1
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Lan Y, Zou Z, Yang Z. Single Cell mass spectrometry: Towards quantification of small molecules in individual cells. Trends Analyt Chem 2024; 174:117657. [PMID: 39391010 PMCID: PMC11465888 DOI: 10.1016/j.trac.2024.117657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Studying cell heterogeneity can provide a deeper understanding of biological activities, but appropriate studies cannot be performed using traditional bulk analysis methods. The development of diverse single cell bioanalysis methods is in urgent need and of great significance. Mass spectrometry (MS) has been recognized as a powerful technique for bioanalysis for its high sensitivity, wide applicability, label-free detection, and capability for quantitative analysis. In this review, the general development of single cell mass spectrometry (SCMS) field is covered. First, multiple existing SCMS techniques are described and compared. Next, the development of SCMS field is discussed in a chronological order. Last, the latest quantification studies on small molecules using SCMS have been described in detail.
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Affiliation(s)
| | | | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
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2
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LaLone V, Smith D, Diaz-Espinosa J, Rosania GR. Quantitative Raman chemical imaging of intracellular drug-membrane aggregates and small molecule drug precipitates in cytoplasmic organelles. Adv Drug Deliv Rev 2023; 202:115107. [PMID: 37769851 PMCID: PMC10841539 DOI: 10.1016/j.addr.2023.115107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Raman confocal microscopes have been used to visualize the distribution of small molecule drugs within different subcellular compartments. This visualization allows the discovery, characterization, and detailed analysis of the molecular transport phenomena underpinning the Volume of Distribution - a key parameter governing the systemic pharmacokinetics of small molecule drugs. In the specific case of lipophilic small molecules with large Volumes of Distribution, chemical imaging studies using Raman confocal microscopes have revealed how weakly basic, poorly soluble drug molecules can accumulate inside cells by forming stable, supramolecular complexes in association with cytoplasmic membranes or by precipitating out within organelles. To study the self-assembly and function of the resulting intracellular drug inclusions, Raman chemical imaging methods have been developed to measure and map the mass, concentration, and ionization state of drug molecules at a microscopic, subcellular level. Beyond the field of drug delivery, Raman chemical imaging techniques relevant to the study of microscopic drug precipitates and drug-lipid complexes which form inside cells are also being developed by researchers with seemingly unrelated scientific interests. Highlighting advances in data acquisition, calibration methods, and computational data management and analysis tools, this review will cover a decade of technological developments that enable the conversion of spectral signals obtained from Raman confocal microscopes into new discoveries and information about previously unknown, concentrative drug transport pathways driven by soluble-to-insoluble phase transitions occurring within the cytoplasmic organelles of eukaryotic cells.
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Affiliation(s)
- Vernon LaLone
- Cambium Analytica Research Laboratories, Traverse City, MI, United States
| | - Doug Smith
- Cambium Analytica Research Laboratories, Traverse City, MI, United States
| | - Jennifer Diaz-Espinosa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Gus R Rosania
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States.
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3
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Siuzdak G. Subcellular quantitative imaging of metabolites at the organelle level. Nat Metab 2023; 5:1446-1448. [PMID: 37679555 DOI: 10.1038/s42255-023-00882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Affiliation(s)
- Gary Siuzdak
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.
- Center for Metabolomics, Scripps Research Institute, La Jolla, CA, USA.
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4
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Huang S, Chen K, Leung JK, Guagliardo P, Chen W, Song W, Clode P, Xu J, Young SG, Jiang H. Subcellular Partitioning of Arsenic Trioxide Revealed by Label-Free Imaging. Anal Chem 2022; 94:13889-13896. [PMID: 36189785 DOI: 10.1021/acs.analchem.2c02770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subcellular partitioning of therapeutic agents is highly relevant to their interactions with target molecules and drug efficacy, but studying subcellular partitioning is an enormous challenge. Here, we describe the application of nanoscale secondary ion mass spectrometry (NanoSIMS) analysis to define the subcellular pharmacokinetics of a cytotoxic chemotherapy drug, arsenic trioxide (ATO). We reasoned that defining the partitioning of ATO would yield valuable insights into the mechanisms underlying ATO efficacy. NanoSIMS imaging made it possible to define the intracellular fate of ATO in a label-free manner─and with high resolution and high sensitivity. Our studies of ATO-treated cells revealed that arsenic accumulates in the nucleolus. After prolonged ATO exposure, ∼40 nm arsenic- and sulfur-rich protein aggregates appeared in the cell nucleolus, nucleus, and membrane-free compartments in the cytoplasm, and our studies suggested that the partitioning of nanoscale aggregates could be relevant to cell survival. All-trans retinoic acid increased intracellular ATO levels and accelerated the nanoscale aggregate formation in the nucleolus. This study yielded fresh insights into the subcellular pharmacokinetics of an important cancer therapeutic agent and the potential impact of drug partitioning and pharmacokinetics on drug activity.
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Affiliation(s)
- Song Huang
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Kai Chen
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia.,Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Jong-Kai Leung
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - Weihua Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Wenxin Song
- Department of Medicine, University of California, Los Angeles, California 90095, United States
| | - Peta Clode
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia.,School of Biological Sciences, University of Western Australia, Perth 6009, Australia
| | - Jiake Xu
- School of Biological Sciences, University of Western Australia, Perth 6009, Australia
| | - Stephen G Young
- Department of Medicine, University of California, Los Angeles, California 90095, United States.,School of Biomedical Sciences, University of Western Australia, Perth 6009, Australia.,Department of Human Genetics, University of California, Los Angeles, California 90095, United States
| | - Haibo Jiang
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia.,Department of Chemistry, The University of Hong Kong, Hong Kong, China
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5
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Becquart C, Stulz R, Thomen A, Dost M, Najafinobar N, Dahlén A, Andersson S, Ewing AG, Kurczy ME. Intracellular Absolute Quantification of Oligonucleotide Therapeutics by NanoSIMS. Anal Chem 2022; 94:10549-10556. [PMID: 35830231 DOI: 10.1021/acs.analchem.2c02111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antisense oligonucleotide (ASO)-based therapeutics hold great potential for the treatment of a variety of diseases. Therefore, a better understanding of cellular delivery, uptake, and trafficking mechanisms of ASOs is highly important for early-stage drug discovery. In particular, understanding the biodistribution and quantifying the abundance of ASOs at the subcellular level are needed to fully characterize their activity. Here, we used a combination of electron microscopy and NanoSIMS to assess the subcellular concentrations of a 34S-labeled GalNAc-ASO and a naked ASO in the organelles of primary human hepatocytes. We first cross-validated the method by including a 127I-labeled ASO, finding that the absolute concentration of the lysosomal ASO using two independent labeling strategies gave matching results, demonstrating the strength of our approach. This work also describes the preparation of external standards for absolute quantification by NanoSIMS. For both the 34S and 127I approaches used for our quantification methodology, we established the limit of detection (5 and 2 μM, respectively) and the lower limit of quantification (14 and 5 μM, respectively).
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Affiliation(s)
- Cécile Becquart
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Rouven Stulz
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | | | - Maryam Dost
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Neda Najafinobar
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 43138 Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Michael E Kurczy
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism CVRM, BioPharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
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6
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Nguyen TD, Mellander L, Lork A, Thomen A, Philipsen M, Kurczy ME, Phan NT, Ewing AG. Visualization of Partial Exocytotic Content Release and Chemical Transport into Nanovesicles in Cells. ACS NANO 2022; 16:4831-4842. [PMID: 35189057 PMCID: PMC8945366 DOI: 10.1021/acsnano.2c00344] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
For decades, "all-or-none" and "kiss-and-run" were thought to be the only major exocytotic release modes in cell-to-cell communication, while the significance of partial release has not yet been widely recognized and accepted owing to the lack of direct evidence for exocytotic partial release. Correlative imaging with transmission electron microscopy and NanoSIMS imaging and a dual stable isotope labeling approach was used to study the cargo status of vesicles before and after exocytosis; demonstrating a measurable loss of transmitter in individual vesicles following stimulation due to partial release. Model secretory cells were incubated with 13C-labeled l-3,4-dihydroxyphenylalanine, resulting in the loading of 13C-labeled dopamine into their vesicles. A second label, di-N-desethylamiodarone, having the stable isotope 127I, was introduced during stimulation. A significant drop in the level of 13C-labeled dopamine and a reduction in vesicle size, with an increasing level of 127I-, was observed in vesicles of stimulated cells. Colocalization of 13C and 127I- in several vesicles was observed after stimulation. Thus, chemical visualization shows transient opening of vesicles to the exterior of the cell without full release the dopamine cargo. We present a direct calculation for the fraction of neurotransmitter release from combined imaging data. The average vesicular release is 60% of the total catecholamine. An important observation is that extracellular molecules can be introduced to cells during the partial exocytotic release process. This nonendocytic transport process appears to be a general route of entry that might be exploited pharmacologically.
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Affiliation(s)
- Tho Duc
Khanh Nguyen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Lisa Mellander
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Alicia Lork
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Aurélien Thomen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Mai Philipsen
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg SE-412 96, Sweden
| | - Michael E. Kurczy
- DMPK,
Research and Early Development, Cardiovascular, Renal and Metabolism
(CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg S-431 83, Sweden
| | - Nhu T.N. Phan
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Andrew G. Ewing
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
- E-mail:
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7
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Subirana MA, Riemschneider S, Hause G, Dobritzsch D, Schaumlöffel D, Herzberg M. High spatial resolution imaging of subcellular macro and trace element distribution during phagocytosis. Metallomics 2022; 14:6530650. [PMID: 35179212 DOI: 10.1093/mtomcs/mfac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022]
Abstract
The bioavailability of trace elements in the course of evolution had an essential influence on the emergence of life itself. This is reflected in the co-evolution between eukaryotes and prokaryotes. In this study, the influence and cellular distribution of bioelements during phagocytosis at the host-pathogen interface was investigated using high-resolution nanoscale secondary ion mass spectrometry (NanoSIMS) and quantitative inductively coupled plasma mass spectrometry (ICP-MS). In the eukaryotic murine macrophages (RAW 264.7 cell line), the cellular Fe / Zn ratio was found to be balanced, whereas the dominance of iron in the prokaryotic cells of the pathogen Salmonella enterica Serovar Enteritidis was about 90% compared to zinc. This confirms the evolutionary increased zinc requirement of the eukaryotic animal cell. Using NanoSIMS, the Cs+ primary ion source allowed high spatial resolution mapping of cell morphology down to subcellular level. At a comparable resolution, several low abundant trace elements could be mapped during phagocytosis with a RF plasma O- primary ion source. An enrichment of copper and nickel could be detected in the prokaryotic cells. Surprisingly, an accumulation of cobalt in the area of nuclear envelope was observed indicating an interesting but still unknown distribution of this trace element in murine macrophages.
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Affiliation(s)
- Maria Angels Subirana
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France
| | - Sina Riemschneider
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103 Leipzig, Germany
| | - Gerd Hause
- Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Dirk Dobritzsch
- Martin-Luther-University Halle-Wittenberg, Core Facility - Proteomic Mass Spectrometry, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Dirk Schaumlöffel
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France.,Peoples' Friendship University of Russia (RUDN University), Mklukho-Maklaya str. 6, 117198 Moscow, Russia
| | - Martin Herzberg
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany
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8
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Zhu X, Xu T, Peng C, Wu S. Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues. Front Chem 2022; 9:782432. [PMID: 35186891 PMCID: PMC8850921 DOI: 10.3389/fchem.2021.782432] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or imaging mass spectrometry (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, and map hundreds of biomolecules, such as peptides, proteins, lipid, and other organic compounds in cells and tissues. So far, although several soft ionization techniques, such as desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS) have been used for imaging biomolecules, matrix-assisted laser desorption/ionization (MALDI) is still the most widespread MSI scanning method. Here, we aim to provide a comprehensive review of MALDI-MSI with an emphasis on its advances of the instrumentation, methods, application, and future directions in single cell and biological tissues.
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Affiliation(s)
- Xiaoping Zhu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianyi Xu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Shihua Wu, ; Shihua Wu,
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9
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Noun M, Akoumeh R, Abbas I. Cell and Tissue Imaging by TOF-SIMS and MALDI-TOF: An Overview for Biological and Pharmaceutical Analysis. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-26. [PMID: 34809729 DOI: 10.1017/s1431927621013593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of mass spectrometry imaging (MSI) has been demonstrated in cell and tissue research since 1970. MSI can reveal the spatial distribution of a wide range of atomic and molecular ions detected from biological sample surfaces, it is a powerful and valuable technique used to monitor and detect diverse chemical and biological compounds, such as drugs, lipids, proteins, and DNA. MSI techniques, notably matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and time of flight secondary ion mass spectrometry (TOF-SIMS), witnessed a dramatic upsurge in studying and investigating biological samples especially, cells and tissue sections. This advancement is attributed to the submicron lateral resolution, the high sensitivity, the good precision, and the accurate chemical specificity, which make these techniques suitable for decoding and understanding complex mechanisms of certain diseases, as well as monitoring the spatial distribution of specific elements, and compounds. While the application of both techniques for the analysis of cells and tissues is thoroughly discussed, a briefing of MALDI-TOF and TOF-SIMS basis and the adequate sampling before analysis are briefly covered. The importance of MALDI-TOF and TOF-SIMS as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields is highlighted through representative published studies.
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Affiliation(s)
- Manale Noun
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Rayane Akoumeh
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Imane Abbas
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
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10
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Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
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Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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11
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Taskin MB, Ahmad T, Wistlich L, Meinel L, Schmitz M, Rossi A, Groll J. Bioactive Electrospun Fibers: Fabrication Strategies and a Critical Review of Surface-Sensitive Characterization and Quantification. Chem Rev 2021; 121:11194-11237. [DOI: 10.1021/acs.chemrev.0c00816] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mehmet Berat Taskin
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Taufiq Ahmad
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Laura Wistlich
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry and Helmholtz Institute for RNA Based Infection Research, 97074 Würzburg, Germany
| | - Michael Schmitz
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Angela Rossi
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Jürgen Groll
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
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12
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He C, Migawa MT, Chen K, Weston TA, Tanowitz M, Song W, Guagliardo P, Iyer KS, Bennett CF, Fong LG, Seth PP, Young SG, Jiang H. High-resolution visualization and quantification of nucleic acid-based therapeutics in cells and tissues using Nanoscale secondary ion mass spectrometry (NanoSIMS). Nucleic Acids Res 2021; 49:1-14. [PMID: 33275144 PMCID: PMC7797060 DOI: 10.1093/nar/gkaa1112] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/27/2020] [Accepted: 11/04/2020] [Indexed: 01/19/2023] Open
Abstract
Nucleic acid therapeutics (NATs) have proven useful in promoting the degradation of specific transcripts, modifying gene expression, and regulating mRNA splicing. In each situation, efficient delivery of nucleic acids to cells, tissues and intracellular compartments is crucial—both for optimizing efficacy and reducing side effects. Despite successes in NATs, our understanding of their cellular uptake and distribution in tissues is limited. Current methods have yielded insights into distribution of NATs within cells and tissues, but the sensitivity and resolution of these approaches are limited. Here, we show that nanoscale secondary ion mass spectrometry (NanoSIMS) imaging can be used to define the distribution of 5-bromo-2′-deoxythymidine (5-BrdT) modified antisense oligonucleotides (ASO) in cells and tissues with high sensitivity and spatial resolution. This approach makes it possible to define ASO uptake and distribution in different subcellular compartments and to quantify the impact of targeting ligands designed to promote ASO uptake by cells. Our studies showed that phosphorothioate ASOs are associated with filopodia and the inner nuclear membrane in cultured cells, and also revealed substantial cellular and subcellular heterogeneity of ASO uptake in mouse tissues. NanoSIMS imaging represents a significant advance in visualizing uptake and distribution of NATs; this approach will be useful in optimizing efficacy and delivery of NATs for treating human disease.
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Affiliation(s)
- Cuiwen He
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Kai Chen
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Thomas A Weston
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Wenxin Song
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | | | - Loren G Fong
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Stephen G Young
- Department of Medicine, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Haibo Jiang
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia.,Department of Chemistry, The University of Hong Kong, Hong Kong, China
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13
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Correlative light electron ion microscopy reveals in vivo localisation of bedaquiline in Mycobacterium tuberculosis-infected lungs. PLoS Biol 2020; 18:e3000879. [PMID: 33382684 PMCID: PMC7810513 DOI: 10.1371/journal.pbio.3000879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/15/2021] [Accepted: 12/22/2020] [Indexed: 12/26/2022] Open
Abstract
Correlative light, electron, and ion microscopy (CLEIM) offers huge potential to track the intracellular fate of antibiotics, with organelle-level resolution. However, a correlative approach that enables subcellular antibiotic visualisation in pathogen-infected tissue is lacking. Here, we developed correlative light, electron, and ion microscopy in tissue (CLEIMiT) and used it to identify the cell type–specific accumulation of an antibiotic in lung lesions of mice infected with Mycobacterium tuberculosis. Using CLEIMiT, we found that the anti-tuberculosis (TB) drug bedaquiline (BDQ) is localised not only in foamy macrophages in the lungs during infection but also accumulate in polymorphonuclear (PMN) cells. This study uses correlative light, electron and ion microscopy (CLEIM) in vivo to reveal the intracellular fate of an antibiotic in lung lesions of mice infected with Mycobacterium tuberculosis, with organelle-level resolution.
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14
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Lorenz M, Wagner R, Jesse S, Marsh JM, Mamak M, Proksch R, Ovchinnikova OS. Nanoscale Mass Spectrometry Multimodal Imaging via Tip-Enhanced Photothermal Desorption. ACS NANO 2020; 14:16791-16802. [PMID: 33232114 DOI: 10.1021/acsnano.0c05019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Materials ranging from adhesives, pharmaceuticals, lubricants, and personal care products are traditionally studied using macroscopic characterization techniques. However, their functionality is in reality defined by details of chemical organization on often noncrystalline matter with characteristic length scales on the order of microns to nanometers. Additionally, these materials are traditionally difficult to analyze using standard vacuum-based approaches that provide nanoscale chemical characterization due to their volatile and beam-sensitive nature. Therefore, approaches that operate under ambient conditions need to be developed that allow probing of nanoscale chemical phenomena and correlated functionality. Here, we demonstrate a tool for probing and visualizing local chemical environments and correlating them to material structure and functionality using advanced multimodal chemical imaging on a combined atomic force microscopy (AFM) and mass spectrometry (MS) system using tip-enhanced photothermal desorption with atmospheric pressure chemical ionization (APCI). We demonstrate enhanced performance metrics of the technique for correlated imaging and point sampling and illustrate the applicability for the analysis of trace chemicals on a human hair, additives in adhesives on paper, and pharmaceuticals samples notoriously difficult to analyze in a vacuum environment. Overall, this approach of correlating local chemical environments to structure and functionality is key to advancing research in many fields ranging from biology, to medicine, to material science.
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Affiliation(s)
- Matthias Lorenz
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ryan Wagner
- Asylum Research an Oxford Instruments Company, Santa Barbara, California 93117, United States
| | - Stephen Jesse
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | | | - Marc Mamak
- Procter & Gamble Company, Cincinnati, Ohio 45202, United States
| | - Roger Proksch
- Asylum Research an Oxford Instruments Company, Santa Barbara, California 93117, United States
| | - Olga S Ovchinnikova
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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15
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Zhang L, Jiang H, Wang WX. Subcellular Imaging of Localization and Transformation of Silver Nanoparticles in the Oyster Larvae. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11434-11442. [PMID: 32786557 DOI: 10.1021/acs.est.0c03342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To accurately assess the behavior and toxicity of silver nanoparticles (AgNPs), it is essential to understand their subcellular distribution and biotransformation. We combined both nanoscale secondary ion mass spectrometry (NanoSIMS) and electron microscopy to investigate the subcellular localization of Ag and in situ chemical distribution in the oyster larvae Crassostrea angulata after exposure to isotopically enriched 109AgNPs. Oyster larvae directly ingested particulate Ag, and in vivo dissolution of AgNPs occurred. The results collectively showed that AgNPs were much less bioavailable than Ag+, and the intracellular Ag was mainly originated from the soluble Ag, especially those dissolved from the ingested AgNPs. AgNPs absorbed on the cell membranes continued to release Ag ions, forming inorganic Ag-S complexes extracellularly, while Ag-organosulfur complexes were predominantly formed intracellularly. The internalized Ag could bind to the sulfur-rich molecules (S-donors) in the cytosol and/or be sequestered in the lysosomes of velum, esophagus, and stomach cells, as well as in the digestive vacuoles of digestive cells, which could act as a detoxification pathway for the oyster larvae. Ag was also occasionally incorporated into the phosphate granules, rough endoplasmic reticulum, and mitochondria. Our work provided definite evidence for the partial sulfidation of AgNPs after interaction with oyster larvae and shed new light on the bioavailability and fate of nanoparticles in marine environment.
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Affiliation(s)
- Luqing Zhang
- Marine Environmental Laboratory, Shenzhen Research Institute, HKUST, Shenzhen 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Haibo Jiang
- School of Molecular Sciences, University of Western Australia, Perth, Washington 6009, Australia
| | - Wen-Xiong Wang
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hongkong, Kowloon, Hong Kong
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16
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Agudelo CW, Samaha G, Garcia-Arcos I. Alveolar lipids in pulmonary disease. A review. Lipids Health Dis 2020; 19:122. [PMID: 32493486 PMCID: PMC7268969 DOI: 10.1186/s12944-020-01278-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Lung lipid metabolism participates both in infant and adult pulmonary disease. The lung is composed by multiple cell types with specialized functions and coordinately acting to meet specific physiologic requirements. The alveoli are the niche of the most active lipid metabolic cell in the lung, the type 2 cell (T2C). T2C synthesize surfactant lipids that are an absolute requirement for respiration, including dipalmitoylphosphatidylcholine. After its synthesis and secretion into the alveoli, surfactant is recycled by the T2C or degraded by the alveolar macrophages (AM). Surfactant biosynthesis and recycling is tightly regulated, and dysregulation of this pathway occurs in many pulmonary disease processes. Alveolar lipids can participate in the development of pulmonary disease from their extracellular location in the lumen of the alveoli, and from their intracellular location in T2C or AM. External insults like smoke and pollution can disturb surfactant homeostasis and result in either surfactant insufficiency or accumulation. But disruption of surfactant homeostasis is also observed in many chronic adult diseases, including chronic obstructive pulmonary disease (COPD), and others. Sustained damage to the T2C is one of the postulated causes of idiopathic pulmonary fibrosis (IPF), and surfactant homeostasis is disrupted during fibrotic conditions. Similarly, surfactant homeostasis is impacted during acute respiratory distress syndrome (ARDS) and infections. Bioactive lipids like eicosanoids and sphingolipids also participate in chronic lung disease and in respiratory infections. We review the most recent knowledge on alveolar lipids and their essential metabolic and signaling functions during homeostasis and during some of the most commonly observed pulmonary diseases.
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Affiliation(s)
- Christina W Agudelo
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, 11203, USA
| | - Ghassan Samaha
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, 11203, USA
| | - Itsaso Garcia-Arcos
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, 11203, USA.
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17
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Thomen A, Najafinobar N, Penen F, Kay E, Upadhyay PP, Li X, Phan NTN, Malmberg P, Klarqvist M, Andersson S, Kurczy ME, Ewing AG. Subcellular Mass Spectrometry Imaging and Absolute Quantitative Analysis across Organelles. ACS NANO 2020; 14:4316-4325. [PMID: 32239916 PMCID: PMC7199216 DOI: 10.1021/acsnano.9b09804] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/02/2020] [Indexed: 05/22/2023]
Abstract
Mass spectrometry imaging is a field that promises to become a mainstream bioanalysis technology by allowing the combination of single-cell imaging and subcellular quantitative analysis. The frontier of single-cell imaging has advanced to the point where it is now possible to compare the chemical contents of individual organelles in terms of raw or normalized ion signal. However, to realize the full potential of this technology, it is necessary to move beyond this concept of relative quantification. Here we present a nanoSIMS imaging method that directly measures the absolute concentration of an organelle-associated, isotopically labeled, pro-drug directly from a mass spectrometry image. This is validated with a recently developed nanoelectrochemistry method for single organelles. We establish a limit of detection based on the number of isotopic labels used and the volume of the organelle of interest, also offering this calculation as a web application. This approach allows subcellular quantification of drugs and metabolites, an overarching and previously unmet goal in cell science and pharmaceutical development.
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Affiliation(s)
- Aurélien Thomen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
| | - Neda Najafinobar
- Medicinal
Chemistry, Research and Early Development, Respiratory, Inflammation,
and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Florent Penen
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg, 412 96, Sweden
| | - Emma Kay
- Bioscience,
Research and Early Development, Cardiovascular, Renal and Metabolism,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Pratik P. Upadhyay
- Pharmaceutical
Technolgy and Development, AstraZeneca R&D, Gothenburg, 430 52, Sweden
| | - Xianchan Li
- Center
for Imaging and Systems Biology, College of Life and Environmental
Sciences, Minzu University of China, Beijing, 100081, China
| | - Nhu T. N. Phan
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
| | - Per Malmberg
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg, 412 96, Sweden
| | - Magnus Klarqvist
- Early
Product Development, Pharmaceutical Science, R&D, AstraZeneca, Gothenburg, 431 50, Sweden
| | - Shalini Andersson
- New Modalities,
Discovery Sciences, R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Michael E. Kurczy
- DMPK,
Research and Early Development, Cardiovascular, Renal and Metabolism,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Andrew G. Ewing
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
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18
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Subcellular Chemical Imaging: New Avenues in Cell Biology. Trends Cell Biol 2020; 30:173-188. [DOI: 10.1016/j.tcb.2019.12.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/10/2019] [Accepted: 12/17/2019] [Indexed: 12/31/2022]
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19
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Exploring the Fundamental Structures of Life: Non-Targeted, Chemical Analysis of Single Cells and Subcellular Structures. Angew Chem Int Ed Engl 2019; 58:9348-9364. [PMID: 30500998 PMCID: PMC6542728 DOI: 10.1002/anie.201811951] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 01/14/2023]
Abstract
Cells are a basic functional and structural unit of living organisms. Both unicellular communities and multicellular species produce an astonishing chemical diversity, enabling a wide range of divergent functions, yet each cell shares numerous aspects that are common to all living organisms. While there are many approaches for studying this chemical diversity, only a few are non-targeted and capable of analyzing hundreds of different chemicals at cellular resolution. Here, we review the non-targeted approaches used to perform comprehensive chemical analyses, provide chemical imaging information, or obtain high-throughput single-cell profiling data. Single-cell measurement capabilities are rapidly increasing in terms of throughput, limits of detection, and completeness of the chemical analyses; these improvements enable their application to understand ever more complex physiological phenomena, such as learning, memory, and behavior.
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Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Thanh D. Do
- Department of Chemistry, 1420 Circle Drive, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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20
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LaLone V, Fawaz MV, Morales-Mercado J, Mourão MA, Snyder CS, Kim SY, Lieberman AP, Tuteja A, Mehta G, Standiford TJ, Raghavendran K, Shedden K, Schwendeman A, Stringer KA, Rosania GR. Inkjet-printed micro-calibration standards for ultraquantitative Raman spectral cytometry. Analyst 2019; 144:3790-3799. [PMID: 31116195 PMCID: PMC6711383 DOI: 10.1039/c9an00500e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report the development of a cytometric analysis platform for measuring the contents of individual cells in absolute (picogram) scales; this study represents the first report of Raman-based quantitation of the absolute mass - or the total amount - of multiple endogenous biomolecules within single-cells. To enable ultraquantitative calibration, we engineered single-cell-sized micro-calibration standards of known composition by inkjet-printer deposition of biomolecular components in microarrays across the surface of silicon chips. We demonstrate clinical feasibility by characterizing the compositional phenotype of human skin fibroblast and porcine alveolar macrophage cell populations in the respective contexts of Niemann-Pick disease and drug-induced phospholipidosis: two types of lipid storage disorders. We envision this microanalytical platform as the foundation for many future biomedical applications, ranging from diagnostic assays to pathological analysis to advanced pharmaco/toxicokinetic research studies.
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Affiliation(s)
- Vernon LaLone
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Maria V Fawaz
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jomar Morales-Mercado
- School of Sciences, Technology, and Environment, Universidad Ana G. Méndez Cupey Campus, San Juan, Puerto Rico
| | - Márcio A Mourão
- CSCAR Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Catherine S Snyder
- Department of Materials Science and Engineering, College of Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sang Yeop Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Andrew P Lieberman
- Department of Pathology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Anish Tuteja
- Department of Materials Science and Engineering, College of Engineering, University of Michigan, Ann Arbor, MI 48109, USA and Biointerfaces Institute, Macromolecular Science and Engineering, Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Geeta Mehta
- Department of Materials Science and Engineering, College of Engineering, University of Michigan, Ann Arbor, MI 48109, USA and Department of Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Theodore J Standiford
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Krishnan Raghavendran
- Department of Surgery, Michigan Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Kerby Shedden
- CSCAR Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Kathleen A Stringer
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI 48109, USA and Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gus R Rosania
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
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21
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Erforschung der fundamentalen Strukturen des Lebens: Nicht zielgerichtete chemische Analyse von Einzelzellen und subzellulären Strukturen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Thanh D. Do
- Department of ChemistryUniversity of Tennessee 1420 Circle Drive Knoxville TN 37996 USA
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
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22
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Schulz S, Becker M, Groseclose MR, Schadt S, Hopf C. Advanced MALDI mass spectrometry imaging in pharmaceutical research and drug development. Curr Opin Biotechnol 2019; 55:51-59. [DOI: 10.1016/j.copbio.2018.08.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/21/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
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23
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Belianinov A, Ievlev AV, Lorenz M, Borodinov N, Doughty B, Kalinin SV, Fernández FM, Ovchinnikova OS. Correlated Materials Characterization via Multimodal Chemical and Functional Imaging. ACS NANO 2018; 12:11798-11818. [PMID: 30422627 PMCID: PMC9850281 DOI: 10.1021/acsnano.8b07292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Multimodal chemical imaging simultaneously offers high-resolution chemical and physical information with nanoscale and, in select cases, atomic resolution. By coupling modalities that collect physical and chemical information, we can address scientific problems in biological systems, battery and fuel cell research, catalysis, pharmaceuticals, photovoltaics, medicine, and many others. The combined systems enable the local correlation of material properties with chemical makeup, making fundamental questions of how chemistry and structure drive functionality approachable. In this Review, we present recent progress and offer a perspective for chemical imaging used to characterize a variety of samples by a number of platforms. Specifically, we present cases of infrared and Raman spectroscopies combined with scanning probe microscopy; optical microscopy and mass spectrometry; nonlinear optical microscopy; and, finally, ion, electron, and probe microscopies with mass spectrometry. We also discuss the challenges associated with the use of data originated by the combinatorial hardware, analysis, and machine learning as well as processing tools necessary for the interpretation of multidimensional data acquired from multimodal studies.
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Affiliation(s)
- Alex Belianinov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Anton V. Ievlev
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Matthias Lorenz
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nikolay Borodinov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Benjamin Doughty
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sergei V. Kalinin
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology and Petit Institute for Biochemistry and Bioscience, Atlanta, Georgia 30332, United States
| | - Olga S. Ovchinnikova
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Corresponding Author:
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24
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Lenz B, Braendli-Baiocco A, Engelhardt J, Fant P, Fischer H, Francke S, Fukuda R, Gröters S, Harada T, Harleman H, Kaufmann W, Kustermann S, Nolte T, Palazzi X, Pohlmeyer-Esch G, Popp A, Romeike A, Schulte A, Lima BS, Tomlinson L, Willard J, Wood CE, Yoshida M. Characterizing Adversity of Lysosomal Accumulation in Nonclinical Toxicity Studies: Results from the 5th ESTP International Expert Workshop. Toxicol Pathol 2018; 46:224-246. [PMID: 29471779 DOI: 10.1177/0192623317749452] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lysosomes have a central role in cellular catabolism, trafficking, and processing of foreign particles. Accumulation of endogenous and exogenous materials in lysosomes represents a common finding in nonclinical toxicity studies. Histologically, these accumulations often lack distinctive features indicative of lysosomal or cellular dysfunction, making it difficult to consistently interpret and assign adverse dose levels. To help address this issue, the European Society of Toxicologic Pathology organized a workshop where representative types of lysosomal accumulation induced by pharmaceuticals and environmental chemicals were presented and discussed. The expert working group agreed that the diversity of lysosomal accumulations requires a case-by-case weight-of-evidence approach and outlined several factors to consider in the adversity assessment, including location and type of cell affected, lysosomal contents, severity of the accumulation, and related pathological effects as evidence of cellular or organ dysfunction. Lysosomal accumulations associated with cytotoxicity, inflammation, or fibrosis were generally considered to be adverse, while those found in isolation (without morphologic or functional consequences) were not. Workshop examples highlighted the importance of thoroughly characterizing the biological context of lysosomal effects, including mechanistic data and functional in vitro readouts if available. The information provided here should facilitate greater consistency and transparency in the interpretation of lysosomal effects.
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Affiliation(s)
- B Lenz
- 1 Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - A Braendli-Baiocco
- 1 Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - J Engelhardt
- 2 Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - P Fant
- 3 Charles River Laboratories, Lyon, France
| | - H Fischer
- 1 Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - S Francke
- 4 Center for Food Safety and Applied Nutrition (CFSAN), U.S. Food and Drug Administration, College Park, Maryland, USA
| | - R Fukuda
- 5 Axcelead Drug Discovery Partners, Inc., Kanagawa, Japan
| | - S Gröters
- 6 Department of Experimental Toxicology and Ecology, BASF SE, Ludwigshafen, Germany
| | - T Harada
- 7 Institute of Environmental Toxicology, Ibaraki, Japan
| | - H Harleman
- 8 Global Medical, Clinical and Regulatory Affairs, Global Preclinical Development and Management, Fresenius-Kabi Deutschland GmbH, Bad Homburg, Germany
| | | | - S Kustermann
- 1 Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - T Nolte
- 10 Nonclinical Drug Safety Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - X Palazzi
- 11 Global Pathology, DSRD, Pfizer WRD, Groton, Connecticut, USA
| | - G Pohlmeyer-Esch
- 10 Nonclinical Drug Safety Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - A Popp
- 12 Global Preclinical Safety, AbbVie, Ludwigshafen, Germany
| | - A Romeike
- 13 Covance Laboratories, Inc., Rueil-Malmaison, France
| | - A Schulte
- 14 Department of Chemicals and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - B Silva Lima
- 15 Department of Pharmacological Sciences, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - L Tomlinson
- 11 Global Pathology, DSRD, Pfizer WRD, Groton, Connecticut, USA
| | - J Willard
- 16 CDER, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - C E Wood
- 17 Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - M Yoshida
- 18 Food Safety Commission, Cabinet Office, Tokyo, Japan
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25
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Nuñez JR, Anderton CR, Renslow RS. Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data. PLoS One 2018; 13:e0199239. [PMID: 30067751 PMCID: PMC6070163 DOI: 10.1371/journal.pone.0199239] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/04/2018] [Indexed: 11/24/2022] Open
Abstract
Color vision deficiency (CVD) affects more than 4% of the population and leads to a different visual perception of colors. Though this has been known for decades, colormaps with many colors across the visual spectra are often used to represent data, leading to the potential for misinterpretation or difficulty with interpretation by someone with this deficiency. Until the creation of the module presented here, there were no colormaps mathematically optimized for CVD using modern color appearance models. While there have been some attempts to make aesthetically pleasing or subjectively tolerable colormaps for those with CVD, our goal was to make optimized colormaps for the most accurate perception of scientific data by as many viewers as possible. We developed a Python module, cmaputil, to create CVD-optimized colormaps, which imports colormaps and modifies them to be perceptually uniform in CVD-safe colorspace while linearizing and maximizing the brightness range. The module is made available to the science community to enable others to easily create their own CVD-optimized colormaps. Here, we present an example CVD-optimized colormap created with this module that is optimized for viewing by those without a CVD as well as those with red-green colorblindness. This colormap, cividis, enables nearly-identical visual-data interpretation to both groups, is perceptually uniform in hue and brightness, and increases in brightness linearly.
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Affiliation(s)
- Jamie R. Nuñez
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Christopher R. Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ryan S. Renslow
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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26
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Imaging Mass Microscopy of Kidneys from Azithromycin-Treated Rats with Phospholipidosis. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1993-2003. [PMID: 29981744 DOI: 10.1016/j.ajpath.2018.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 05/11/2018] [Accepted: 05/29/2018] [Indexed: 11/23/2022]
Abstract
Drug-induced phospholipidosis is a lysosomal storage disorder characterized by the excess accumulation of tissue phospholipids. Although azithromycin can be used to induce phospholipidosis, no experimental studies evaluating the relationship between drug accumulation and phospholipid localization have been performed. In this study, azithromycin was orally administered to rats for 7 days, and the relationship between drug and phospholipid accumulation was performed using imaging mass microscopy. The administration of azithromycin induced tubular epithelial vacuolation in the inner stripe of the outer medulla of the kidney, consistent with the lamellar bodies that are typical manifestations of drug-induced phospholipidosis. Azithromycin and phospholipid tissue levels were extensively elevated in the kidneys of azithromycin-treated rats. Imaging mass microscopy revealed that both azithromycin and its metabolites were found in the kidneys of azithromycin-treated rats but not in control animals. The vacuolated areas of the kidneys were primarily found in the inner stripe of the outer medulla, consistent with the areas of high azithromycin concentration. Azithromycin was colocalized with several phospholipids-phosphatidylinositol (18:0/20:4), phosphatidylethanolamine (18:0/20:4 and 16:0/20:4), and possibly didocosahexaenoyl (C22:6)-bis(monoacylglycerol) phosphate, a putative biomarker of drug-induced phospholipidosis. In summary, we found correlations between regions of kidney damage and the accumulation of azithromycin, its metabolites, and phospholipids using imaging mass microscopy. Such analyses may help reveal the mechanism and identify putative biomarkers of drug-induced phospholipidosis.
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Montes-Bayón M, Sharar M, Corte-Rodriguez M. Trends on (elemental and molecular) mass spectrometry based strategies for speciation and metallomics. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.09.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhang L, Vertes A. Einzelzell‐Massenspektrometrie zur Untersuchung zellulärer Heterogenität. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709719] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Linwen Zhang
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Akos Vertes
- Department of Chemistry The George Washington University Washington DC 20052 USA
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Zhang L, Vertes A. Single‐Cell Mass Spectrometry Approaches to Explore Cellular Heterogeneity. Angew Chem Int Ed Engl 2018; 57:4466-4477. [DOI: 10.1002/anie.201709719] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/27/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Linwen Zhang
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Akos Vertes
- Department of Chemistry The George Washington University Washington DC 20052 USA
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30
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Howes SC, Koning RI, Koster AJ. Correlative microscopy for structural microbiology. Curr Opin Microbiol 2018; 43:132-138. [PMID: 29414444 DOI: 10.1016/j.mib.2018.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/12/2018] [Accepted: 01/14/2018] [Indexed: 10/18/2022]
Abstract
Understanding how microbes utilize their environment is aided by visualizing them in their natural context at high resolution. Correlative imaging enables efficient targeting and identification of labelled viral and bacterial components by light microscopy combined with high resolution imaging by electron microscopy. Advances in genetic and bioorthogonal labelling, improved workflows for targeting and image correlation, and large-scale data collection are increasing the applicability of correlative imaging methods. Furthermore, developments in mass spectroscopy and soft X-ray imaging are expanding the correlative imaging modalities available. Investigating the structure and organization of microbes within their host by combined imaging methods provides important insights into mechanisms of infection and disease which cannot be obtained by other techniques.
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Affiliation(s)
- Stuart C Howes
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Roman I Koning
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands; Netherlands Centre for Electron Nanoscopy, Institute of Biology, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Abraham J Koster
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands; Netherlands Centre for Electron Nanoscopy, Institute of Biology, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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Sekine R, Moore KL, Matzke M, Vallotton P, Jiang H, Hughes GM, Kirby JK, Donner E, Grovenor CRM, Svendsen C, Lombi E. Complementary Imaging of Silver Nanoparticle Interactions with Green Algae: Dark-Field Microscopy, Electron Microscopy, and Nanoscale Secondary Ion Mass Spectrometry. ACS NANO 2017; 11:10894-10902. [PMID: 29061049 DOI: 10.1021/acsnano.7b04556] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Increasing consumer use of engineered nanomaterials has led to significantly increased efforts to understand their potential impact on the environment and living organisms. Currently, no individual technique can provide all the necessary information such as their size, distribution, and chemistry in complex biological systems. Consequently, there is a need to develop complementary instrumental imaging approaches that provide enhanced understanding of these "bio-nano" interactions to overcome the limitations of individual techniques. Here we used a multimodal imaging approach incorporating dark-field light microscopy, high-resolution electron microscopy, and nanoscale secondary ion mass spectrometry (NanoSIMS). The aim was to gain insight into the bio-nano interactions of surface-functionalized silver nanoparticles (Ag-NPs) with the green algae Raphidocelis subcapitata, by combining the fidelity, spatial resolution, and elemental identification offered by the three techniques, respectively. Each technique revealed that Ag-NPs interact with the green algae with a dependence on the size (10 nm vs 60 nm) and surface functionality (tannic acid vs branched polyethylenimine, bPEI) of the NPs. Dark-field light microscopy revealed the presence of strong light scatterers on the algal cell surface, and SEM imaging confirmed their nanoparticulate nature and localization at nanoscale resolution. NanoSIMS imaging confirmed their chemical identity as Ag, with the majority of signal concentrated at the cell surface. Furthermore, SEM and NanoSIMS provided evidence of 10 nm bPEI Ag-NP internalization at higher concentrations (40 μg/L), correlating with the highest toxicity observed from these NPs. This multimodal approach thus demonstrated an effective approach to complement dose-response studies in nano-(eco)-toxicological investigations.
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Affiliation(s)
- Ryo Sekine
- Future Industries Institute, University of South Australia , Building X, Mawson Lakes Campus, Adelaide, SA 5095, Australia
- Centre for Ecology and Hydrology , Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, United Kingdom
| | - Katie L Moore
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
- School of Materials, The University of Manchester , Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Marianne Matzke
- Centre for Ecology and Hydrology , Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, United Kingdom
| | - Pascal Vallotton
- Institute für Biochemie, ETH Zurich , Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia , 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Haibo Jiang
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
- CSIRO Land and Water, Environmental Contaminant Mitigation and Biotechnology Program , Waite Campus, Waite Road, Perth, SA 5064, Australia
| | - Gareth M Hughes
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
| | - Jason K Kirby
- CSIRO Land and Water, Environmental Contaminant Mitigation and Biotechnology Program , Waite Campus, Waite Road, Perth, SA 5064, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia , Building X, Mawson Lakes Campus, Adelaide, SA 5095, Australia
| | - Chris R M Grovenor
- Department of Materials, The University of Oxford , Parks Road, Oxford, OX1 3PH, United Kingdom
| | - Claus Svendsen
- Centre for Ecology and Hydrology , Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, United Kingdom
| | - Enzo Lombi
- Future Industries Institute, University of South Australia , Building X, Mawson Lakes Campus, Adelaide, SA 5095, Australia
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Passarelli MK, Pirkl A, Moellers R, Grinfeld D, Kollmer F, Havelund R, Newman CF, Marshall PS, Arlinghaus H, Alexander MR, West A, Horning S, Niehuis E, Makarov A, Dollery CT, Gilmore IS. The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power. Nat Methods 2017; 14:1175-1183. [DOI: 10.1038/nmeth.4504] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
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Abstract
Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.
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