1
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Lincy-Bianchi L, Häfner M, Becquart C, Tängemo C, Kurczy ME, Munier CC, Knerr L. Incorporation of Intracellular NanoSIMS Tracers to Oligonucleotide Conjugates via Strain Promoted Sydnone-Alkyne Cycloaddition. Bioconjug Chem 2024; 35:912-921. [PMID: 38860868 DOI: 10.1021/acs.bioconjchem.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Extensive efforts have been dedicated to developing cell-specific targeting ligands that can be conjugated to therapeutic cargo, offering a promising yet still challenging strategy to deliver oligonucleotide therapeutics beyond the liver. Indeed, while the cargo and the ligand are crucial, the third component, the linker, is integral but is often overlooked. Here, we present strain-promoted sydnone-alkyne cycloaddition as a versatile linker chemistry for oligonucleotide synthesis, expanding the choices for bioconjugation of therapeutics while enabling subcellular detection of the linker and payload using nanoscale secondary ion mass spectrometry (NanoSIMS) imaging. This strategy was successfully applied to peptide and lipid ligands and profiled using the well characterized N-acetylgalactosamine (GalNAc) targeting ligand. The linker did not affect the expected activity of the conjugate and was detectable and distinguishable from the labeled cargo. Finally, this work not only offers a practical bioconjugation method but also enables the assessment of the linker's subcellular behavior, facilitating NanoSIMS imaging to monitor the three key components of therapeutic conjugates.
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Affiliation(s)
- Loujahine Lincy-Bianchi
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Maximilian Häfner
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Cécile Becquart
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Carolina Tängemo
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Michael E Kurczy
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Claire C Munier
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
| | - Laurent Knerr
- Medicinal Chemistry, Research and Development, Early Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden
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2
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Lu C, Chen G, Song W, Chen K, Hee C, Nikan M, Guagliardo P, Bennett CF, Seth P, Iyer KS, Young SG, Qi X, Jiang H. Tool to Resolve Distortions in Elemental and Isotopic Imaging. J Am Chem Soc 2024. [PMID: 38985464 DOI: 10.1021/jacs.4c05384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Nanoscale secondary ion mass spectrometry (NanoSIMS) makes it possible to visualize elements and isotopes in a wide range of samples at a high resolution. However, the fidelity and quality of NanoSIMS images often suffer from distortions because of a requirement to acquire and integrate multiple image frames. We developed an optical flow-based algorithm tool, NanoSIMS Stabilizer, for all-channel postacquisition registration of images. The NanoSIMS Stabilizer effectively deals with the distortions and artifacts, resulting in a high-resolution visualization of isotope and element distribution. It is open source with an easy-to-use ImageJ plugin and is accompanied by a Python version with GPU acceleration.
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Affiliation(s)
- Chixiang Lu
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Gu Chen
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Wenxin Song
- Departments of Medicine, University of California, Los Angeles, California 90095, United States
| | - Kai Chen
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Charmaine Hee
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Mehran Nikan
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth 6009, Australia
| | - C Frank Bennett
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | - Punit Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010, United States
| | | | - Stephen G Young
- Departments of Medicine, University of California, Los Angeles, California 90095, United States
- Human Genetics, University of California, Los Angeles, California 90095, United States
| | - Xiaojuan Qi
- Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Haibo Jiang
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
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3
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Chan YH, Pathmasiri KC, Pierre-Jacques D, Hibbard MC, Tao N, Fischer JL, Yang E, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics. Nat Commun 2024; 15:5036. [PMID: 38866734 PMCID: PMC11169460 DOI: 10.1038/s41467-024-49384-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
A technique capable of label-free detection, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of native biomolecules in intact specimens. However, MSI has often been precluded from single-cell applications due to the spatial resolution limit set forth by the physical and instrumental constraints of the method. By taking advantage of the reversible interaction between the analytes and a superabsorbent hydrogel, we have developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome the spatial resolution limits of modern mass spectrometers. With GAMSI, we show that the spatial resolution of MALDI-MSI can be enhanced ~3-6-fold to the sub-micrometer level without changing the existing mass spectrometry hardware or analysis pipeline. This approach will vastly enhance the accessibility of MSI-based spatial analysis at the cellular scale.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | - Maddison C Hibbard
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | | | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA.
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4
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Gewurz B, Guo R, Lim M, Shah H, Paulo J, Zhang Y, Yang H, Wang LW, Strebinger D, Smith N, Li M, Leong M, Lutchenkov M, Liang JH, Li Z, Wang Y, Puri R, Melnick A, Green M, Asara J, Papathanassiu A, Gygi S, Mootha V. Multi-omic Analysis of Human B-cell Activation Reveals a Key Lysosomal BCAT1 Role in mTOR Hyperactivation by B-cell receptor and TLR9. RESEARCH SQUARE 2024:rs.3.rs-4413958. [PMID: 38854072 PMCID: PMC11160916 DOI: 10.21203/rs.3.rs-4413958/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
B-lymphocytes play major adaptive immune roles, producing antibody and driving T-cell responses. However, how immunometabolism networks support B-cell activation and differentiation in response to distinct receptor stimuli remains incompletely understood. To gain insights, we systematically investigated acute primary human B-cell transcriptional, translational and metabolomic responses to B-cell receptor (BCR), Toll-like receptor 9 (TLR9), CD40-ligand (CD40L), interleukin-4 (IL4) or combinations thereof. T-independent BCR/TLR9 co-stimulation, which drives malignant and autoimmune B-cell states, jointly induced PD-L1 plasma membrane expression, supported by NAD metabolism and oxidative phosphorylation. BCR/TLR9 also highly induced the transaminase BCAT1, which localized to lysosomal membranes to support branched chain amino acid synthesis and mTORC1 hyperactivation. BCAT1 inhibition blunted BCR/TLR9, but not CD40L/IL4-triggered B-cell proliferation, IL10 expression and BCR/TLR pathway-driven lymphoma xenograft outgrowth. These results provide a valuable resource, reveal receptor-mediated immunometabolism remodeling to support key B-cell phenotypes including PD-L1 checkpoint signaling, and identify BCAT1 as a novel B-cell therapeutic target.
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Affiliation(s)
| | | | - Matthew Lim
- Department of Cell Biology, Harvard Medical School
| | | | | | | | - Haopeng Yang
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center
| | | | | | | | - Meng Li
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine
| | | | | | | | | | | | - Rishi Puri
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University
| | | | - Michael Green
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center
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5
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Pegoraro C, Domingo-Ortí I, Conejos-Sánchez I, Vicent MJ. Unlocking the Mitochondria for Nanomedicine-based Treatments: Overcoming Biological Barriers, Improving Designs, and Selecting Verification Techniques. Adv Drug Deliv Rev 2024; 207:115195. [PMID: 38325562 DOI: 10.1016/j.addr.2024.115195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Enhanced targeting approaches will support the treatment of diseases associated with dysfunctional mitochondria, which play critical roles in energy generation and cell survival. Obstacles to mitochondria-specific targeting include the presence of distinct biological barriers and the need to pass through (or avoid) various cell internalization mechanisms. A range of studies have reported the design of mitochondrially-targeted nanomedicines that navigate the complex routes required to influence mitochondrial function; nonetheless, a significant journey lies ahead before mitochondrially-targeted nanomedicines become suitable for clinical use. Moving swiftly forward will require safety studies, in vivo assays confirming effectiveness, and methodologies to validate mitochondria-targeted nanomedicines' subcellular location/activity. From a nanomedicine standpoint, we describe the biological routes involved (from administration to arrival within the mitochondria), the features influencing rational design, and the techniques used to identify/validate successful targeting. Overall, rationally-designed mitochondria-targeted-based nanomedicines hold great promise for precise subcellular therapeutic delivery.
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Affiliation(s)
- Camilla Pegoraro
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inés Domingo-Ortí
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inmaculada Conejos-Sánchez
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - María J Vicent
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
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6
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Sun X, Yu Y, Qian K, Wang J, Huang L. Recent Progress in Mass Spectrometry-Based Single-Cell Metabolic Analysis. SMALL METHODS 2024; 8:e2301317. [PMID: 38032130 DOI: 10.1002/smtd.202301317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Single-cell analysis enables the measurement of biomolecules at the level of individual cells, facilitating in-depth investigations into cellular heterogeneity and precise interpretation of the related biological mechanisms. Among these biomolecules, cellular metabolites exhibit remarkable sensitivity to environmental and biochemical changes, unveiling a hidden world underlying cellular heterogeneity and allowing for the determination of cell physiological states. However, the metabolic analysis of single cells is challenging due to the extremely low concentrations, substantial content variations, and rapid turnover rates of cellular metabolites. Mass spectrometry (MS), characterized by its high sensitivity, wide dynamic range, and excellent selectivity, is employed in single-cell metabolic analysis. This review focuses on recent advances and applications of MS-based single-cell metabolic analysis, encompassing three key steps of single-cell isolation, detection, and application. It is anticipated that MS will bring profound implications in biomedical practices, serving as advanced tools to depict the single-cell metabolic landscape.
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Affiliation(s)
- Xuming Sun
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Yi Yu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
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7
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Gorman BL, Torti SV, Torti FM, Anderton CR. Mass spectrometry imaging of metals in tissues and cells: Methods and biological applications. Biochim Biophys Acta Gen Subj 2024; 1868:130329. [PMID: 36791830 PMCID: PMC10423302 DOI: 10.1016/j.bbagen.2023.130329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/24/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Metals are pervasive throughout biological processes, where they play essential structural and catalytic roles. Metals can also exhibit deleterious effects on human health. Powerful analytical techniques, such as mass spectrometry imaging (MSI), are required to map metals due to their low concentrations within biological tissue. SCOPE OF REVIEW This Mini Review focuses on key MSI technology that can image metal distributions in situ, describing considerations for each technique (e.g., resolution, sensitivity, etc.). We highlight recent work using MSI for mapping trace metals in tissues, detecting metal-based drugs, and simultaneously imaging metals and biomolecules. MAJOR CONCLUSIONS MSI has enabled significant advances in locating bioactive metals at high spatial resolution and correlating their distributions with that of biomolecules. The use of metal-based immunochemistry has enabled simultaneous high-throughput protein and biomolecule imaging. GENERAL SIGNIFICANCE The techniques and examples described herein can be applied to many biological questions concerning the important biological roles of metals, metal toxicity, and localization of metal-based drugs.
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Affiliation(s)
- Brittney L Gorman
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States of America
| | - Suzy V Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, United States of America
| | - Frank M Torti
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, United States of America
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States of America.
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8
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Rajbhandari P, Neelakantan TV, Hosny N, Stockwell BR. Spatial pharmacology using mass spectrometry imaging. Trends Pharmacol Sci 2024; 45:67-80. [PMID: 38103980 PMCID: PMC10842749 DOI: 10.1016/j.tips.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The emerging and powerful field of spatial pharmacology can map the spatial distribution of drugs and their metabolites, as well as their effects on endogenous biomolecules including metabolites, lipids, proteins, peptides, and glycans, without the need for labeling. This is enabled by mass spectrometry imaging (MSI) that provides previously inaccessible information in diverse phases of drug discovery and development. We provide a perspective on how MSI technologies and computational tools can be implemented to reveal quantitative spatial drug pharmacokinetics and toxicology, tissue subtyping, and associated biomarkers. We also highlight the emerging potential of comprehensive spatial pharmacology through integration of multimodal MSI data with other spatial technologies. Finally, we describe how to overcome challenges including improving reproducibility and compound annotation to generate robust conclusions that will improve drug discovery and development processes.
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Affiliation(s)
- Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Noreen Hosny
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA; Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Chemistry, Columbia University, New York, NY, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
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9
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Zhang YW, Schönberger K, Cabezas‐Wallscheid N. Bidirectional interplay between metabolism and epigenetics in hematopoietic stem cells and leukemia. EMBO J 2023; 42:e112348. [PMID: 38010205 PMCID: PMC10711668 DOI: 10.15252/embj.2022112348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 11/29/2023] Open
Abstract
During the last decades, remarkable progress has been made in further understanding the complex molecular regulatory networks that maintain hematopoietic stem cell (HSC) function. Cellular and organismal metabolisms have been shown to directly instruct epigenetic alterations, and thereby dictate stem cell fate, in the bone marrow. Epigenetic regulatory enzymes are dependent on the availability of metabolites to facilitate DNA- and histone-modifying reactions. The metabolic and epigenetic features of HSCs and their downstream progenitors can be significantly altered by environmental perturbations, dietary habits, and hematological diseases. Therefore, understanding metabolic and epigenetic mechanisms that regulate healthy HSCs can contribute to the discovery of novel metabolic therapeutic targets that specifically eliminate leukemia stem cells while sparing healthy HSCs. Here, we provide an in-depth review of the metabolic and epigenetic interplay regulating hematopoietic stem cell fate. We discuss the influence of metabolic stress stimuli, as well as alterations occurring during leukemic development. Additionally, we highlight recent therapeutic advancements toward eradicating acute myeloid leukemia cells by intervening in metabolic and epigenetic pathways.
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Affiliation(s)
- Yu Wei Zhang
- Max Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
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10
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Zeng Q, Xia MC, Yin X, Cheng S, Xue Z, Tan S, Gong X, Ye Z. Recent developments in ionization techniques for single-cell mass spectrometry. Front Chem 2023; 11:1293533. [PMID: 38130875 PMCID: PMC10733462 DOI: 10.3389/fchem.2023.1293533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The variation among individual cells plays a significant role in many biological functions. Single-cell analysis is advantageous for gaining insight into intricate biochemical mechanisms rarely accessible when studying tissues as a whole. However, measurement on a unicellular scale is still challenging due to unicellular complex composition, minute substance quantities, and considerable differences in compound concentrations. Mass spectrometry has recently gained extensive attention in unicellular analytical fields due to its exceptional sensitivity, throughput, and compound identification abilities. At present, single-cell mass spectrometry primarily concentrates on the enhancement of ionization methods. The principal ionization approaches encompass nanoelectrospray ionization (nano-ESI), laser desorption ionization (LDI), secondary ion mass spectrometry (SIMS), and inductively coupled plasma (ICP). This article summarizes the most recent advancements in ionization techniques and explores their potential directions within the field of single-cell mass spectrometry.
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Affiliation(s)
- Qingli Zeng
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Meng-Chan Xia
- National Anti-Drug Laboratory Beijing Regional Center, Beijing, China
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Simin Cheng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Zhichao Xue
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
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11
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Gupta G, Kaur J, Bhattacharya K, Chambers BJ, Gazzi A, Furesi G, Rauner M, Fuoco C, Orecchioni M, Delogu LG, Haag L, Stehr JE, Thomen A, Bordes R, Malmberg P, Seisenbaeva GA, Kessler VG, Persson M, Fadeel B. Exploiting Mass Spectrometry to Unlock the Mechanism of Nanoparticle-Induced Inflammasome Activation. ACS NANO 2023; 17:17451-17467. [PMID: 37643371 PMCID: PMC10510732 DOI: 10.1021/acsnano.3c05600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Nanoparticles (NPs) elicit sterile inflammation, but the underlying signaling pathways are poorly understood. Here, we report that human monocytes are particularly vulnerable to amorphous silica NPs, as evidenced by single-cell-based analysis of peripheral blood mononuclear cells using cytometry by time-of-flight (CyToF), while silane modification of the NPs mitigated their toxicity. Using human THP-1 cells as a model, we observed cellular internalization of silica NPs by nanoscale secondary ion mass spectrometry (nanoSIMS) and this was confirmed by transmission electron microscopy. Lipid droplet accumulation was also noted in the exposed cells. Furthermore, time-of-flight secondary ion mass spectrometry (ToF-SIMS) revealed specific changes in plasma membrane lipids, including phosphatidylcholine (PC) in silica NP-exposed cells, and subsequent studies suggested that lysophosphatidylcholine (LPC) acts as a cell autonomous signal for inflammasome activation in the absence of priming with a microbial ligand. Moreover, we found that silica NPs elicited NLRP3 inflammasome activation in monocytes, whereas cell death transpired through a non-apoptotic, lipid peroxidation-dependent mechanism. Together, these data further our understanding of the mechanism of sterile inflammation.
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Affiliation(s)
- Govind Gupta
- Institute
of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jasreen Kaur
- Institute
of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kunal Bhattacharya
- Institute
of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | | | - Arianna Gazzi
- Department
of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Giulia Furesi
- Department
of Medicine III and Center for Healthy Aging, TU Dresden, 01307 Dresden, Germany
| | - Martina Rauner
- Department
of Medicine III and Center for Healthy Aging, TU Dresden, 01307 Dresden, Germany
| | - Claudia Fuoco
- Department
of Biology, University of Rome Tor Vergata, Rome 00173, Italy
| | - Marco Orecchioni
- Division
of Inflammation Biology, La Jolla Institute
for Immunology, La Jolla, California 92037, United States
| | - Lucia Gemma Delogu
- Department
of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Lars Haag
- Department
of Laboratory Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Jan Eric Stehr
- Department
of Physics, Chemistry and Biology, Linköping
University, 581 83 Linköping, Sweden
| | - Aurélien Thomen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, 412 96 Göteborg, Sweden
| | - Romain Bordes
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | - Per Malmberg
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | - Gulaim A. Seisenbaeva
- Department
of Molecular Sciences, Swedish University
of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Vadim G. Kessler
- Department
of Molecular Sciences, Swedish University
of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Michael Persson
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | - Bengt Fadeel
- Institute
of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
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12
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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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13
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Shao X, Meng C, Song W, Zhang T, Chen Q. Subcellular visualization: Organelle-specific targeted drug delivery and discovery. Adv Drug Deliv Rev 2023; 199:114977. [PMID: 37391014 DOI: 10.1016/j.addr.2023.114977] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Organelles perform critical biological functions due to their distinct molecular composition and internal environment. Disorders in organelles or their interacting networks have been linked to the incidence of numerous diseases, and the research of pharmacological actions at the organelle level has sparked pharmacists' interest. Currently, cell imaging has evolved into a critical tool for drug delivery, drug discovery, and pharmacological research. The introduction of advanced imaging techniques in recent years has provided researchers with richer biological information for viewing and studying the ultrastructure of organelles, protein interactions, and gene transcription activities, leading to the design and delivery of precision-targeted drugs. Therefore, this reviews the research on organelles-targeted drugs based upon imaging technologies and development of fluorescent molecules for medicinal purposes. We also give a thorough analysis of a number of subcellular-level elements of drug development, including subcellular research instruments and methods, organelle biological event investigation, subcellular target and drug identification, and design of subcellular delivery systems. This review will make it possible to promote drug research from the individual/cellular level to the subcellular level, as well as give a new focus based on newly found organelle activities.
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Affiliation(s)
- Xintian Shao
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Caicai Meng
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Wenjing Song
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China; School of Pharmaceutical Sciences & Institute of Materia Medica, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Key Laboratory for Biotechnology Drugs of National Health Commission, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Tao Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province 250014, PR China
| | - Qixin Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Key Laboratory for Biotechnology Drugs of National Health Commission, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China.
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14
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Chan YH, Pathmasiri KC, Pierre-Jacques D, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543480. [PMID: 37398444 PMCID: PMC10312618 DOI: 10.1101/2023.06.02.543480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Compatible with label-free detection and quantification, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of biomolecules in intact specimens. Yet, the spatial resolution of MSI is limited by the method's physical and instrumental constraints, which often preclude it from single-cell and subcellular applications. By taking advantage of the reversible interaction of analytes with superabsorbent hydrogels, we developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome these limits. With GAMSI, the spatial resolution of lipid and protein MALDI-MSI can be enhanced severalfold without changing the existing mass spectrometry hardware and analysis pipeline. This approach will further enhance the accessibility to (sub)cellular-scale MALDI-MSI-based spatial omics.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
| | | | | | - Stephanie M. Cologna
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago; Chicago, IL 60607, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago; Chicago, IL 60607, USA
- Department of Biological Sciences, University of Illinois Chicago; Chicago, IL 60607, USA
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15
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He X, Ewing AG. Hofmeister Series: From Aqueous Solution of Biomolecules to Single Cells and Nanovesicles. Chembiochem 2023; 24:e202200694. [PMID: 37043703 DOI: 10.1002/cbic.202200694] [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] [Received: 12/07/2022] [Revised: 01/30/2023] [Indexed: 04/14/2023]
Abstract
Hofmeister effects play a critical role in numerous physicochemical and biological phenomena, including the solubility and/or accumulation of proteins, the activities of enzymes, ion transport in biochannels, the structure of lipid bilayers, and the dynamics of vesicle opening and exocytosis. This minireview focuses on how ionic specificity affects the physicochemical properties of biomolecules to regulate cellular exocytosis, vesicular content, and nanovesicle opening. We summarize recent progress in further understanding Hofmeister effects on biomacromolecules and their applications in biological systems. These important steps have increased our understanding of the Hofmeister effects on cellular exocytosis, vesicular content, and nanovesicle opening. Increasing evidence is firmly establishing that the ions along the Hofmeister series play an important role in living organisms that has often been ignored.
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Affiliation(s)
- Xiulan He
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296, Gothenburg, Sweden
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16
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Pognan F, Beilmann M, Boonen HCM, Czich A, Dear G, Hewitt P, Mow T, Oinonen T, Roth A, Steger-Hartmann T, Valentin JP, Van Goethem F, Weaver RJ, Newham P. The evolving role of investigative toxicology in the pharmaceutical industry. Nat Rev Drug Discov 2023; 22:317-335. [PMID: 36781957 PMCID: PMC9924869 DOI: 10.1038/s41573-022-00633-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
For decades, preclinical toxicology was essentially a descriptive discipline in which treatment-related effects were carefully reported and used as a basis to calculate safety margins for drug candidates. In recent years, however, technological advances have increasingly enabled researchers to gain insights into toxicity mechanisms, supporting greater understanding of species relevance and translatability to humans, prediction of safety events, mitigation of side effects and development of safety biomarkers. Consequently, investigative (or mechanistic) toxicology has been gaining momentum and is now a key capability in the pharmaceutical industry. Here, we provide an overview of the current status of the field using case studies and discuss the potential impact of ongoing technological developments, based on a survey of investigative toxicologists from 14 European-based medium-sized to large pharmaceutical companies.
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Affiliation(s)
- Francois Pognan
- Discovery and Investigative Safety, Novartis Pharma AG, Basel, Switzerland.
| | - Mario Beilmann
- Nonclinical Drug Safety Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Harrie C M Boonen
- Drug Safety, Dept of Exploratory Toxicology, Lundbeck A/S, Valby, Denmark
| | | | - Gordon Dear
- In Vitro In Vivo Translation, GlaxoSmithKline David Jack Centre for Research, Ware, UK
| | - Philip Hewitt
- Chemical and Preclinical Safety, Merck Healthcare KGaA, Darmstadt, Germany
| | - Tomas Mow
- Safety Pharmacology and Early Toxicology, Novo Nordisk A/S, Maaloev, Denmark
| | - Teija Oinonen
- Preclinical Safety, Orion Corporation, Espoo, Finland
| | - Adrian Roth
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | | | - Freddy Van Goethem
- Predictive, Investigative & Translational Toxicology, Nonclinical Safety, Janssen Research & Development, Beerse, Belgium
| | - Richard J Weaver
- Innovation Life Cycle Management, Institut de Recherches Internationales Servier, Suresnes, France
| | - Peter Newham
- Clinical Pharmacology and Safety Sciences, AstraZeneca R&D, Cambridge, UK.
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17
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Borges R, Gu C, Machado JD, Ewing AG. The dynamic nature of exocytosis from large secretory vesicles. A view from electrochemistry and imaging. Cell Calcium 2023; 110:102699. [PMID: 36708611 DOI: 10.1016/j.ceca.2023.102699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
In this brief review, we discuss the factors that modulate the quantum size and the kinetics of exocytosis. We also discuss the determinants which motivate the type of exocytosis from the so-called kiss-and-run to full fusion and along the intermediate mode of partial release. Kiss-and-run release comprises the transient opening of a nanometer (approx. 2 nm diameter) fusion pore between vesicle and plasma membrane allowing a small amount of release. Partial release comprises a larger more extended opening of the pore to allow a larger fraction of released vesicle content and is what is observed as normal full release in most electrochemical measurements. Partial release appears to be dominant in dense core vesicles and perhaps synaptic vesicles. The concept of partial release leads to the fraction released as a plastic component of exocytosis. Partial vesicular distension and the kinetics of exocytosis can be modulated by second messengers, physiological modulators, and drugs. This concept adds a novel point of regulation for the exocytotic process.
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Affiliation(s)
- Ricardo Borges
- Pharmacology Unit, Medical School, Universidad de la Laguna, Tenerife. Spain
| | - Chaoyi Gu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden
| | - José-David Machado
- Pharmacology Unit, Medical School, Universidad de la Laguna, Tenerife. Spain
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.
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18
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Hou JJ, Zhang ZJ, Wu WY, He QQ, Zhang TQ, Liu YW, Wang ZJ, Gao L, Long HL, Lei M, Wu WY, Guo DA. Mass spectrometry imaging: new eyes on natural products for drug research and development. Acta Pharmacol Sin 2022; 43:3096-3111. [PMID: 36229602 PMCID: PMC9712638 DOI: 10.1038/s41401-022-00990-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
Natural products (NPs) and their structural analogs represent a major source of novel drug development for disease prevention and treatment. The development of new drugs from NPs includes two crucial aspects. One is the discovery of NPs from medicinal plants/microorganisms, and the other is the evaluation of the NPs in vivo at various physiological and pathological states. The heterogeneous spatial distribution of NPs in medicinal plants/microorganisms or in vivo can provide valuable information for drug development. However, few molecular imaging technologies can detect thousands of compounds simultaneously on a label-free basis. Over the last two decades, mass spectrometry imaging (MSI) methods have progressively improved and diversified, thereby allowing for the development of various applications of NPs in plants/microorganisms and in vivo NP research. Because MSI allows for the spatial mapping of the production and distribution of numerous molecules in situ without labeling, it provides a visualization tool for NP research. Therefore, we have focused this mini-review on summarizing the applications of MSI technology in discovering NPs from medicinal plants and evaluating NPs in preclinical studies from the perspective of new drug research and development (R&D). Additionally, we briefly reviewed the factors that should be carefully considered to obtain the desired MSI results. Finally, the future development of MSI in new drug R&D is proposed.
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Affiliation(s)
- Jin-Jun Hou
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zi-Jia Zhang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Yong Wu
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Qing-Qing He
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Teng-Qian Zhang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Wen Liu
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhao-Jun Wang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Gao
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua-Li Long
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Lei
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan-Ying Wu
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - De-An Guo
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Tajik M, Baharfar M, Donald WA. Single-cell mass spectrometry. Trends Biotechnol 2022; 40:1374-1392. [PMID: 35562238 DOI: 10.1016/j.tibtech.2022.04.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 01/21/2023]
Abstract
Owing to recent advances in mass spectrometry (MS), tens to hundreds of proteins, lipids, and small molecules can be measured in single cells. The ability to characterize the molecular heterogeneity of individual cells is necessary to define the full assortment of cell subtypes and identify their function. We review single-cell MS including high-throughput, targeted, mass cytometry-based approaches and antibody-free methods for broad profiling of the proteome and metabolome of single cells. The advantages and disadvantages of different methods are discussed, as well as the challenges and opportunities for further improvements in single-cell MS. These methods is being used in biomedicine in several applications including revealing tumor heterogeneity and high-content drug screening.
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Affiliation(s)
- Mohammad Tajik
- School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Mahroo Baharfar
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052, Australia.
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20
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Brunet MA, Gorman BL, Kraft ML. Depth Correction of 3D NanoSIMS Images Shows Intracellular Lipid and Cholesterol Distributions while Capturing the Effects of Differential Sputter Rate. ACS NANO 2022; 16:16221-16233. [PMID: 36218061 DOI: 10.1021/acsnano.2c05148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Knowledge of the distributions of drugs, metabolites, and drug carriers within cells is a prerequisite for the development of effective disease treatments. Intracellular component distribution may be imaged with high sensitivity and spatial resolution by using a NanoSIMS in the depth profiling mode. Depth correction strategies that capture the effects of differential sputtering without requiring additional measurements could enable producing accurate 3D NanoSIMS depth profiling images of intracellular component distributions. Here we describe an approach for depth correcting 3D NanoSIMS depth profiling images of cells that accounts for differential sputter rates. Our approach uses the secondary ion and secondary electron depth profiling images to reconstruct the cell's morphology at every raster plane. These cell morphology reconstructions are used to adjust the z-positions and heights of the voxels in the component-specific 3D NanoSIMS images. We validated this strategy using AFM topography data and reconstructions created from depth profiling images acquired with focused ion beam-secondary electron microscopy. Good agreement was found for the shapes and relative heights of the reconstructed morphologies. Application of this depth correction strategy to 3D NanoSIMS depth profiling images of a metabolically labeled cell better resolved the transport vesicles, organelles, and organellar membranes containing 18O-cholesterol and 15N-sphingolipids. Accurate 3D NanoSIMS images of intracellular component distributions may now be produced without requiring correlated analyses with separate instruments or the assumption of a constant sputter rate. This will allow visualization of the subcellular distributions of lipids, metabolites, drugs, and nanoparticles in 3D, information pivotal to understanding and treating disease.
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21
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Bar-Peled L, Kory N. Principles and functions of metabolic compartmentalization. Nat Metab 2022; 4:1232-1244. [PMID: 36266543 PMCID: PMC10155461 DOI: 10.1038/s42255-022-00645-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/24/2022] [Indexed: 01/20/2023]
Abstract
Metabolism has historically been studied at the levels of whole cells, whole tissues and whole organisms. As a result, our understanding of how compartmentalization-the spatial and temporal separation of pathways and components-shapes organismal metabolism remains limited. At its essence, metabolic compartmentalization fulfils three important functions or 'pillars': establishing unique chemical environments, providing protection from reactive metabolites and enabling the regulation of metabolic pathways. However, how these pillars are established, regulated and maintained at both the cellular and systemic levels remains unclear. Here we discuss how the three pillars are established, maintained and regulated within the cell and discuss the consequences of dysregulation of metabolic compartmentalization in human disease. Organelles are increasingly emerging as 'command-and-control centres' and the increased understanding of metabolic compartmentalization is revealing new aspects of metabolic homeostasis, with this knowledge being translated into therapies for the treatment of cancer and certain neurodegenerative diseases.
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Affiliation(s)
- Liron Bar-Peled
- Center for Cancer Research, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Nora Kory
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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22
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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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23
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Baijnath S, Kaya I, Nilsson A, Shariatgorji R, Andrén PE. Advances in spatial mass spectrometry enable in-depth neuropharmacodynamics. Trends Pharmacol Sci 2022; 43:740-753. [DOI: 10.1016/j.tips.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/06/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022]
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24
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Grujcic V, Taylor GT, Foster RA. One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology. Front Microbiol 2022; 13:881018. [PMID: 35677911 PMCID: PMC9169044 DOI: 10.3389/fmicb.2022.881018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Studying microbes from a single-cell perspective has become a major theme and interest within the field of aquatic microbiology. One emerging trend is the unfailing observation of heterogeneity in activity levels within microbial populations. Wherever researchers have looked, intra-population variability in biochemical composition, growth rates, and responses to varying environmental conditions has been evident and probably reflect coexisting genetically distinct strains of the same species. Such observations of heterogeneity require a shift away from bulk analytical approaches and development of new methods or adaptation of existing techniques, many of which were first pioneered in other, unrelated fields, e.g., material, physical, and biomedical sciences. Many co-opted approaches were initially optimized using model organisms. In a field with so few cultivable models, method development has been challenging but has also contributed tremendous insights, breakthroughs, and stimulated curiosity. In this perspective, we present a subset of methods that have been effectively applied to study aquatic microbes at the single-cell level. Opportunities and challenges for innovation are also discussed. We suggest future directions for aquatic microbiological research that will benefit from open access to sophisticated instruments and highly interdisciplinary collaborations.
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Affiliation(s)
- Vesna Grujcic
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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25
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More TH, Hiller K. Complexity of subcellular metabolism: strategies for compartment-specific profiling. Curr Opin Biotechnol 2022; 75:102711. [DOI: 10.1016/j.copbio.2022.102711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/03/2022]
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26
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Lork AA, Vo KLL, Phan NTN. Chemical Imaging and Analysis of Single Nerve Cells by Secondary Ion Mass Spectrometry Imaging and Cellular Electrochemistry. Front Synaptic Neurosci 2022; 14:854957. [PMID: 35651734 PMCID: PMC9149580 DOI: 10.3389/fnsyn.2022.854957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A nerve cell is a unit of neuronal communication in the nervous system and is a heterogeneous molecular structure, which is highly mediated to accommodate cellular functions. Understanding the complex regulatory mechanisms of neural communication at the single cell level requires analytical techniques with high sensitivity, specificity, and spatial resolution. Challenging technologies for chemical imaging and analysis of nerve cells will be described in this review. Secondary ion mass spectrometry (SIMS) allows for non-targeted and targeted molecular imaging of nerve cells and synapses at subcellular resolution. Cellular electrochemistry is well-suited for quantifying the amount of reactive chemicals released from living nerve cells. These techniques will also be discussed regarding multimodal imaging approaches that have recently been shown to be advantageous for the understanding of structural and functional relationships in the nervous system. This review aims to provide an insight into the strengths, limitations, and potentials of these technologies for synaptic and neuronal analyses.
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27
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Angerer TB, Bour J, Biagi JL, Moskovets E, Frache G. Evaluation of 6 MALDI-Matrices for 10 μm Lipid Imaging and On-Tissue MSn with AP-MALDI-Orbitrap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:760-771. [PMID: 35358390 PMCID: PMC9074099 DOI: 10.1021/jasms.1c00327] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Mass spectrometry imaging is a technique uniquely suited to localize and identify lipids in a tissue sample. Using an atmospheric pressure (AP-) matrix-assisted laser desorption ionization (MALDI) source coupled to an Orbitrap Elite, numerous lipid locations and structures can be determined in high mass resolution spectra and at cellular spatial resolution, but careful sample preparation is necessary. We tested 11 protocols on serial brain sections for the commonly used MALDI matrices CHCA, norharmane, DHB, DHAP, THAP, and DAN in combination with tissue washing and matrix additives to determine the lipid coverage, signal intensity, and spatial resolution achievable with AP-MALDI. In positive-ion mode, the most lipids could be detected with CHCA and THAP, while THAP and DAN without additional treatment offered the best signal intensities. In negative-ion mode, DAN showed the best lipid coverage and DHAP performed superiorly for gangliosides. DHB produced intense cholesterol signals in the white matter. One hundred fifty-five lipids were assigned in positive-ion mode (THAP) and 137 in negative-ion mode (DAN), and 76 peaks were identified using on-tissue tandem-MS. The spatial resolution achievable with DAN was 10 μm, confirmed with on tissue line-scans. This enabled the association of lipid species to single neurons in AP-MALDI images. The results show that the performance of AP-MALDI is comparable to vacuum MALDI techniques for lipid imaging.
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Affiliation(s)
- Tina B. Angerer
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
| | - Jerome Bour
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
| | - Jean-Luc Biagi
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
| | | | - Gilles Frache
- Luxembourg
Institute of Science and Technology (LIST), Advanced Characterization platform, Materials Research
and Technology, 41, rue
du Brill, L-4422 Belvaux, Luxembourg
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28
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Du X, Li N, Chen Q, Wu Z, Zhai J, Xie X. Perspective on fluorescence cell imaging with ionophore-based ion-selective nano-optodes. BIOMICROFLUIDICS 2022; 16:031301. [PMID: 35698631 PMCID: PMC9188459 DOI: 10.1063/5.0090599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Inorganic ions are ubiquitous in all kinds of cells with highly dynamic spatial and temporal distribution. Taking advantage of different types of fluorescent probes, fluorescence microscopic imaging and quantitative analysis of ion concentrations in cells have rapidly advanced. A family of fluorescent nanoprobes based on ionophores has emerged in recent years with the potential to establish a unique platform for the analysis of common biological ions including Na+, K+, Ca2+, Cl-, and so on. This article aims at providing a retrospect and outlook of ionophore-based ion-selective nanoprobes and the applications in cell imaging.
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Affiliation(s)
- Xinfeng Du
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Niping Li
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qinghan Chen
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zeying Wu
- School of Chemical Engineering and Material Science, Changzhou Institute of Technology, Changzhou 213032, China
| | - Jingying Zhai
- Authors to whom correspondence should be addressed:; ; and
| | - Xiaojiang Xie
- Authors to whom correspondence should be addressed:; ; and
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29
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He X, Ewing AG. Simultaneous Counting of Molecules in the Halo and Dense-Core of Nanovesicles by Regulating Dynamics of Vesicle Opening. Angew Chem Int Ed Engl 2022; 61:e202116217. [PMID: 35129861 PMCID: PMC9306628 DOI: 10.1002/anie.202116217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Indexed: 01/09/2023]
Abstract
We report the discovery that in the presence of chaotropic anions (SCN−) the opening of nanometer biological vesicles at an electrified interface often becomes a two‐step process (around 30 % doublet peaks). We have then used this to independently count molecules in each subvesicular compartment, the halo and protein dense‐core, and the fraction of catecholamine binding to the dense‐core is 68 %. Moreover, we differentiated two distinct populations of large dense‐core vesicles (LDCVs) and quantified their content, which might correspond to immature (43 %) and mature (30 %) LDCVs, to reveal differences in their biogenesis. We speculate this is caused by an increase in the electrostatic attraction between protonated catecholamine and the negatively charged dense‐core following adsorption of SCN−.
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Affiliation(s)
- Xiulan He
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296, Gothenburg, Sweden
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30
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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: 6] [Impact Index Per Article: 3.0] [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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31
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Kay E, Stulz R, Becquart C, Lovric J, Tängemo C, Thomen A, Baždarević D, Najafinobar N, Dahlén A, Pielach A, Fernandez-Rodriguez J, Strömberg R, Ämmälä C, Andersson S, Kurczy M. NanoSIMS Imaging Reveals the Impact of Ligand-ASO Conjugate Stability on ASO Subcellular Distribution. Pharmaceutics 2022; 14:pharmaceutics14020463. [PMID: 35214195 PMCID: PMC8876276 DOI: 10.3390/pharmaceutics14020463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 01/27/2023] Open
Abstract
The delivery of antisense oligonucleotides (ASOs) to specific cell types via targeted endocytosis is challenging due to the low cell surface expression of target receptors and inefficient escape of ASOs from the endosomal pathway. Conjugating ASOs to glucagon-like peptide 1 (GLP1) leads to efficient target knockdown, specifically in pancreatic β-cells. It is presumed that ASOs dissociate from GLP1 intracellularly to enable an ASO interaction with its target RNA. It is unknown where or when this happens following GLP1-ASO binding to GLP1R and endocytosis. Here, we use correlative nanoscale secondary ion mass spectroscopy (NanoSIMS) and transmission electron microscopy to explore GLP1-ASO subcellular trafficking in GLP1R overexpressing HEK293 cells. We isotopically label both eGLP1 and ASO, which do not affect the eGLP1-ASO conjugate function. We found that the eGLP1 peptide and ASO are not detected at the same level in the same endosomes, within 30 min of GLP1R-HEK293 cell exposure to eGLP1-ASO. When we utilized different linker chemistry to stabilize the GLP1-ASO conjugate, we observed more ASO located with GLP1 compared to cell incubation with the less stable conjugate. Overall, our work suggests that the ASO separates from GLP1 relatively early in the endocytic pathway, and that linker chemistry might impact the GLP1-ASO function.
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Affiliation(s)
- Emma Kay
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Rouven Stulz
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden; (R.S.); (R.S.)
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (A.D.); (S.A.)
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
| | - Cécile Becquart
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 412 96 Gothenburg, Sweden;
| | - Jelena Lovric
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
| | - Carolina Tängemo
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Aurélien Thomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 412 96 Gothenburg, Sweden;
| | - Dženita Baždarević
- Bioscience, Early Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Neda Najafinobar
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (A.D.); (S.A.)
| | - Anna Pielach
- Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden; (A.P.); (J.F.-R.)
| | - Julia Fernandez-Rodriguez
- Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden; (A.P.); (J.F.-R.)
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden; (R.S.); (R.S.)
| | - Carina Ämmälä
- Bioscience, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden;
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (A.D.); (S.A.)
| | - Michael Kurczy
- DMPK, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Gothenburg, Sweden; (C.B.); (J.L.)
- Correspondence:
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32
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He X, Ewing AG. Simultaneous Counting of Molecules in the Halo and Dense‐Core of Nanovesicles by Regulating Dynamics of Vesicle Opening. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiulan He
- Department of Chemistry and Molecular Biology University of Gothenburg Kemivägen 10 41296 Gothenburg Sweden
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology University of Gothenburg Kemivägen 10 41296 Gothenburg Sweden
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33
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Zhao Y, Cheng P, Yang H, Wang M, Meng D, Zhu Y, Zheng R, Li T, Zhang A, Tan S, Huang T, Bian J, Zhan X, Weiss PS, Yang Y. Towards High-Performance Semitransparent Organic Photovoltaics: Dual-Functional p-Type Soft Interlayer. ACS NANO 2022; 15:13220-13229. [PMID: 34932319 DOI: 10.1021/acsnano.1c02922] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Semitransparent organic photovoltaics (OPVs) have drawn significant attention for their promising potential in the field of building integrated photovoltaics such as energy-generating greenhouses. However, the conflict between the need to attain satisfying average visible transmittances for greenhouse applications and the need to maintain high power conversion efficiencies is limiting the commercialization of semitransparent OPVs. A major manifestation of this issue is the undermining of charge carrier extraction efficiency when opaque, visible-light-absorbing electrodes are substituted with semitransparent ones. Here, we incorporated a dual-function p-type compatible interlayer to modify the interface of the hole-transporting layer and the ultrathin electrode of the semitransparent devices. We find that the p-type interlayer not only enhances the charge carrier extraction of the electrode but also increases the light transmittance in the wavelength range of 400-450 nm, which covers most of the photosynthetic absorption spectrum. The modified semitransparent devices reach a power conversion efficiency of 13.7% and an average visible transmittance of 22.2%.
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Affiliation(s)
| | | | - Hangbo Yang
- Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Minhuan Wang
- Key Laboratory of Materials Modification by Laser, Ion, and Electron Beams, Dalian University of Technology, Ministry of Education, School of Physics, Dalian, 116024, China
| | | | | | | | - Tengfei Li
- School of Materials Science and Engineering, Peking University, Beijing, 100871, People's Republic of China
| | | | | | | | - Jiming Bian
- Key Laboratory of Materials Modification by Laser, Ion, and Electron Beams, Dalian University of Technology, Ministry of Education, School of Physics, Dalian, 116024, China
| | - Xiaowei Zhan
- School of Materials Science and Engineering, Peking University, Beijing, 100871, People's Republic of China
| | - Paul S Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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34
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Trefely S, Huber K, Liu J, Noji M, Stransky S, Singh J, Doan MT, Lovell CD, von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao S, Xu JP, Bedi KC, Rame JE, Bogner-Strauss JG, Mesaros C, Sidoli S, Wellen KE, Snyder NW. Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Mol Cell 2022; 82:447-462.e6. [PMID: 34856123 PMCID: PMC8950487 DOI: 10.1016/j.molcel.2021.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 11/03/2021] [Indexed: 01/22/2023]
Abstract
Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.
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Affiliation(s)
- Sophie Trefely
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharina Huber
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Biochemistry, Graz University of Technology, Graz 8010, Austria
| | - Joyce Liu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Noji
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay Singh
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Mary T Doan
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Claudia D Lovell
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eliana von Krusenstiern
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Helen Jiang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Anna Bostwick
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Hannah L Pepper
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Luke Izzo
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven Zhao
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jimmy P Xu
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth C Bedi
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Eduardo Rame
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Clementina Mesaros
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
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35
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Bow JP, Adami V, Marasco A, Gronnevik G, Rivers D, Alvaro G, Riss PJ. A Direct Fixation of CO2 for Isotopic Labelling of Hydantoins Using Iodine-Phosphine Charge Transfer Complexes. Chem Commun (Camb) 2022; 58:7546-7549. [DOI: 10.1039/d2cc01754g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report a method for the isotopic labelling of hydantoins directly from CO2 by means of trimethyl-λ5-phosphine diiodide mediated carbonyl insertion. The method is suitable for 13C-labelling of diverse...
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36
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Localization and Absolute Quantification of Dopamine in Discrete Intravesicular Compartments Using NanoSIMS Imaging. Int J Mol Sci 2021; 23:ijms23010160. [PMID: 35008583 PMCID: PMC8745556 DOI: 10.3390/ijms23010160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022] Open
Abstract
The absolute concentration and the compartmentalization of analytes in cells and organelles are crucial parameters in the development of drugs and drug delivery systems, as well as in the fundamental understanding of many cellular processes. Nanoscale secondary ion mass spectrometry (NanoSIMS) imaging is a powerful technique which allows subcellular localization of chemical species with high spatial and mass resolution, and high sensitivity. In this study, we combined NanoSIMS imaging with spatial oversampling with transmission electron microscopy (TEM) imaging to discern the compartments (dense core and halo) of large dense core vesicles in a model cell line used to study exocytosis, and to localize 13C dopamine enrichment following 4–6 h of 150 μM 13C L-3,4-dihydroxyphenylalanine (L-DOPA) incubation. In addition, the absolute concentrations of 13C dopamine in distinct vesicle domains as well as in entire single vesicles were quantified and validated by comparison to electrochemical data. We found concentrations of 87.5 mM, 16.0 mM and 39.5 mM for the dense core, halo and the whole vesicle, respectively. This approach adds to the potential of using combined TEM and NanoSIMS imaging to perform absolute quantification and directly measure the individual contents of nanometer-scale organelles.
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37
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Gorman BL, Brunet MA, Kraft ML. Depth correction of 3D NanoSIMS images using secondary electron pixel intensities. Biointerphases 2021; 16:041005. [PMID: 34344157 PMCID: PMC8337084 DOI: 10.1116/6.0001092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Strategies that do not require additional characterization to be performed on the sample or the collection of additional secondary ion signals are needed to depth correct 3D SIMS images of cells. Here, we develop a depth correction strategy that uses the pixel intensities in the secondary electron images acquired during negative-ion NanoSIMS depth profiling to reconstruct the sample morphology. This morphology reconstruction was then used to depth correct the 3D SIMS images that show the components of interest in the sample. As a proof of concept, we applied this approach to NanoSIMS depth profiling data that show the 15N-enrichment and 18O-enrichment from 15N-sphingolipids and 18O-cholesterol, respectively, within a metabolically labeled Madin-Darby canine kidney cell. Comparison of the cell morphology reconstruction to the secondary electron images collected with the NanoSIMS revealed that the assumption of a constant sputter rate produced small inaccuracies in sample morphology after approximately 0.66 μm of material was sputtered from the cell. Nonetheless, the resulting 3D renderings of the lipid-specific isotope enrichments better matched the shapes and positions of the subcellular compartments that contained 15N-sphingolipids and 18O-cholesterol than the uncorrected 3D SIMS images. This depth correction of the 3D SIMS images also facilitated the detection of spherical cholesterol-rich compartments that were surrounded by membranes containing cholesterol and sphingolipids. Thus, we expect this approach will facilitate identifying the subcellular structures that are enriched with biomolecules of interest in 3D SIMS images while eliminating the need for correlated analyses or additional secondary ion signals for the depth correction of 3D NanoSIMS images.
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Affiliation(s)
- Brittney L Gorman
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Melanie A Brunet
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Mary L Kraft
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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38
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Gallart-Ayala H, Teav T, Ivanisevic J. Metabolomics meets lipidomics: Assessing the small molecule component of metabolism. Bioessays 2021; 42:e2000052. [PMID: 33230910 DOI: 10.1002/bies.202000052] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 09/11/2020] [Indexed: 12/16/2022]
Abstract
Metabolomics, including lipidomics, is emerging as a quantitative biology approach for the assessment of energy flow through metabolism and information flow through metabolic signaling; thus, providing novel insights into metabolism and its regulation, in health, healthy ageing and disease. In this forward-looking review we provide an overview on the origins of metabolomics, on its role in this postgenomic era of biochemistry and its application to investigate metabolite role and (bio)activity, from model systems to human population studies. We present the challenges inherent to this analytical science, and approaches and modes of analysis that are used to resolve, characterize and measure the infinite chemical diversity contained in the metabolome (including lipidome) of complex biological matrices. In the current outbreak of metabolic diseases such as cardiometabolic disorders, cancer and neurodegenerative diseases, metabolomics appears to be ideally situated for the investigation of disease pathophysiology from a metabolite perspective.
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Affiliation(s)
- Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tony Teav
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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39
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Nitsch S, Zorro Shahidian L, Schneider R. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Rep 2021. [PMID: 34159701 DOI: 10.5252/embr.202152774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Santander, Spain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
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Nitsch S, Zorro Shahidian L, Schneider R. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Rep 2021; 22:e52774. [PMID: 34159701 PMCID: PMC8406397 DOI: 10.15252/embr.202152774] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/08/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC)University of CantabriaSantanderSpain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Faculty of BiologyLudwig‐Maximilians Universität MünchenPlanegg‐MartinsriedGermany
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Abstract
BACKGROUND Precision medicine, space exploration, drug discovery to characterization of dark chemical space of habitats and organisms, metabolomics takes a centre stage in providing answers to diverse biological, biomedical, and environmental questions. With technological advances in mass-spectrometry and spectroscopy platforms that aid in generation of information rich datasets that are complex big-data, data analytics tend to co-evolve to match the pace of analytical instrumentation. Software tools, resources, databases, and solutions help in harnessing the concealed information in the generated data for eventual translational success. AIM OF THE REVIEW In this review, ~ 85 metabolomics software resources, packages, tools, databases, and other utilities that appeared in 2020 are introduced to the research community. KEY SCIENTIFIC CONCEPTS OF REVIEW In Table 1 the computational dependencies and downloadable links of the tools are provided, and the resources are categorized based on their utility. The review aims to keep the community of metabolomics researchers updated with all the resources developed in 2020 at a collated avenue, in line with efforts form 2015 onwards to help them find these at one place for further referencing and use.
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Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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Liu Y, Du J, Wang M, Zhang J, Liu C, Li X. Recent Progress in Quantitatively Monitoring Vesicular Neurotransmitter Release and Storage With Micro/Nanoelectrodes. Front Chem 2021; 8:591311. [PMID: 33505953 PMCID: PMC7831278 DOI: 10.3389/fchem.2020.591311] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/20/2020] [Indexed: 01/31/2023] Open
Abstract
Exocytosis is one of the essential steps for chemical signal transmission between neurons. In this process, vesicles dock and fuse with the plasma membrane and release the stored neurotransmitters through fusion pores into the extracellular space, and all of these steps are governed with various molecules, such as proteins, ions, and even lipids. Quantitatively monitoring vesicular neurotransmitter release in exocytosis and initial neurotransmitter storage in individual vesicles is significant for the study of chemical signal transmission of the central nervous system (CNS) and neurological diseases. Electrochemistry with micro/nanoelectrodes exhibits great spatial-temporal resolution and high sensitivity. It can be used to examine the exocytotic kinetics from the aspect of neurotransmitters and quantify the neurotransmitter storage in individual vesicles. In this review, we first introduce the recent advances of single-cell amperometry (SCA) and the nanoscale interface between two immiscible electrolyte solutions (nanoITIES), which can monitor the quantity and release the kinetics of electrochemically and non-electrochemically active neurotransmitters, respectively. Then, the development and application of the vesicle impact electrochemical cytometry (VIEC) and intracellular vesicle impact electrochemical cytometry (IVIEC) and their combination with other advanced techniques can further explain the mechanism of neurotransmitter storage in vesicles before exocytosis. It has been proved that these electrochemical techniques have great potential in the field of neuroscience.
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Affiliation(s)
| | | | | | | | - Chunlan Liu
- Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Xianchan Li
- Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing, China
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Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM. Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2401-2415. [PMID: 32886506 PMCID: PMC9278956 DOI: 10.1021/jasms.0c00232] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Imaging mass spectrometry has become a mature molecular mapping technology that is used for molecular discovery in many medical and biological systems. While powerful by itself, imaging mass spectrometry can be complemented by the addition of other orthogonal, chemically informative imaging technologies to maximize the information gained from a single experiment and enable deeper understanding of biological processes. Within this review, we describe MALDI, SIMS, and DESI imaging mass spectrometric technologies and how these have been integrated with other analytical modalities such as microscopy, transcriptomics, spectroscopy, and electrochemistry in a field termed multimodal imaging. We explore the future of this field and discuss forthcoming developments that will bring new insights to help unravel the molecular complexities of biological systems, from single cells to functional tissue structures and organs.
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Affiliation(s)
- Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
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Giampà M, Sgobba E. Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry. Molecules 2020; 25:E4979. [PMID: 33126406 PMCID: PMC7662314 DOI: 10.3390/molecules25214979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.
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Affiliation(s)
- Marco Giampà
- MR Cancer Group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Elvira Sgobba
- Genetics and Plant Physiology, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
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Narendra DP, Steinhauser ML. Metabolic Analysis at the Nanoscale with Multi-Isotope Imaging Mass Spectrometry (MIMS). CURRENT PROTOCOLS IN CELL BIOLOGY 2020; 88:e111. [PMID: 32706155 PMCID: PMC7484994 DOI: 10.1002/cpcb.111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Incorporation of a stable-isotope metabolic tracer into cells or tissue can be followed at submicron resolution by multi-isotope imaging mass spectrometry (MIMS), a form of imaging secondary ion microscopy optimized for accurate isotope ratio measurement from microvolumes of sample (as small as ∼30 nm across). In a metabolic MIMS experiment, a cell or animal is metabolically labeled with a tracer containing a stable isotope. Relative accumulation of the heavy isotope in the fixed sample is then measured as an increase over its natural abundance by MIMS. MIMS has been used to measure protein turnover in single organelles, track cellular division in vivo, visualize sphingolipid rafts on the plasma membrane, and measure dopamine incorporation into dense-core vesicles, among other biological applications. In this article, we introduce metabolic analysis using NanoSIMS by focusing on two specific applications: quantifying protein turnover in single organelles of cultured cells and tracking cell replication in mouse tissues in vivo. These examples illustrate the versatility of metabolic analysis with MIMS. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Metabolic labeling for MIMS Basic Protocol 2: Embedding of samples for correlative transmission electron microscopy and MIMS with a genetically encoded reporter Alternate Protocol: Embedding of samples for correlative light microscopy and MIMS Support Protocol: Preparation of silicon wafers as sample supports for MIMS Basic Protocol 3: Analysis of MIMS data.
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Affiliation(s)
- Derek P Narendra
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Matthew L Steinhauser
- Department of Medicine, Aging Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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47
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Gorman BL, Brunet MA, Pham SN, Kraft ML. Measurement of Absolute Concentration at the Subcellular Scale. ACS NANO 2020; 14:6414-6419. [PMID: 32510923 DOI: 10.1021/acsnano.0c04285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The concentration of a pharmaceutical drug or bioactive metabolite within the target organelle influences the effects elicited by the drug or metabolite. Although the relative concentrations of many compounds of interest within subcellular compartments have been measured, measurements of absolute concentrations in the organelle remain elusive. In this Perspective, we discuss a significant advance in using nano secondary ion mass spectrometry (nanoSIMS) to measure the absolute concentration of a 13C-labeled metabolite within secretory vesicles, as reported by Thomen et al. in the April issue of ACS Nano.
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