anal Chem 2021; 93:12243-12249. [PMID: 34449196 DOI: 10.1021/acs.analchem.1c01560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have developed a pre-coated substrate for matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) that enables high spatial resolution mapping of both phospholipids and neutral lipid classes in positive ion mode as metal cation adducts. The MALDI substrates are constructed by depositing a layer of α-cyano-4-hydroxycinnamic acid (CHCA) and potassium salts onto silicon nanopost arrays (NAPA) prior to tissue mounting. The matrix/salt pre-coated NAPA substrate significantly enhances all detected lipid signals allowing lipids to be detected at lower laser energies than bare NAPA. The improved sensitivity at lower laser energy enabled ion images to be generated at 10 μm spatial resolution from rat retinal tissue. Optimization of matrix pre-coated NAPA consisted of testing lithium, sodium, and potassium salts along with various matrices to investigate the increased sensitivity toward lipids for MALDI IMS experiments. It was determined that pre-coating NAPA with CHCA and potassium salts before thaw-mounting of tissue resulted in a signal intensity increase of at least 5.8 ± 0.1-fold for phospholipids and 2.0 ± 0.1-fold for neutral lipids compared to bare NAPA. Pre-coating NAPA with matrix and salt also reduced the necessary laser power to achieve desorption/ionization by ∼35%. This reduced the effective diameter of the ablation area from 13 ± 2 μm down to 8 ± 1 μm, enabling high spatial resolution MALDI IMS. Using pre-coated NAPA with CHCA and potassium salts offers a MALDI IMS substrate with broad molecular coverage of lipids in a single polarity that eliminates the need for extensive sample preparation after sectioning.
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Affiliation(s)
- Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Kevin L Schey
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37205, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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21
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Tideman LEM, Migas LG, Djambazova KV, Patterson NH, Caprioli RM, Spraggins JM, Van de Plas R. Automated biomarker candidate discovery in imaging mass spectrometry data through spatially localized Shapley additive explanations. Anal Chim Acta 2021; 1177:338522. [PMID: 34482894 PMCID: PMC10124144 DOI: 10.1016/j.aca.2021.338522] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/04/2021] [Accepted: 04/11/2021] [Indexed: 01/09/2023]
Abstract
The search for molecular species that are differentially expressed between biological states is an important step towards discovering promising biomarker candidates. In imaging mass spectrometry (IMS), performing this search manually is often impractical due to the large size and high-dimensionality of IMS datasets. Instead, we propose an interpretable machine learning workflow that automatically identifies biomarker candidates by their mass-to-charge ratios, and that quantitatively estimates their relevance to recognizing a given biological class using Shapley additive explanations (SHAP). The task of biomarker candidate discovery is translated into a feature ranking problem: given a classification model that assigns pixels to different biological classes on the basis of their mass spectra, the molecular species that the model uses as features are ranked in descending order of relative predictive importance such that the top-ranking features have a higher likelihood of being useful biomarkers. Besides providing the user with an experiment-wide measure of a molecular species' biomarker potential, our workflow delivers spatially localized explanations of the classification model's decision-making process in the form of a novel representation called SHAP maps. SHAP maps deliver insight into the spatial specificity of biomarker candidates by highlighting in which regions of the tissue sample each feature provides discriminative information and in which regions it does not. SHAP maps also enable one to determine whether the relationship between a biomarker candidate and a biological state of interest is correlative or anticorrelative. Our automated approach to estimating a molecular species' potential for characterizing a user-provided biological class, combined with the untargeted and multiplexed nature of IMS, allows for the rapid screening of thousands of molecular species and the obtention of a broader biomarker candidate shortlist than would be possible through targeted manual assessment. Our biomarker candidate discovery workflow is demonstrated on mouse-pup and rat kidney case studies.
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Affiliation(s)
- Leonoor E M Tideman
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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22
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Wexler AG, Guiberson ER, Beavers WN, Shupe JA, Washington MK, Lacy DB, Caprioli RM, Spraggins JM, Skaar EP. Clostridioides difficile infection induces a rapid influx of bile acids into the gut during colonization of the host. Cell Rep 2021; 36:109683. [PMID: 34496241 PMCID: PMC8445666 DOI: 10.1016/j.celrep.2021.109683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/05/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Clostridioides difficile is the leading cause of nosocomial intestinal infections in the United States. Ingested C. difficile spores encounter host bile acids and other cues that are necessary for germinating into toxin-producing vegetative cells. While gut microbiota disruption (often by antibiotics) is a prerequisite for C. difficile infection (CDI), the mechanisms C. difficile employs for colonization remain unclear. Here, we pioneered the application of imaging mass spectrometry to study how enteric infection changes gut metabolites. We find that CDI induces an influx of bile acids into the gut within 24 h of the host ingesting spores. In response, the host reduces bile acid biosynthesis gene expression. These bile acids drive C. difficile outgrowth, as mice receiving the bile acid sequestrant cholestyramine display delayed colonization and reduced germination. Our findings indicate that C. difficile may facilitate germination upon infection and suggest that altering flux through bile acid pathways can modulate C. difficile outgrowth in CDI-prone patients.
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Affiliation(s)
- Aaron G Wexler
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Shupe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - D Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; The Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Vanderbilt University, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
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23
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Ullman JC, Arguello A, Getz JA, Bhalla A, Mahon CS, Wang J, Giese T, Bedard C, Kim DJ, Blumenfeld JR, Liang N, Ravi R, Nugent AA, Davis SS, Ha C, Duque J, Tran HL, Wells RC, Lianoglou S, Daryani VM, Kwan W, Solanoy H, Nguyen H, Earr T, Dugas JC, Tuck MD, Harvey JL, Reyzer ML, Caprioli RM, Hall S, Poda S, Sanchez PE, Dennis MS, Gunasekaran K, Srivastava A, Sandmann T, Henne KR, Thorne RG, Di Paolo G, Astarita G, Diaz D, Silverman AP, Watts RJ, Sweeney ZK, Kariolis MS, Henry AG. Brain delivery and activity of a lysosomal enzyme using a blood-brain barrier transport vehicle in mice. Sci Transl Med 2021; 12:12/545/eaay1163. [PMID: 32461331 DOI: 10.1126/scitranslmed.aay1163] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 02/10/2020] [Accepted: 04/02/2020] [Indexed: 12/20/2022]
Abstract
Most lysosomal storage diseases (LSDs) involve progressive central nervous system (CNS) impairment, resulting from deficiency of a lysosomal enzyme. Treatment of neuronopathic LSDs remains a considerable challenge, as approved intravenously administered enzyme therapies are ineffective in modifying CNS disease because they do not effectively cross the blood-brain barrier (BBB). We describe a therapeutic platform for increasing the brain exposure of enzyme replacement therapies. The enzyme transport vehicle (ETV) is a lysosomal enzyme fused to an Fc domain that has been engineered to bind to the transferrin receptor, which facilitates receptor-mediated transcytosis across the BBB. We demonstrate that ETV fusions containing iduronate 2-sulfatase (ETV:IDS), the lysosomal enzyme deficient in mucopolysaccharidosis type II, exhibited high intrinsic activity and degraded accumulated substrates in both IDS-deficient cell and in vivo models. ETV substantially improved brain delivery of IDS in a preclinical model of disease, enabling enhanced cellular distribution to neurons, astrocytes, and microglia throughout the brain. Improved brain exposure for ETV:IDS translated to a reduction in accumulated substrates in these CNS cell types and peripheral tissues and resulted in a complete correction of downstream disease-relevant pathologies in the brain, including secondary accumulation of lysosomal lipids, perturbed gene expression, neuroinflammation, and neuroaxonal damage. These data highlight the therapeutic potential of the ETV platform for LSDs and provide preclinical proof of concept for TV-enabled therapeutics to treat CNS diseases more broadly.
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Affiliation(s)
- Julie C Ullman
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Annie Arguello
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Jennifer A Getz
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Akhil Bhalla
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Cathal S Mahon
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Junhua Wang
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Tina Giese
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Catherine Bedard
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Do Jin Kim
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Jessica R Blumenfeld
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Nicholas Liang
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Ritesh Ravi
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Alicia A Nugent
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Sonnet S Davis
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Connie Ha
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Joseph Duque
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Hai L Tran
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Robert C Wells
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Steve Lianoglou
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Vinay M Daryani
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Wanda Kwan
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Hilda Solanoy
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Hoang Nguyen
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Timothy Earr
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Jason C Dugas
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Michael D Tuck
- Mass Spectrometry Research Center, Vanderbilt University, 9160 MRB III, 465 21 Avenue South, Nashville, TN 37240, USA
| | - Jennifer L Harvey
- Mass Spectrometry Research Center, Vanderbilt University, 9160 MRB III, 465 21 Avenue South, Nashville, TN 37240, USA
| | - Michelle L Reyzer
- Mass Spectrometry Research Center, Vanderbilt University, 9160 MRB III, 465 21 Avenue South, Nashville, TN 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, 9160 MRB III, 465 21 Avenue South, Nashville, TN 37240, USA
| | - Sejal Hall
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Suresh Poda
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Pascal E Sanchez
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Mark S Dennis
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Kannan Gunasekaran
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Ankita Srivastava
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Thomas Sandmann
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Kirk R Henne
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Robert G Thorne
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Gilbert Di Paolo
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Giuseppe Astarita
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Dolores Diaz
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Adam P Silverman
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Ryan J Watts
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Zachary K Sweeney
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Mihalis S Kariolis
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA.
| | - Anastasia G Henry
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA 94080, USA.
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24
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Al-Rohil RN, Moore JL, Patterson NH, Nicholson S, Verbeeck N, Claesen M, Muhammad JZ, Caprioli RM, Norris JL, Kantrow S, Compton M, Robbins J, Alomari AK. Diagnosis of melanoma by imaging mass spectrometry: Development and validation of a melanoma prediction model. J Cutan Pathol 2021; 48:1455-1462. [PMID: 34151458 DOI: 10.1111/cup.14083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/24/2021] [Accepted: 05/30/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND The definitive diagnosis of melanocytic neoplasia using solely histopathologic evaluation can be challenging. Novel techniques that objectively confirm diagnoses are needed. This study details the development and validation of a melanoma prediction model from spatially resolved multivariate protein expression profiles generated by imaging mass spectrometry (IMS). METHODS Three board-certified dermatopathologists blindly evaluated 333 samples. Samples with triply concordant diagnoses were included in this study, divided into a training set (n = 241) and a test set (n = 92). Both the training and test sets included various representative subclasses of unambiguous nevi and melanomas. A prediction model was developed from the training set using a linear support vector machine classification model. RESULTS We validated the prediction model on the independent test set of 92 specimens (75 classified correctly, 2 misclassified, and 15 indeterminate). IMS detects melanoma with a sensitivity of 97.6% and a specificity of 96.4% when evaluating each unique spot. IMS predicts melanoma at the sample level with a sensitivity of 97.3% and a specificity of 97.5%. Indeterminate results were excluded from sensitivity and specificity calculations. CONCLUSION This study provides evidence that IMS-based proteomics results are highly concordant to diagnostic results obtained by careful histopathologic evaluation from a panel of expert dermatopathologists.
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Affiliation(s)
- Rami N Al-Rohil
- Departments of Pathology and Dermatology, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Nathan Heath Patterson
- Frontier Diagnostics, LLC, Nashville, Tennessee, USA.,Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | | | | | | | | | - Richard M Caprioli
- Frontier Diagnostics, LLC, Nashville, Tennessee, USA.,Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeremy L Norris
- Frontier Diagnostics, LLC, Nashville, Tennessee, USA.,Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Sara Kantrow
- Pathology Associates of Saint Thomas, Nashville, Tennessee, USA
| | - Margaret Compton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jason Robbins
- Pathology Associates of Saint Thomas, Nashville, Tennessee, USA
| | - Ahmed K Alomari
- Departments of Pathology and Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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25
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Hollingshead BD, Tomlinson L, Finley J, Doshna C, Ritenour C, Barricklow J, Oppenheimer SR, O'Neil SP, Moore JL, Patterson NH, Nicholson SP, Norris JL, Caprioli RM, Beaumont K, King-Ahmad AJ, Vispute S, Cook JC, Radi Z, Schuler M. An orthogonal methods assessment of topical drug concentrations in skin and the impact for risk assessment in the viable epidermis. Regul Toxicol Pharmacol 2021; 123:104934. [PMID: 33872740 DOI: 10.1016/j.yrtph.2021.104934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022]
Abstract
Systemic toxicity assessments for oral or parenteral drugs often utilize the concentration of drug in plasma to enable safety margin calculations for human risk assessment. For topical drugs, there is no standard method for measuring drug concentrations in the stratum basale of the viable epidermis. This is particularly important since the superficial part of the epidermis, the stratum corneum (SC), is nonviable and where most of a topically applied drug remains, never penetrating deeper into the skin. We investigated the relative concentrations of a prototype kinase inhibitor using punch biopsy, laser capture microdissection, and imaging mass spectrometry methods in the SC, stratum basale, and dermis of minipig skin following topical application as a cream formulation. The results highlight the value of laser capture microdissection and mass spectrometry imaging in quantifying the large difference in drug concentration across the skin and even within the epidermis, and supports use of these methods for threshold-based toxicity risk assessments in specific anatomic locations of the skin, like of the stratum basale.
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Affiliation(s)
- Brett D Hollingshead
- Pfizer Drug Safety Research and Development, 1 Portland Street, Cambridge, MA, 02139, USA.
| | - Lindsay Tomlinson
- Pfizer Drug Safety Research and Development, 1 Portland Street, Cambridge, MA, 02139, USA
| | - Jim Finley
- Pfizer Drug Safety Research and Development, Eastern Point Road, Groton, CT, 06340, USA
| | - Colleen Doshna
- Pfizer Drug Safety Research and Development, Eastern Point Road, Groton, CT, 06340, USA
| | - Casey Ritenour
- Pfizer Drug Safety Research and Development, Eastern Point Road, Groton, CT, 06340, USA
| | - Jason Barricklow
- Pfizer Pharmacokinetics, Dynamics and Metabolism, Eastern Point Road, Groton, CT, 06340, USA
| | | | - Shawn P O'Neil
- Pfizer Drug Safety Research and Development, 1 Portland Street, Cambridge, MA, 02139, USA
| | - Jessica L Moore
- Frontier Diagnostics, 345 Hill Ave, Nashville, TN, 37210, USA
| | | | | | - Jeremy L Norris
- Frontier Diagnostics, 345 Hill Ave, Nashville, TN, 37210, USA
| | | | - Kevin Beaumont
- Pfizer Pharmacokinetics, Dynamics and Metabolism, 1 Portland Street, Cambridge, MA, 02139, USA
| | - Amanda J King-Ahmad
- Pfizer Pharmacokinetics, Dynamics and Metabolism, Eastern Point Road, Groton, CT, 06340, USA
| | - Saurabh Vispute
- Pfizer Drug Safety Research and Development, Eastern Point Road, Groton, CT, 06340, USA
| | - Jon C Cook
- Pfizer Drug Safety Research and Development, Eastern Point Road, Groton, CT, 06340, USA
| | - Zaher Radi
- Pfizer Drug Safety Research and Development, 1 Portland Street, Cambridge, MA, 02139, USA
| | - Maik Schuler
- Pfizer Drug Safety Research and Development, Eastern Point Road, Groton, CT, 06340, USA
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26
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Bisht K, Moore JL, Caprioli RM, Skaar EP, Wakeman CA. Impact of temperature-dependent phage expression on Pseudomonas aeruginosa biofilm formation. NPJ Biofilms Microbiomes 2021; 7:22. [PMID: 33727555 PMCID: PMC7966754 DOI: 10.1038/s41522-021-00194-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen that forms robust biofilms in the different niches it occupies. Numerous physiological adaptations are required as this organism shifts from soil or aquatic environments to a host-associated lifestyle. While many conditions differ between these niches, temperature shifts are a factor that can contribute to physiological stress during this transition. To understand how temperature impacts biofilm formation in this pathogen, we used proteomic and transcriptomic tools to elucidate physiological responses in environment-relevant vs. host-relevant temperatures. These studies uncovered differential expression of various proteins including a phage protein that is associated with the EPS matrix in P. aeruginosa. This filamentous phage was induced at host temperatures and was required for full biofilm-forming capacity specifically at human body temperature. These data highlight the importance of temperature shift in biofilm formation and suggest bacteriophage proteins could be a possible therapeutic target in biofilm-associated infections.
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Affiliation(s)
- Karishma Bisht
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jessica L Moore
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | | | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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27
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Manzo T, Prentice BM, Anderson KG, Raman A, Schalck A, Codreanu GS, Nava Lauson CB, Tiberti S, Raimondi A, Jones MA, Reyzer M, Bates BM, Spraggins JM, Patterson NH, McLean JA, Rai K, Tacchetti C, Tucci S, Wargo JA, Rodighiero S, Clise-Dwyer K, Sherrod SD, Kim M, Navin NE, Caprioli RM, Greenberg PD, Draetta G, Nezi L. Accumulation of long-chain fatty acids in the tumor microenvironment drives dysfunction in intrapancreatic CD8+ T cells. J Exp Med 2021; 217:151833. [PMID: 32491160 PMCID: PMC7398173 DOI: 10.1084/jem.20191920] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/14/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
CD8+ T cells are master effectors of antitumor immunity, and their presence at tumor sites correlates with favorable outcomes. However, metabolic constraints imposed by the tumor microenvironment (TME) can dampen their ability to control tumor progression. We describe lipid accumulation in the TME areas of pancreatic ductal adenocarcinoma (PDA) populated by CD8+ T cells infiltrating both murine and human tumors. In this lipid-rich but otherwise nutrient-poor TME, access to using lipid metabolism becomes particularly valuable for sustaining cell functions. Here, we found that intrapancreatic CD8+ T cells progressively accumulate specific long-chain fatty acids (LCFAs), which, rather than provide a fuel source, impair their mitochondrial function and trigger major transcriptional reprogramming of pathways involved in lipid metabolism, with the subsequent reduction of fatty acid catabolism. In particular, intrapancreatic CD8+ T cells specifically exhibit down-regulation of the very-long-chain acyl-CoA dehydrogenase (VLCAD) enzyme, which exacerbates accumulation of LCFAs and very-long-chain fatty acids (VLCFAs) that mediate lipotoxicity. Metabolic reprogramming of tumor-specific T cells through enforced expression of ACADVL enabled enhanced intratumoral T cell survival and persistence in an engineered mouse model of PDA, overcoming one of the major hurdles to immunotherapy for PDA.
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Affiliation(s)
- Teresa Manzo
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boone M Prentice
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Kristin G Anderson
- Clinical Research Division and Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA.,Departments of Medicine/Oncology and Immunology, University of Washington School of Medicine, Seattle, WA
| | - Ayush Raman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Aislyn Schalck
- Department of Genetics and Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Carina B Nava Lauson
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy
| | - Silvia Tiberti
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy
| | - Andrea Raimondi
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, San Raffaele Vita-Salute University, Milano, Italy
| | - Marissa A Jones
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Michelle Reyzer
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Breanna M Bates
- Clinical Research Division and Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA.,Departments of Medicine/Oncology and Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jeffrey M Spraggins
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Nathan H Patterson
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - John A McLean
- Center for Innovative Technology, Vanderbilt University, Nashville, TN
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carlo Tacchetti
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, San Raffaele Vita-Salute University, Milano, Italy
| | - Sara Tucci
- Laboratory of Clinical Biochemistry and Metabolism Center for Pediatrics and Adolescent Medicine, University of Freiburg, Freiburg, Germany
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Simona Rodighiero
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stacy D Sherrod
- Center for Innovative Technology, Vanderbilt University, Nashville, TN
| | - Michael Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nicholas E Navin
- Department of Genetics and Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Richard M Caprioli
- Department of Biochemistry, Mass Spectrometry Research Center, Department of Chemistry, Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN
| | - Philip D Greenberg
- Clinical Research Division and Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA.,Departments of Medicine/Oncology and Immunology, University of Washington School of Medicine, Seattle, WA
| | - Giulio Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luigi Nezi
- Department of Experimental Oncology, IRCCS European Institute of Oncology, Milano, Italy.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
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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: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Staphylococcus aureus is a common cause of invasive and life-threatening infections that are often multidrug resistant. To develop novel treatment approaches, a detailed understanding of the complex host-pathogen interactions during infection is essential. This is particularly true for the molecular processes that govern the formation of tissue abscesses, as these heterogeneous structures are important contributors to staphylococcal pathogenicity. To fully characterize the developmental process leading to mature abscesses, temporal and spatial analytical approaches are required. Spatially targeted proteomic technologies such as micro-liquid extraction surface analysis offer insight into complex biological systems including detection of bacterial proteins and their abundance in the host environment. By analyzing the proteomic constituents of different abscess regions across the course of infection, we defined the immune response and bacterial contribution to abscess development through spatial and temporal proteomic assessment. The information gathered was mapped to biochemical pathways to characterize the metabolic processes and immune strategies employed by the host. These data provide insights into the physiological state of bacteria within abscesses and elucidate pathogenic processes at the host-pathogen interface.
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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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Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM. Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. J Am Soc Mass Spectrom 2020; 31:2401-2415. [PMID: 32886506 PMCID: PMC9278956 DOI: 10.1021/jasms.0c00232] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Imaging mass spectrometry has become a mature molecular mapping technology that is used for molecular discovery in many medical and biological systems. While powerful by itself, imaging mass spectrometry can be complemented by the addition of other orthogonal, chemically informative imaging technologies to maximize the information gained from a single experiment and enable deeper understanding of biological processes. Within this review, we describe MALDI, SIMS, and DESI imaging mass spectrometric technologies and how these have been integrated with other analytical modalities such as microscopy, transcriptomics, spectroscopy, and electrochemistry in a field termed multimodal imaging. We explore the future of this field and discuss forthcoming developments that will bring new insights to help unravel the molecular complexities of biological systems, from single cells to functional tissue structures and organs.
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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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30
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Anderson DMG, Messinger JD, Patterson NH, Rivera ES, Kotnala A, Spraggins JM, Caprioli RM, Curcio CA, Schey KL. Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:2426-2436. [PMID: 32628476 PMCID: PMC8161663 DOI: 10.1021/jasms.0c00119] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The human retina provides vision at light levels ranging from starlight to sunlight. Its supporting tissues regulate plasma-delivered lipophilic essentials for vision, including retinoids. The macula is an anatomic specialization for high-acuity and color vision that is also vulnerable to prevalent blinding diseases. The retina's exquisite architecture comprises numerous cell types that are aligned horizontally, yielding structurally distinct cell, synaptic, and vascular layers that are visible in histology and in diagnostic clinical imaging. MALDI imaging mass spectrometry (IMS) is now capable of uniting low micrometer spatial resolution with high levels of chemical specificity. In this study, a multimodal imaging approach fortified with accurate multi-image registration was used to localize lipids in human retina tissue at laminar, cellular, and subcellular levels. Multimodal imaging results indicate differences in distributions and abundances of lipid species across and within single cell types. Of note are distinct localizations of signals within specific layers of the macula. For example, phosphatidylethanolamine and phosphatidylinositol lipids were localized to central RPE cells, whereas specific plasmalogen lipids were localized to cells of the perifoveal RPE and Henle fiber layer. Subcellular compartments of photoreceptors were distinguished by PE(20:0_22:5) in the outer nuclear layer, PE(18:0_22:6) in outer and inner segments, and cardiolipin CL(70:5) in the mitochondria-rich inner segments. Several lipids, differing by a single double bond, have markedly different distributions between the central fovea and the ganglion cell and inner nuclear layers. A lipid atlas, initiated in this study, can serve as a reference database for future examination of diseased tissues.
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Affiliation(s)
- David M G Anderson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jeffrey D Messinger
- Department of Ophthalmology and Visual Science, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Nathan H Patterson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Emilio S Rivera
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Ankita Kotnala
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department of Ophthalmology and Visual Science, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Richard M Caprioli
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Christine A Curcio
- Department of Ophthalmology and Visual Science, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Kevin L Schey
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37240, United States
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31
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Rivera ES, Djambazova KV, Neumann EK, Caprioli RM, Spraggins JM. Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. J Mass Spectrom 2020; 55:e4614. [PMID: 32955134 PMCID: PMC8211109 DOI: 10.1002/jms.4614] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 05/02/2023]
Abstract
Imaging mass spectrometry (IMS) technologies are capable of mapping a wide array of biomolecules in diverse cellular and tissue environments. IMS has emerged as an essential tool for providing spatially targeted molecular information due to its high sensitivity, wide molecular coverage, and chemical specificity. One of the major challenges for mapping the complex cellular milieu is the presence of many isomers and isobars in these samples. This challenge is traditionally addressed using orthogonal liquid chromatography (LC)-based analysis, though, common approaches such as chromatography and electrophoresis are not able to be performed at timescales that are compatible with most imaging applications. Ion mobility offers rapid, gas-phase separations that are readily integrated with IMS workflows in order to provide additional data dimensionality that can improve signal-to-noise, dynamic range, and specificity. Here, we highlight recent examples of ion mobility coupled to IMS and highlight their importance to the field.
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Key Words
- IMS
- desorption electrospray ionization, DESI
- drift tube ion mobility spectrometry, DTIMS
- high-field asymmetric waveform ion mobility, FAIMS
- imaging mass spectrometry
- infrared matrix-assisted laser desorption electrospray ionization, IR-MALDESI
- ion mobility
- laser ablation electrospray ionization, LAESI
- lipids
- liquid extraction surface analysis, LESA
- liquid microjunction, (LMJ)
- matrix-assisted laser desorption electrospray ionization, MALDI
- metabolites
- proteins
- tissue analysis
- trapped ion mobility spectrometry, TIMS
- travelling wave ion mobility spectrometry, TWIMS
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Affiliation(s)
- Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
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McMillen JC, Fincher JA, Klein DR, Spraggins JM, Caprioli RM. Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. J Mass Spectrom 2020; 55:e4663. [PMID: 33241625 DOI: 10.26434/chemrxiv.12494705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/14/2020] [Indexed: 05/18/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, untargeted detection of many hundreds of analytes from tissue. Recently, laser postionization (MALDI-2) has been developed for increased ion yield and sensitivity for lipid IMS. However, the dependence of MALDI-2 performance on the various lipid classes is largely unknown. To understand the effect of the applied matrix on MALDI-2 analysis of lipids, samples including an equimolar lipid standard mixture, various tissue homogenates, and intact rat kidney tissue sections were analyzed using the following matrices: α-cyano-4-hydroxycinnamic acid, 2',5'-dihydroxyacetophenone, 2',5'-dihydroxybenzoic acid (DHB), and norharmane (NOR). Lipid signal enhancement of protonated species using MALDI-2 technology varied based on the matrix used. Although signal improvements were observed for all matrices, the most dramatic effects using MALDI-2 were observed using NOR and DHB. For lipid standards analyzed by MALDI-2, NOR provided the broadest coverage, enabling the detection of all 13 protonated standards, including nonpolar lipids, whereas DHB gave less coverage but gave the highest signal increase for those lipids recorded. With respect to tissue homogenates and rat kidney tissue, mass spectra were compared and showed that the number and intensity of neutral lipids tentatively identified with MALDI-2 using NOR increased significantly (e.g., fivefold intensity increase for triacylglycerol). In the cases of DHB with MALDI-2, the number of protonated lipids identified from tissue homogenates doubled with 152 on average compared with 76 with MALDI alone. High spatial resolution imaging (~20 μm) of rat kidney tissue showed similar results using DHB with 125 lipids tentatively identified from MALDI-2 spectra versus just 72 using standard MALDI. From the four matrices tested, NOR provided the greatest increase in sensitivity for neutral lipids (triacylglycerol, diacylglycerol, monoacylglycerol, and cholesterol ester), and DHB provided the highest overall number of lipids detected using MALDI-2 technology.
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Affiliation(s)
- Josiah C McMillen
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
| | - Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
- Department of Pharmacology, Vanderbilt University
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, 37232, USA
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33
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McMillen JC, Fincher JA, Klein DR, Spraggins JM, Caprioli RM. Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. J Mass Spectrom 2020; 55:e4663. [PMID: 33241625 PMCID: PMC8099046 DOI: 10.1002/jms.4663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/14/2020] [Indexed: 05/04/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, untargeted detection of many hundreds of analytes from tissue. Recently, laser postionization (MALDI-2) has been developed for increased ion yield and sensitivity for lipid IMS. However, the dependence of MALDI-2 performance on the various lipid classes is largely unknown. To understand the effect of the applied matrix on MALDI-2 analysis of lipids, samples including an equimolar lipid standard mixture, various tissue homogenates, and intact rat kidney tissue sections were analyzed using the following matrices: α-cyano-4-hydroxycinnamic acid, 2',5'-dihydroxyacetophenone, 2',5'-dihydroxybenzoic acid (DHB), and norharmane (NOR). Lipid signal enhancement of protonated species using MALDI-2 technology varied based on the matrix used. Although signal improvements were observed for all matrices, the most dramatic effects using MALDI-2 were observed using NOR and DHB. For lipid standards analyzed by MALDI-2, NOR provided the broadest coverage, enabling the detection of all 13 protonated standards, including nonpolar lipids, whereas DHB gave less coverage but gave the highest signal increase for those lipids recorded. With respect to tissue homogenates and rat kidney tissue, mass spectra were compared and showed that the number and intensity of neutral lipids tentatively identified with MALDI-2 using NOR increased significantly (e.g., fivefold intensity increase for triacylglycerol). In the cases of DHB with MALDI-2, the number of protonated lipids identified from tissue homogenates doubled with 152 on average compared with 76 with MALDI alone. High spatial resolution imaging (~20 μm) of rat kidney tissue showed similar results using DHB with 125 lipids tentatively identified from MALDI-2 spectra versus just 72 using standard MALDI. From the four matrices tested, NOR provided the greatest increase in sensitivity for neutral lipids (triacylglycerol, diacylglycerol, monoacylglycerol, and cholesterol ester), and DHB provided the highest overall number of lipids detected using MALDI-2 technology.
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Affiliation(s)
- Josiah C. McMillen
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jarod A. Fincher
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Dustin R. Klein
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jeffrey M. Spraggins
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Pharmacology, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
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Fernández-Vega A, Chicano-Gálvez E, Prentice BM, Anderson D, Priego-Capote F, López-Bascón MA, Calderón-Santiago M, Avendaño MS, Guzmán-Ruiz R, Tena-Sempere M, Fernández JA, Caprioli RM, Malagón MM. Optimization of a MALDI-Imaging protocol for studying adipose tissue-associated disorders. Talanta 2020; 219:121184. [PMID: 32887102 DOI: 10.1016/j.talanta.2020.121184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is increasingly recognized for its potential in the discovery of novel biomarkers directly from tissue sections. However, there are no MALDI IMS studies as yet on the adipose tissue, a lipid-enriched tissue that plays a pivotal role in the development of obesity-associated disorders. Herein, we aimed at developing an optimized method for analyzing adipose tissue lipid composition under both physiological and pathological conditions by MALDI IMS. Our studies showed an exacerbated lipid delocalization from adipose tissue sections when conventional strategies were applied. However, our optimized method using conductive-tape sampling and 2,5-dihydroxybenzoic acid (DHB) as a matrix, preserved the anatomical organization and minimized lipid diffusion from sample sections. This method enabled the identification of a total of 625 down-regulated and 328 up-regulated m/z values in the adipose tissue from a rat model of extreme obesity as compared to lean animals. Combination of MALDI IMS and liquid chromatography (LC)-MS/MS data identified 44 differentially expressed lipid species between lean and obese animals, including phospholipids and sphingomyelins. Among the lipids identified, SM(d18:0_18:2), PE(P-16:0_20:0), and PC(O-16:0_16:1) showed a differential spatial distribution in the adipose tissue of lean vs. obese animals. In sum, our method provides a valuable new tool for research on adipose tissue that may pave the way for the identification of novel biomarkers of obesity and metabolic disease.
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Affiliation(s)
- A Fernández-Vega
- Dept. Cell Biology, Physiology, and Immunology, IMIBIC/University of Cordoba (UCO)/Reina Sofia University Hospital (HURS), Cordoba, Spain; CIBER Physiopathology of Obesity and Nutrition (CIBERobn), ISCIII, Spain
| | | | - B M Prentice
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - D Anderson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - F Priego-Capote
- Department of Analytical Chemistry, IMIBIC/UCO/HURS, Cordoba, Spain
| | - M A López-Bascón
- Department of Analytical Chemistry, IMIBIC/UCO/HURS, Cordoba, Spain
| | | | - M S Avendaño
- Dept. Cell Biology, Physiology, and Immunology, IMIBIC/University of Cordoba (UCO)/Reina Sofia University Hospital (HURS), Cordoba, Spain; CIBER Physiopathology of Obesity and Nutrition (CIBERobn), ISCIII, Spain
| | - R Guzmán-Ruiz
- Dept. Cell Biology, Physiology, and Immunology, IMIBIC/University of Cordoba (UCO)/Reina Sofia University Hospital (HURS), Cordoba, Spain; CIBER Physiopathology of Obesity and Nutrition (CIBERobn), ISCIII, Spain
| | - M Tena-Sempere
- Dept. Cell Biology, Physiology, and Immunology, IMIBIC/University of Cordoba (UCO)/Reina Sofia University Hospital (HURS), Cordoba, Spain; CIBER Physiopathology of Obesity and Nutrition (CIBERobn), ISCIII, Spain
| | - J A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - R M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA; Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain; Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37232, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA; Department of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - M M Malagón
- Dept. Cell Biology, Physiology, and Immunology, IMIBIC/University of Cordoba (UCO)/Reina Sofia University Hospital (HURS), Cordoba, Spain; CIBER Physiopathology of Obesity and Nutrition (CIBERobn), ISCIII, Spain.
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35
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Neumann EK, Migas LG, Allen JL, Caprioli RM, Van de Plas R, Spraggins JM. Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Mass Spectrometry. Anal Chem 2020. [PMID: 32668145 DOI: 10.26434/chemrxiv.12118644.v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Low molecular weight metabolites are essential for defining the molecular phenotypes of cells. However, spatial metabolomics tools often lack the sensitivity, specify, and spatial resolution to provide comprehensive descriptions of these species in tissue. MALDI imaging mass spectrometry (IMS) of low molecular weight ions is particularly challenging as MALDI matrix clusters are often nominally isobaric with multiple metabolite ions, requiring high resolving power instrumentation or derivatization to circumvent this issue. An alternative to this is to perform ion mobility separation before ion detection, enabling the visualization of metabolites without the interference of matrix ions. Additional difficulties surrounding low weight metabolite visualization include high resolution imaging, while maintaining sufficient ion numbers for broad and representative analysis of the tissue chemical complement. Here, we use MALDI timsTOF IMS to image low molecular weight metabolites at higher spatial resolution than most metabolite MALDI IMS experiments (20 μm) while maintaining broad coverage within the human kidney. We demonstrate that trapped ion mobility spectrometry (TIMS) can resolve matrix peaks from metabolite signal and separate both isobaric and isomeric metabolites with different distributions within the kidney. The added ion mobility data dimension dramatically increased the peak capacity for spatial metabolomics experiments. Through this improved sensitivity, we have found >40 low molecular weight metabolites in human kidney tissue, such as argininic acid, acetylcarnitine, and choline that localize to the cortex, medulla, and renal pelvis, respectively. Future work will involve further exploring metabolomic profiles of human kidneys as a function of age, sex, and race.
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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
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, Building 34, 2628 CD Delft, The Netherlands
| | - Jamie L Allen
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Raf Van de Plas
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, Building 34, 2628 CD Delft, The Netherlands
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
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36
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Djambazova KV, Klein DR, Migas LG, Neumann EK, Rivera ES, Van de Plas R, Caprioli RM, Spraggins JM. Resolving the Complexity of Spatial Lipidomics Using MALDI TIMS Imaging Mass Spectrometry. Anal Chem 2020; 92:13290-13297. [PMID: 32808523 DOI: 10.26434/chemrxiv.12331652.v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows for direct mapping of biomolecules in tissues. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here, we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) mass spectrometer with trapped ion mobility spectrometry (TIMS) enables a >250% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn backbone isomers, acyl chain isomers, and double-bond position and stereoisomers, is demonstrated. As a proof of concept, in situ separation and imaging of lipid isomers with distinct spatial distributions were performed using tissue sections from a whole-body mouse pup.
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Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Emilio S Rivera
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
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37
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Prentice BM, Ryan DJ, Grove KJ, Cornett DS, Caprioli RM, Spraggins JM. Dynamic Range Expansion by Gas-Phase Ion Fractionation and Enrichment for Imaging Mass Spectrometry. Anal Chem 2020; 92:13092-13100. [PMID: 32845133 PMCID: PMC8340028 DOI: 10.1021/acs.analchem.0c02121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the analysis of biological tissue by imaging mass spectrometry (IMS), the limit of detection and dynamic range are of paramount importance in obtaining experimental results that provide insight into underlying biological processes. Many important biomolecules are present in the tissue milieu in low concentrations and in complex mixtures with other compounds of widely ranging abundances, challenging the limits of analytical technologies. In many IMS experiments, the ion signal can be dominated by a few highly abundant ion species. On trap-based instrument platforms that accumulate ions prior to mass analysis, these high abundance ions can diminish the detection and dynamic range of lower abundance ions. Herein, we describe two strategies for combating these challenges during IMS experiments on a hybrid QhFT-ICR MS. In one iteration, the mass resolving capabilities of a quadrupole mass filter are used to selectively enrich ions of interest via a technique previously termed continuous accumulation of selected ions. Second, we have introduced a supplemental dipolar AC waveform to the quadrupole mass filter of a commercial QhFT-ICR mass spectrometer to perform selected ion ejection prior to the ion accumulation region. This setup allows the selective ejection of the most abundant ion species prior to ion accumulation, thereby greatly improving the molecular depth with which IMS can probe tissue samples. The gain in sensitivity of both of these approaches roughly scales with the number of accumulated laser shots up to the charge capacity of the ion accumulation cell. The efficiencies of these two strategies are described here by performing lipid imaging mass spectrometry analyses of a rat brain.
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Affiliation(s)
- Boone M Prentice
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Daniel J Ryan
- ExxonMobil Research and Engineering Company, Annandale, New Jersey 08801, United States
| | - Kerri J Grove
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Pharmacology and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
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38
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Neumann EK, Migas LG, Allen JL, Caprioli RM, Van de Plas R, Spraggins JM. Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Mass Spectrometry. Anal Chem 2020; 92:13084-13091. [PMID: 32668145 DOI: 10.1021/acs.analchem.0c02051] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Low molecular weight metabolites are essential for defining the molecular phenotypes of cells. However, spatial metabolomics tools often lack the sensitivity, specify, and spatial resolution to provide comprehensive descriptions of these species in tissue. MALDI imaging mass spectrometry (IMS) of low molecular weight ions is particularly challenging as MALDI matrix clusters are often nominally isobaric with multiple metabolite ions, requiring high resolving power instrumentation or derivatization to circumvent this issue. An alternative to this is to perform ion mobility separation before ion detection, enabling the visualization of metabolites without the interference of matrix ions. Additional difficulties surrounding low weight metabolite visualization include high resolution imaging, while maintaining sufficient ion numbers for broad and representative analysis of the tissue chemical complement. Here, we use MALDI timsTOF IMS to image low molecular weight metabolites at higher spatial resolution than most metabolite MALDI IMS experiments (20 μm) while maintaining broad coverage within the human kidney. We demonstrate that trapped ion mobility spectrometry (TIMS) can resolve matrix peaks from metabolite signal and separate both isobaric and isomeric metabolites with different distributions within the kidney. The added ion mobility data dimension dramatically increased the peak capacity for spatial metabolomics experiments. Through this improved sensitivity, we have found >40 low molecular weight metabolites in human kidney tissue, such as argininic acid, acetylcarnitine, and choline that localize to the cortex, medulla, and renal pelvis, respectively. Future work will involve further exploring metabolomic profiles of human kidneys as a function of age, sex, and race.
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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
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, Building 34, 2628 CD Delft, The Netherlands
| | - Jamie L Allen
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States.,Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Raf Van de Plas
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Delft Center for Systems and Control, Delft University of Technology, Mekelweg 2, Building 34, 2628 CD Delft, The Netherlands
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
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39
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Djambazova KV, Klein DR, Migas LG, Neumann EK, Rivera ES, Van de Plas R, Caprioli RM, Spraggins JM. Resolving the Complexity of Spatial Lipidomics Using MALDI TIMS Imaging Mass Spectrometry. Anal Chem 2020; 92:13290-13297. [PMID: 32808523 DOI: 10.1021/acs.analchem.0c02520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows for direct mapping of biomolecules in tissues. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here, we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) mass spectrometer with trapped ion mobility spectrometry (TIMS) enables a >250% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn backbone isomers, acyl chain isomers, and double-bond position and stereoisomers, is demonstrated. As a proof of concept, in situ separation and imaging of lipid isomers with distinct spatial distributions were performed using tissue sections from a whole-body mouse pup.
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Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Emilio S Rivera
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States.,Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
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40
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Palmer LD, Minor KE, Mettlach JA, Rivera ES, Boyd KL, Caprioli RM, Spraggins JM, Dalebroux ZD, Skaar EP. Modulating Isoprenoid Biosynthesis Increases Lipooligosaccharides and Restores Acinetobacter baumannii Resistance to Host and Antibiotic Stress. Cell Rep 2020; 32:108129. [PMID: 32905776 PMCID: PMC7519801 DOI: 10.1016/j.celrep.2020.108129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/19/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is a leading cause of ventilator-associated pneumonia and a critical threat due to multidrug resistance. The A. baumannii outer membrane is an asymmetric lipid bilayer composed of inner leaflet glycerophospholipids and outer leaflet lipooligosaccharides. Deleting mlaF of the maintenance of lipid asymmetry (Mla) system causes A. baumannii to become more susceptible to pulmonary surfactants and antibiotics and decreases bacterial survival in the lungs of mice. Spontaneous suppressor mutants isolated from infected mice contain an ISAba11 insertion upstream of the ispB initiation codon, an essential isoprenoid biosynthesis gene. The insertion restores antimicrobial resistance and virulence to ΔmlaF. The suppressor strain increases lipooligosaccharides, suggesting that the mechanism involves balancing the glycerophospholipids/lipooligosaccharides ratio on the bacterial surface. An identical insertion exists in an extensively drug-resistant A. baumannii isolate, demonstrating its clinical relevance. These data show that the stresses bacteria encounter during infection select for genomic rearrangements that increase resistance to antimicrobials.
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Affiliation(s)
- Lauren D Palmer
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Keaton E Minor
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joshua A Mettlach
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Emilio S Rivera
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Kelli L Boyd
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Zachary D Dalebroux
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA.
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41
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Zhang L, Yang C, Pfeifer JD, Caprioli RM, Judd AM, Patterson NH, Reyzer ML, Norris JL, Maluf HM. Histopathologic, immunophenotypic, and proteomics characteristics of low-grade phyllodes tumor and fibroadenoma: more similarities than differences. NPJ Breast Cancer 2020; 6:27. [PMID: 32613078 PMCID: PMC7319981 DOI: 10.1038/s41523-020-0169-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/26/2020] [Indexed: 12/18/2022] Open
Abstract
Distinguishing low-grade phyllodes tumor from fibroadenoma is practically challenging due to their overlapping histologic features. However, the final interpretation is essential to surgeons, who base their management on the final pathology report. Patients who receive a diagnosis of fibroadenoma might not undergo any additional intervention while lumpectomy with wide margins is the standard of care for phyllodes tumor, which can have significant cosmetic consequences. We studied the clinical, immunophenotypic, and proteomics profiles of 31 histologically confirmed low-grade phyllodes tumor and 30 fibroadenomas. Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) and immunohistochemistry for Ki-67, p53, β-catenin, and E-cadherin were performed on all cases. After the mass spectra for all 31 cases of low-grade phyllodes tumor and 30 cases of fibroadenoma were collected, an average peak value for all cases was generated. There was no significant difference in the overall mass spectra pattern in any of the peaks identified. There was also overlap in the percentage of cells staining positive for Ki-67, p53, β-catenin, and E-cadherin. The two groups of patients showed no statistically significant difference in age, tumor size, or disease-free survival. Neither group developed malignant transformation, distant metastases, or disease-related mortality. We have demonstrated low-grade phyllodes tumor and fibroadenoma to show significant overlapping clinical and proteomics features.
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Affiliation(s)
- Lingxin Zhang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Present Address: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Chen Yang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Present Address: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - John D. Pfeifer
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235 USA
| | - Audra M. Judd
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235 USA
| | - Nathan H. Patterson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235 USA
| | - Michelle L. Reyzer
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235 USA
| | - Jeremy L. Norris
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235 USA
| | - Horacio M. Maluf
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Present Address: Department of Pathology, Cedars Sinai Medical Center, Los Angeles, CA 90048 USA
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42
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Jones MA, Cho SH, Patterson NH, Van de Plas R, Spraggins JM, Boothby MR, Caprioli RM. Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry. Anal Chem 2020; 92:7079-7086. [PMID: 32298091 PMCID: PMC7456589 DOI: 10.1021/acs.analchem.0c00446] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Identifying the spatial distributions of biomolecules in tissue is crucial for understanding integrated function. Imaging mass spectrometry (IMS) allows simultaneous mapping of thousands of biosynthetic products such as lipids but has needed a means of identifying specific cell-types or functional states to correlate with molecular localization. We report, here, advances starting from identity marking with a genetically encoded fluorophore. The fluorescence emission data were integrated with IMS data through multimodal image processing with advanced registration techniques and data-driven image fusion. In an unbiased analysis of spleens, this integrated technology enabled identification of ether lipid species preferentially enriched in germinal centers. We propose that this use of genetic marking for microanatomical regions of interest can be paired with molecular information from IMS for any tissue, cell-type, or activity state for which fluorescence is driven by a gene-tracking allele and ultimately with outputs of other means of spatial mapping.
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Affiliation(s)
- Marissa A Jones
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
| | - Sung Hoon Cho
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN AA-4214B, MCN A-5301, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control (DCSC), Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Mark R Boothby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN AA-4214B, MCN A-5301, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
- Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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Palmer LD, Jordan AT, Maloney KN, Farrow MA, Gutierrez DB, Gant-Branum R, Burns WJ, Romer CE, Tsui T, Allen JL, Beavers WN, Nei YW, Sherrod SD, Lacy DB, Norris JL, McLean JA, Caprioli RM, Skaar EP. Zinc intoxication induces ferroptosis in A549 human lung cells. Metallomics 2020; 11:982-993. [PMID: 30968088 DOI: 10.1039/c8mt00360b] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Zinc (Zn) is an essential trace metal required for all forms of life, but is toxic at high concentrations. While the toxic effects of high levels of Zn are well documented, the mechanism of cell death appears to vary based on the study and concentration of Zn. Zn has been proposed as an anti-cancer treatment against non-small cell lung cancer (NSCLC). The goal of this analysis was to determine the effects of Zn on metabolism and cell death in A549 cells. Here, high throughput multi-omics analysis identified the molecular effects of Zn intoxication on the proteome, metabolome, and transcriptome of A549 human NSCLC cells after 5 min to 24 h of Zn exposure. Multi-omics analysis combined with additional experimental evidence suggests Zn intoxication induces ferroptosis, an iron and lipid peroxidation-dependent programmed cell death, demonstrating the utility of multi-omics analysis to identify cellular response to intoxicants.
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Affiliation(s)
- Lauren D Palmer
- Vanderbilt Institute for Infection, Immunology and Inflammation and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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44
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Cho SH, Jones M, Spraggins J, Caprioli RM, Boothby MR. Identification of germinal center-specific lipid species. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.151.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Germinal centers (GCs) are microanatomic structures that B cells proliferate, are selected for affinity maturation, undergo antibody (Ab) class-switch recombination and differentiate into Ab-secreting plasma cells and memory B cells. Nutrient availability, metabolic reprogramming process, and spatial localizations of biomolecules can impact on GC response and quality of humoral immune response. By using matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS), we identified that the ether lipid species are preferentially enriched in germinal centers, and the perturbation of ether lipid synthesis attenuatedGC response and antigen-specific Ab production. These results suggest that molecular programing of GC lymphocytes is tied to increased ether lipid synthesis and that these species are functionally important in humoral immunity.
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Affiliation(s)
- Sung Hoon Cho
- 1Pathology, Microbiology & Immunology; Vanderbilt University Medical Center, Nashville, TN
| | | | | | | | - Mark Robin Boothby
- 1Pathology, Microbiology & Immunology; Vanderbilt University Medical Center, Nashville, TN
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45
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Verbeeck N, Caprioli RM, Van de Plas R. Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. Mass Spectrom Rev 2020; 39:245-291. [PMID: 31602691 PMCID: PMC7187435 DOI: 10.1002/mas.21602] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/27/2018] [Indexed: 05/20/2023]
Abstract
Imaging mass spectrometry (IMS) is a rapidly advancing molecular imaging modality that can map the spatial distribution of molecules with high chemical specificity. IMS does not require prior tagging of molecular targets and is able to measure a large number of ions concurrently in a single experiment. While this makes it particularly suited for exploratory analysis, the large amount and high-dimensional nature of data generated by IMS techniques make automated computational analysis indispensable. Research into computational methods for IMS data has touched upon different aspects, including spectral preprocessing, data formats, dimensionality reduction, spatial registration, sample classification, differential analysis between IMS experiments, and data-driven fusion methods to extract patterns corroborated by both IMS and other imaging modalities. In this work, we review unsupervised machine learning methods for exploratory analysis of IMS data, with particular focus on (a) factorization, (b) clustering, and (c) manifold learning. To provide a view across the various IMS modalities, we have attempted to include examples from a range of approaches including matrix assisted laser desorption/ionization, desorption electrospray ionization, and secondary ion mass spectrometry-based IMS. This review aims to be an entry point for both (i) analytical chemists and mass spectrometry experts who want to explore computational techniques; and (ii) computer scientists and data mining specialists who want to enter the IMS field. © 2019 The Authors. Mass Spectrometry Reviews published by Wiley Periodicals, Inc. Mass SpecRev 00:1-47, 2019.
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Affiliation(s)
- Nico Verbeeck
- Delft Center for Systems and ControlDelft University of Technology ‐ TU DelftDelftThe Netherlands
- Aspect Analytics NVGenkBelgium
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT)KU LeuvenLeuvenBelgium
| | - Richard M. Caprioli
- Mass Spectrometry Research CenterVanderbilt UniversityNashvilleTN
- Department of BiochemistryVanderbilt UniversityNashvilleTN
- Department of ChemistryVanderbilt UniversityNashvilleTN
- Department of PharmacologyVanderbilt UniversityNashvilleTN
- Department of MedicineVanderbilt UniversityNashvilleTN
| | - Raf Van de Plas
- Delft Center for Systems and ControlDelft University of Technology ‐ TU DelftDelftThe Netherlands
- Mass Spectrometry Research CenterVanderbilt UniversityNashvilleTN
- Department of BiochemistryVanderbilt UniversityNashvilleTN
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46
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Perry WJ, Patterson NH, Prentice BM, Neumann EK, Caprioli RM, Spraggins JM. Uncovering matrix effects on lipid analyses in MALDI imaging mass spectrometry experiments. J Mass Spectrom 2020; 55:e4491. [PMID: 31860760 PMCID: PMC7383219 DOI: 10.1002/jms.4491] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/25/2019] [Accepted: 12/16/2019] [Indexed: 05/04/2023]
Abstract
The specific matrix used in matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) can have an effect on the molecules ionized from a tissue sample. The sensitivity for distinct classes of biomolecules can vary when employing different MALDI matrices. Here, we compare the intensities of various lipid subclasses measured by Fourier transform ion cyclotron resonance (FT-ICR) IMS of murine liver tissue when using 9-aminoacridine (9AA), 5-chloro-2-mercaptobenzothiazole (CMBT), 1,5-diaminonaphthalene (DAN), 2,5-Dihydroxyacetophenone (DHA), and 2,5-dihydroxybenzoic acid (DHB). Principal component analysis and receiver operating characteristic curve analysis revealed significant matrix effects on the relative signal intensities observed for different lipid subclasses and adducts. Comparison of spectral profiles and quantitative assessment of the number and intensity of species from each lipid subclass showed that each matrix produces unique lipid signals. In positive ion mode, matrix application methods played a role in the MALDI analysis for different cationic species. Comparisons of different methods for the application of DHA showed a significant increase in the intensity of sodiated and potassiated analytes when using an aerosol sprayer. In negative ion mode, lipid profiles generated using DAN were significantly different than all other matrices tested. This difference was found to be driven by modification of phosphatidylcholines during ionization that enables them to be detected in negative ion mode. These modified phosphatidylcholines are isomeric with common phosphatidylethanolamines confounding MALDI IMS analysis when using DAN. These results show an experimental basis of MALDI analyses when analyzing lipids from tissue and allow for more informed selection of MALDI matrices when performing lipid IMS experiments.
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Affiliation(s)
- William J. Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN
- Department of Chemistry, Vanderbilt University, Nashville, TN
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN
- Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Boone M. Prentice
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN
- Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Elizabeth K. Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN
- Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN
- Department of Chemistry, Vanderbilt University, Nashville, TN
- Department of Biochemistry, Vanderbilt University, Nashville, TN
- Department of Pharmacology, Vanderbilt University, Nashville, TN
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN
- Department of Chemistry, Vanderbilt University, Nashville, TN
- Department of Biochemistry, Vanderbilt University, Nashville, TN
- Corresponding Author Address reprint requests to Jeffrey M. Spraggins, V9140 MRBIII, 465 21 Ave South, Nashville, TN 37232, (615) 343-7333,
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47
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Perry WJ, Weiss A, Van de Plas R, Spraggins JM, Caprioli RM, Skaar EP. Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review. Curr Opin Chem Biol 2020; 55:127-135. [PMID: 32087551 PMCID: PMC7237308 DOI: 10.1016/j.cbpa.2020.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/25/2019] [Accepted: 01/14/2020] [Indexed: 02/08/2023]
Abstract
Metals play an essential role in biological systems and are required as structural or catalytic co-factors in many proteins. Disruption of the homeostatic control and/or spatial distributions of metals can lead to disease. Imaging technologies have been developed to visualize elemental distributions across a biological sample. Measurement of elemental distributions by imaging mass spectrometry and imaging X-ray fluorescence are increasingly employed with technologies that can assess histological features and molecular compositions. Data from several modalities can be interrogated as multimodal images to correlate morphological, elemental, and molecular properties. Elemental and molecular distributions have also been axially resolved to achieve three-dimensional volumes, dramatically increasing the biological information. In this review, we provide an overview of recent developments in the field of metal imaging with an emphasis on multimodal studies in two and three dimensions. We specifically highlight studies that present technological advancements and biological applications of how metal homeostasis affects human health.
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Affiliation(s)
- William J Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Andy Weiss
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA; Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands; Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37232, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA; Department of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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48
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Laut CL, Perry WJ, Metzger AL, Weiss A, Stauff DL, Walker S, Caprioli RM, Skaar EP. Bacillus anthracis Responds to Targocil-Induced Envelope Damage through EdsRS Activation of Cardiolipin Synthesis. mBio 2020; 11:e03375-19. [PMID: 32234818 PMCID: PMC7157781 DOI: 10.1128/mbio.03375-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/27/2020] [Indexed: 01/08/2023] Open
Abstract
Bacillus anthracis is a spore-forming bacterium that causes devastating infections and has been used as a bioterror agent. This pathogen can survive hostile environments through the signaling activity of two-component systems, which couple environmental sensing with transcriptional activation to initiate a coordinated response to stress. In this work, we describe the identification of a two-component system, EdsRS, which mediates the B. anthracis response to the antimicrobial compound targocil. Targocil is a cell envelope-targeting compound that is toxic to B. anthracis at high concentrations. Exposure to targocil causes damage to the cellular barrier and activates EdsRS to induce expression of a previously uncharacterized cardiolipin synthase, which we have named ClsT. Both EdsRS and ClsT are required for protection against targocil-dependent damage. Induction of clsT by EdsRS during targocil treatment results in an increase in cardiolipin levels, which protects B. anthracis from envelope damage. Together, these results reveal that a two-component system signaling response to an envelope-targeting antimicrobial induces production of a phospholipid associated with stabilization of the membrane. Cardiolipin is then used to repair envelope damage and promote B. anthracis viability.IMPORTANCE Compromising the integrity of the bacterial cell barrier is a common action of antimicrobials. Targocil is an antimicrobial that is active against the bacterial envelope. We hypothesized that Bacillus anthracis, a potential weapon of bioterror, senses and responds to targocil to alleviate targocil-dependent cell damage. Here, we show that targocil treatment increases the permeability of the cellular envelope and is particularly toxic to B. anthracis spores during outgrowth. In vegetative cells, two-component system signaling through EdsRS is activated by targocil. This results in an increase in the production of cardiolipin via a cardiolipin synthase, ClsT, which restores the loss of barrier function, thereby reducing the effectiveness of targocil. By elucidating the B. anthracis response to targocil, we have uncovered an intrinsic mechanism that this pathogen employs to resist toxicity and have revealed therapeutic targets that are important for bacterial defense against structural damage.
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Affiliation(s)
- Clare L Laut
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William J Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Devin L Stauff
- Department of Biology, Grove City College, Grove City, Pennsylvania, USA
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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49
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Abstract
Imaging mass spectrometry (IMS) has emerged as an important imaging modality because of its broad non-specific nature for molecular detection from highly complex samples. Within this broad field, new sub-categories of technologies have been developed incorporating many different molecular ionization processes. This article will focus on one of the major ionization processes, matrix-assisted laser desorption ionization (MALDI). IMS provides a critically important technology that brings new insight into complex biological samples and opens the door to new discoveries. Applications range widely, from fundamental studies in biology to specific clinical issues, all addressing the need to understand molecular spatial distributions at the tissue and cellular levels.
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Affiliation(s)
- Richard M Caprioli
- Biochemistry Department, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8576, USA
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50
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Woodhams DC, Rollins-Smith LA, Reinert LK, Lam BA, Harris RN, Briggs CJ, Vredenburg VT, Patel BT, Caprioli RM, Chaurand P, Hunziker P, Bigler L. Probiotics Modulate a Novel Amphibian Skin Defense Peptide That Is Antifungal and Facilitates Growth of Antifungal Bacteria. Microb Ecol 2020; 79:192-202. [PMID: 31093727 DOI: 10.1007/s00248-019-01385-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Probiotics can ameliorate diseases of humans and wildlife, but the mechanisms remain unclear. Host responses to interventions that change their microbiota are largely uncharacterized. We applied a consortium of four natural antifungal bacteria to the skin of endangered Sierra Nevada yellow-legged frogs, Rana sierrae, before experimental exposure to the pathogenic fungus Batrachochytrium dendrobatidis (Bd). The probiotic microbes did not persist, nor did they protect hosts, and skin peptide sampling indicated immune modulation. We characterized a novel skin defense peptide brevinin-1Ma (FLPILAGLAANLVPKLICSITKKC) that was downregulated by the probiotic treatment. Brevinin-1Ma was tested against a range of amphibian skin cultures and found to inhibit growth of fungal pathogens Bd and B. salamandrivorans, but enhanced the growth of probiotic bacteria including Janthinobacterium lividum, Chryseobacterium ureilyticum, Serratia grimesii, and Pseudomonas sp. While commonly thought of as antimicrobial peptides, here brevinin-1Ma showed promicrobial function, facilitating microbial growth. Thus, skin exposure to probiotic bacterial cultures induced a shift in skin defense peptide profiles that appeared to act as an immune response functioning to regulate the microbiome. In addition to direct microbial antagonism, probiotic-host interactions may be a critical mechanism affecting disease resistance.
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Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Louise A Rollins-Smith
- Departments of Pathology, Microbiology and Immunology and Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Biological Science, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Laura K Reinert
- Departments of Pathology, Microbiology and Immunology and Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Briana A Lam
- Department of Biology, James Madison University, Harrisonburg, VA, 22807, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, 22807, USA
| | - Cheryl J Briggs
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106-9610, USA
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, 94132-1722, USA
| | - Bhumi T Patel
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232-8575, USA
| | - Pierre Chaurand
- Department of Chemistry, Université de Montréal, Montreal, QC, H3T 1J4, Canada
| | - Peter Hunziker
- Functional Genomics Center Zurich, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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