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Li Z, Li Q. Study on the Anti-Inflammatory Mechanism of Coumarins in Peucedanum decursivum Based on Spatial Metabolomics Combined with Network Pharmacology. Molecules 2024; 29:3346. [PMID: 39064924 PMCID: PMC11280318 DOI: 10.3390/molecules29143346] [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: 06/01/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024] Open
Abstract
Peucedanum decursivum (Miq.) Maxim (P. decursivum) is a traditional Chinese medicinal plant with pharmacological effects such as anti-inflammatory and anti-tumor effects, the root of which is widely used as medicine. Determining the spatial distribution and pharmacological mechanisms of metabolites is necessary when studying the effective substances of medicinal plants. As a means of obtaining spatial distribution information of metabolites, mass spectrometry imaging has high sensitivity and allows for molecule visualization. In this study, matrix-assisted laser desorption mass spectrometry (MALDI-TOF-MSI) and network pharmacology were used for the first time to visually study the spatial distribution and anti-inflammatory mechanism of coumarins, which are metabolites of P. decursivum, to determine their tissue localization and mechanism of action. A total of 27 coumarins were identified by MALDI-TOF-MSI, which mainly concentrated in the cortex, periderm, and phloem of the root of P. decursivum. Network pharmacology studies have identified key targets for the anti-inflammatory effect of P. decursivum, such as TNF, PTGS2, and PRAKA. GO enrichment and KEGG pathway analyses indicated that coumarins in P. decursivum mainly participated in biological processes such as inflammatory response, positive regulation of protein kinase B signaling, chemical carcinogenesis receptor activation, pathways in cancer, and other biological pathways. The molecular docking results indicated that there was good binding between components and targets. This study provides a basis for understanding the spatial distribution and anti-inflammatory mechanism of coumarins in P. decursivum.
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Affiliation(s)
| | - Qian Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
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2
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Wei J, Zhu K, Wang T, Qi T, Wang Z, Li J, Zong S, Cui Y. Highly Accurate Profiling of Exosome Phenotypes Using Super-resolution Tricolor Fluorescence Co-localization. ACS NANO 2024; 18:10206-10215. [PMID: 38536943 DOI: 10.1021/acsnano.4c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Exosomes contain a wealth of proteomic information, presenting promising biomarkers for the noninvasive early diagnosis of diseases, especially cancer. However, it remains a great challenge to accurately and reliably distinguish exosomes secreted from different types of cell lines. Fluorescence immunoassay is frequently used for exosome detection. Nonspecific adsorption in immunoassays is unavoidable and affects the reliability of assay results. Despite the fact that various methods have been proposed to reduce nonspecific adsorption, a more effective method that can eliminate the influence of nonspecific adsorption is still lacking. Here, we report a more convenient way (named SR-TFC) to remove the artifacts caused by nonspecific adsorption, which combines tricolor fluorescence labeling of target exosomes, tricolor super-resolution imaging, and pixel counting. The pixel counting method (named CFPP) is realized by MATLAB and can eliminate nonspecific binding sites at the single-pixel level, which has never been achieved before and could improve the reliability of detection to the maximum extent. Furthermore, as a proof-of-concept, profiling of exosomal membrane proteins and identification of breast cancer subpopulations are demonstrated. To enable multiplex breast cancer phenotypic analysis, three kinds of specific proteins are labeled to obtain the 3D phenotypic information on various exosomes. Breast cancer subtypes can be accurately identified according to the super-resolution images of some clinically relevant exosomal proteins. Worth mentioning is that, by selecting other biomarkers, classification of other cancers could also be realized using SR-TFC. Hence, the present work holds great potential in clinical cancer diagnosis and precision medicine.
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Affiliation(s)
- Jinxiu Wei
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Kai Zhu
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Tingyu Wang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Tongsheng Qi
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Zhuyuan Wang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Jia Li
- Department of Ultrasonography, Zhongda Hospital, Medical School Southeast University, Nanjing, Jiangsu 210009, China
| | - Shenfei Zong
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yiping Cui
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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3
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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: 3] [Impact Index Per Article: 3.0] [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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4
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Dragic H, Chaveroux C, Cosset E, Manie SN. Modelling cancer metabolism in vitro: current improvements and future challenges. FEBS J 2024; 291:402-411. [PMID: 36516350 DOI: 10.1111/febs.16704] [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: 09/09/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Advances in cancer biology over the past decades have revealed that metabolic adaptation of cancer cells is an essential aspect of tumorigenesis. However, recent insights into tumour metabolism in vivo have revealed dissimilarities with results obtained in vitro. This is partly due to the reductionism of in vitro cancer models that struggle to reproduce the complexity of tumour tissues. This review describes some of the discrepancies in cancer cell metabolism between in vitro and in vivo conditions, and presents current methodological approaches and tools used to bridge the gap with the clinically relevant microenvironment. As such, these approaches should generate new knowledge that could be more effectively translated into therapeutic opportunities.
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Affiliation(s)
- Helena Dragic
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Cedric Chaveroux
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Erika Cosset
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
| | - Serge N Manie
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS 5286, Centre Léon Bérard, Univ Lyon, Université Claude Bernard Lyon 1, France
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5
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Li W, Shao C, Li C, Zhou H, Yu L, Yang J, Wan H, He Y. Metabolomics: A useful tool for ischemic stroke research. J Pharm Anal 2023; 13:968-983. [PMID: 37842657 PMCID: PMC10568109 DOI: 10.1016/j.jpha.2023.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/14/2023] [Accepted: 05/29/2023] [Indexed: 10/17/2023] Open
Abstract
Ischemic stroke (IS) is a multifactorial and heterogeneous disease. Despite years of studies, effective strategies for the diagnosis, management and treatment of stroke are still lacking in clinical practice. Metabolomics is a growing field in systems biology. It is starting to show promise in the identification of biomarkers and in the use of pharmacometabolomics to help patients with certain disorders choose their course of treatment. The development of metabolomics has enabled further and more biological applications. Particularly, metabolomics is increasingly being used to diagnose diseases, discover new drug targets, elucidate mechanisms, and monitor therapeutic outcomes and its potential effect on precision medicine. In this review, we reviewed some recent advances in the study of metabolomics as well as how metabolomics might be used to identify novel biomarkers and understand the mechanisms of IS. Then, the use of metabolomics approaches to investigate the molecular processes and active ingredients of Chinese herbal formulations with anti-IS capabilities is summarized. We finally summarized recent developments in single cell metabolomics for exploring the metabolic profiles of single cells. Although the field is relatively young, the development of single cell metabolomics promises to provide a powerful tool for unraveling the pathogenesis of IS.
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Affiliation(s)
- Wentao Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chongyu Shao
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chang Li
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Huifen Zhou
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Li Yu
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiehong Yang
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Haitong Wan
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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6
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Kern C, Kern S, Henss A, Rohnke M. Secondary ion mass spectrometry for bone research. Biointerphases 2023; 18:041203. [PMID: 37489909 DOI: 10.1116/6.0002820] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/29/2023] [Indexed: 07/26/2023] Open
Abstract
The purpose of this Tutorial is to highlight the suitability of time-of-flight secondary ion mass spectrometry (ToF-SIMS) and OrbiTrap™ SIMS (Orbi-SIMS) in bone research by introducing fundamentals and best practices of bone analysis with these mass spectrometric imaging (MSI) techniques. The Tutorial includes sample preparation, determination of best-suited measurement settings, data acquisition, and data evaluation, as well as a brief overview of SIMS applications in bone research in the current literature. SIMS is a powerful analytical technique that allows simultaneous analysis and visualization of mineralized and nonmineralized bone tissue, bone marrow as well as implanted biomaterials, and interfaces between bone and implants. Compared to histological staining, which is the standard analytical procedure in bone research, SIMS provides chemical imaging of nonstained bone sections that offers insights beyond what is conventionally obtained. The Tutorial highlights the versatility of ToF- and Orbi-SIMS in addressing important questions in bone research. By illustrating the value of these MSI techniques, it demonstrates how they can contribute to advance progress in bone research.
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Affiliation(s)
- Christine Kern
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Stefanie Kern
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Anja Henss
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Center for Materials Research, Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
| | - Marcus Rohnke
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Center for Materials Research, Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
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7
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Liu J, Hu W, Han Y, Nie H. Recent advances in mass spectrometry imaging of single cells. Anal Bioanal Chem 2023:10.1007/s00216-023-04774-9. [PMID: 37269305 DOI: 10.1007/s00216-023-04774-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/05/2023]
Abstract
Mass spectrometry imaging (MSI) is a sensitive, specific, label-free imaging analysis technique that can simultaneously obtain the spatial distribution, relative content, and structural information of hundreds of biomolecules in cells and tissues, such as lipids, small drug molecules, peptides, proteins, and other compounds. The study of molecular mapping of single cells can reveal major scientific issues such as the activity pattern of living organisms, disease pathogenesis, drug-targeted therapy, and cellular heterogeneity. Applying MSI technology to the molecular mapping of single cells can provide new insights and ideas for the study of single-cell metabolomics. This review aims to provide an informative resource for those in the MSI community who are interested in single-cell imaging. Particularly, we discuss advances in imaging schemes and sample preparation, instrumentation improvements, data processing and analysis, and 3D MSI over the past few years that have allowed MSI to emerge as a powerful technique in the molecular imaging of single cells. Also, we highlight some of the most cutting-edge studies in single-cell MSI, demonstrating the future potential of single-cell MSI. Visualizing molecular distribution at the single-cell or even sub-cellular level can provide us with richer cell information, which strongly contributes to advancing research fields such as biomedicine, life sciences, pharmacodynamic testing, and metabolomics. At the end of the review, we summarize the current development of single-cell MSI technology and look into the future of this technology.
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Affiliation(s)
- Jikun Liu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Analytical Instrumental Center, Peking University, Beijing, 100871, China
| | - Wenya Hu
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Analytical Instrumental Center, Peking University, Beijing, 100871, China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, 102249, China.
| | - Honggang Nie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Analytical Instrumental Center, Peking University, Beijing, 100871, China.
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8
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Deng G, Zha H, Luo H, Zhou Y. Aptamer-conjugated gold nanoparticles and their diagnostic and therapeutic roles in cancer. Front Bioeng Biotechnol 2023; 11:1118546. [PMID: 36741760 PMCID: PMC9892635 DOI: 10.3389/fbioe.2023.1118546] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
The burden of incidence rate and mortality of cancer is increasing rapidly, and the development of precise intervention measures for cancer detection and treatment will help reduce the burden and pain of cancer. At present, the sensitivity and specificity of tumor markers such as CEA and CA-125 used clinically are low, while PET, SPECT, and other imaging diagnoses with high sensitivity possess shortcomings, including long durations to obtain formal reports and the inability to identify the molecular pathological type of cancer. Cancer surgery is limited by stage and easy to recur. Radiotherapy and chemotherapy often cause damage to normal tissues, leading to evident side effects. Aptamers can selectively and exclusively bind to biomarkers and have, therefore, gained attention as ligands to be targeted for cancer detection and treatment. Gold nanoparticles (AuNPs) are considered as promising nano carriers for cancer diagnosis and treatment due to their strong light scattering characteristics, effective biocompatibility, and easy surface modification with targeted agents. The aptamer-gold nanoparticles targeting delivery system developed herein can combine the advantages of aptamers and gold nanoparticles, and shows excellent targeting, high specificity, low immunogenicity, minor side effects, etc., which builds a bridge for cancer markers to be used in early and efficient diagnosis and precise treatment. In this review, we summarize the latest progress in the application of aptamer-modified gold nanoparticles in cancer targeted diagnosis and delivery of therapeutic agents to cancer cells and emphasize the prospects and challenges of transforming these studies into clinical applications.
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Affiliation(s)
- Guozhen Deng
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - He Zha
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Hongzhi Luo
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Yi Zhou
- Department of Orthopaedics, Jian Yang Hospital of Traditional Chinese Medicine, JianYang, Sichuan, China
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9
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Lusk HJ, Levy SE, Bergsten TM, Burdette JE, Sanchez LM. Home-Built Spinning Apparatus for Drying Agarose-Based Imaging Mass Spectrometry Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1325-1328. [PMID: 35640101 PMCID: PMC9262851 DOI: 10.1021/jasms.2c00044] [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: 05/07/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a useful technique for mapping the spatial distribution of molecules across biological samples. Sample preparation is crucial for MALDI-IMS; samples must be flat, dry, and cocrystallized with a matrix prior to analysis. Agarose-based samples can be difficult to consistently prepare as they are susceptible to environmental changes, which can lead to inconsistent drying and wrinkling on the sample surface. Small height differences may cause low ionization of target analytes or introduce artifacts in imaging data depending on the instrument used for analysis. To overcome the variations, a home-built robotic spinner was constructed and applied to agarose-based samples. This robotic spinner is inexpensive and easy to assemble, and when it was applied to agarose-based samples, accelerated the drying process and reduced wrinkles, improving the overall quality of the resulting IMS data.
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Affiliation(s)
- Hannah J. Lusk
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St, Santa Cruz, CA 95064, United States
| | - Sarah E. Levy
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St, Santa Cruz, CA 95064, United States
| | - Tova M. Bergsten
- Department of Pharmaceutical Sciences, University of Illinois at Chicago College of Pharmacy, 900 S Ashland Ave, Chicago IL 60607, United States
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, University of Illinois at Chicago College of Pharmacy, 900 S Ashland Ave, Chicago IL 60607, United States
| | - Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St, Santa Cruz, CA 95064, United States
- Corresponding author:
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10
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Mikolasch TA, Oballa E, Vahdati-Bolouri M, Jarvis E, Cui Y, Cahn A, Terry RL, Sahota J, Thakrar R, Marshall P, Porter JC. Mass spectrometry detection of inhaled drug in distal fibrotic lung. Respir Res 2022; 23:118. [PMID: 35546672 PMCID: PMC9092847 DOI: 10.1186/s12931-022-02026-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Background Currently the only available therapies for fibrotic Interstitial Lung Disease are administered systemically, often causing significant side effects. Inhaled therapy could avoid these but to date there is no evidence that drug can be effectively delivered to distal, fibrosed lung. We set out to combine mass spectrometry and histopathology with rapid sample acquisition using transbronchial cryobiopsy to determine whether an inhaled drug can be delivered to fibrotic, distal lung parenchyma in participants with Interstitial Lung Disease. Methods Patients with radiologically and multidisciplinary team confirmed fibrotic Interstitial Lung Disease were eligible for this study. Transbronchial cryobiopsies and endobronchial biopsies were taken from five participants, with Interstitial Lung Disease, within 70 min of administration of a single dose of nebulised ipratropium bromide. Thin tissue cryosections were analysed by Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry imaging and correlated with histopathology. The remainder of the cryobiopsies were homogenised and analysed by Liquid Chromatography—tandem Mass Spectrometry. Results Drug was detected in proximal and distal lung samples from all participants. Fibrotic regions were identified in research samples of four of the five participants. Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry imaging showed co-location of ipratropium with fibrotic regions in samples from three participants. Conclusions In this proof of concept study, using mass spectrometry, we demonstrate for the first-time that an inhaled drug can deposit in distal fibrotic lung parenchyma in patients with Interstitial Lung Disease. This suggests that drugs to treat pulmonary fibrosis could potentially be administered by the inhaled route. Trial registration A prospective clinical study approved by London Camden and Kings Cross Research Ethics Committee and registered on clinicaltrials.gov (NCT03136120) Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02026-5.
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Affiliation(s)
- Theresia A Mikolasch
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK. .,University College London Hospitals NHS Foundation Trust, London, UK.
| | - Eunice Oballa
- Discovery Medicine, Clinical Pharmacology and Experimental Medicine, GSK Research and Development, Stevenage, UK
| | | | - Emily Jarvis
- Development Biostatistics, GSK Development, Stevenage, UK
| | - Yi Cui
- Safety and Medical Governance, Pharma Safety, GSK Development, Stevenage, UK
| | - Anthony Cahn
- Discovery Medicine, Clinical Pharmacology and Experimental Medicine, GSK Research and Development, Stevenage, UK
| | - Rebecca L Terry
- Pathology, In Vitro/In Vivo Translation, GSK Research, Stevenage, UK
| | - Jagdeep Sahota
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK.,University College London Hospitals NHS Foundation Trust, London, UK
| | - Ricky Thakrar
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Peter Marshall
- Bioimaging, In Vitro/In Vivo Translation, GSK Research, Stevenage, UK
| | - Joanna C Porter
- Centre for Inflammation and Tissue Repair, UCL Respiratory, University College London, London, UK.,University College London Hospitals NHS Foundation Trust, London, UK
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11
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Zhu X, Xu T, Peng C, Wu S. Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues. Front Chem 2022; 9:782432. [PMID: 35186891 PMCID: PMC8850921 DOI: 10.3389/fchem.2021.782432] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or imaging mass spectrometry (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, and map hundreds of biomolecules, such as peptides, proteins, lipid, and other organic compounds in cells and tissues. So far, although several soft ionization techniques, such as desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS) have been used for imaging biomolecules, matrix-assisted laser desorption/ionization (MALDI) is still the most widespread MSI scanning method. Here, we aim to provide a comprehensive review of MALDI-MSI with an emphasis on its advances of the instrumentation, methods, application, and future directions in single cell and biological tissues.
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Affiliation(s)
- Xiaoping Zhu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianyi Xu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Shihua Wu, ; Shihua Wu,
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12
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Noun M, Akoumeh R, Abbas I. Cell and Tissue Imaging by TOF-SIMS and MALDI-TOF: An Overview for Biological and Pharmaceutical Analysis. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-26. [PMID: 34809729 DOI: 10.1017/s1431927621013593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of mass spectrometry imaging (MSI) has been demonstrated in cell and tissue research since 1970. MSI can reveal the spatial distribution of a wide range of atomic and molecular ions detected from biological sample surfaces, it is a powerful and valuable technique used to monitor and detect diverse chemical and biological compounds, such as drugs, lipids, proteins, and DNA. MSI techniques, notably matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and time of flight secondary ion mass spectrometry (TOF-SIMS), witnessed a dramatic upsurge in studying and investigating biological samples especially, cells and tissue sections. This advancement is attributed to the submicron lateral resolution, the high sensitivity, the good precision, and the accurate chemical specificity, which make these techniques suitable for decoding and understanding complex mechanisms of certain diseases, as well as monitoring the spatial distribution of specific elements, and compounds. While the application of both techniques for the analysis of cells and tissues is thoroughly discussed, a briefing of MALDI-TOF and TOF-SIMS basis and the adequate sampling before analysis are briefly covered. The importance of MALDI-TOF and TOF-SIMS as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields is highlighted through representative published studies.
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Affiliation(s)
- Manale Noun
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Rayane Akoumeh
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Imane Abbas
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
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13
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Engel KM, Prabutzki P, Leopold J, Nimptsch A, Lemmnitzer K, Vos DRN, Hopf C, Schiller J. A new update of MALDI-TOF mass spectrometry in lipid research. Prog Lipid Res 2022; 86:101145. [PMID: 34995672 DOI: 10.1016/j.plipres.2021.101145] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 01/06/2023]
Abstract
Matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS) is an indispensable tool in modern lipid research since it is fast, sensitive, tolerates sample impurities and provides spectra without major analyte fragmentation. We will discuss some methodological aspects, the related ion-forming processes and the MALDI MS characteristics of the different lipid classes (with the focus on glycerophospholipids) and the progress, which was achieved during the last ten years. Particular attention will be given to quantitative aspects of MALDI MS since this is widely considered as the most serious drawback of the method. Although the detailed role of the matrix is not yet completely understood, it will be explicitly shown that the careful choice of the matrix is crucial (besides the careful evaluation of the positive and negative ion mass spectra) in order to be able to detect all lipid classes of interest. Two developments will be highlighted: spatially resolved Imaging MS is nowadays well established and the distribution of lipids in tissues merits increasing interest because lipids are readily detectable and represent ubiquitous compounds. It will also be shown that a combination of MALDI MS with thin-layer chromatography (TLC) enables a fast spatially resolved screening of an entire TLC plate which makes the method competitive with LC/MS.
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Affiliation(s)
- Kathrin M Engel
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Patricia Prabutzki
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Jenny Leopold
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Ariane Nimptsch
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Katharina Lemmnitzer
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - D R Naomi Vos
- Center for Biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, D-68163 Mannheim, Germany
| | - Carsten Hopf
- Center for Biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, D-68163 Mannheim, Germany
| | - Jürgen Schiller
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany.
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14
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Robinson E, Giffen P, Hassall D, Ball D, Reid H, Coe D, Teague S, Terry R, Earl M, Marchand J, Farrer B, Havelund R, Gilmore IS, Marshall PS. Multimodal imaging of drug and excipients in rat lungs following an inhaled administration of controlled-release drug laden PLGA microparticles. Analyst 2021; 146:3378-3390. [PMID: 33876155 DOI: 10.1039/d0an02333g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Controlled-release formulations, in the form of micro- or nanoparticles, are increasingly attractive to the pharmaceutical industry for drug delivery. For respiratory illnesses, controlled-release microparticle formulations provide an opportunity to deliver a higher percentage of an inhaled medicament dose to the lung, thus potentially reducing the therapeutic dose, frequency of dosing, and minimising side-effects. We describe the use of a multimodal approach consisting of MALDI MS imaging, 3D depth profiling TOF-SIMS analysis, and histopathology to monitor the distribution of drug and excipients in sections taken from excised rat lungs following an inhaled administration of drug-laden microparticles. Following a single dose, the administered drug was detected in the lung via both MALDI MS and TOF-SIMS over a range of time points. Both imaging techniques enabled the characterisation of the distribution and retention of drug particles and identified differences in the capabilities of both imaging modalities. Histochemical staining of consecutive sections was used to provide biological context to the findings and will also be discussed in this presentation. We demonstrate how this multimodal approach could be used to help increase our understanding of the use of controlled release microparticles.
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Affiliation(s)
- Eve Robinson
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK.
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15
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Nguyen DP, Nguyen HTH, Do LH. Tools and Methods for Investigating Synthetic Metal-Catalyzed Reactions in Living Cells. ACS Catal 2021; 11:5148-5165. [PMID: 34824879 PMCID: PMC8612649 DOI: 10.1021/acscatal.1c00438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although abiotic catalysts are capable of promoting numerous new-to-nature reactions, only a small subset has so far been successfully integrated into living systems. Research in intracellular catalysis requires an interdisciplinary approach that takes advantage of both chemical and biological tools as well as state-of-the-art instrumentations. In this perspective, we will focus on the techniques that have made studying metal-catalyzed reactions in cells possible using representative examples from the literature. Although the lack of quantitative data in vitro and in vivo has somewhat limited progress in the catalyst development process, recent advances in characterization methods should help overcome some of these deficiencies. Given its tremendous potential, we believe that intracellular catalysis will play a more prominent role in the development of future biotechnologies and therapeutics.
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Affiliation(s)
- Dat P. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Huong T. H. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Loi H. Do
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
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16
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Nabi MM, Mamun MA, Islam A, Hasan MM, Waliullah ASM, Tamannaa Z, Sato T, Kahyo T, Setou M. Mass spectrometry in the lipid study of cancer. Expert Rev Proteomics 2021; 18:201-219. [PMID: 33793353 DOI: 10.1080/14789450.2021.1912602] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Cancer is a heterogeneous disease that exploits various metabolic pathways to meet the demand for increased energy and structural components. Lipids are biomolecules that play essential roles as high energy sources, mediators, and structural components of biological membranes. Accumulating evidence has established that altered lipid metabolism is a hallmark of cancer.Areas covered: Mass spectrometry (MS) is a label-free analytical tool that can simultaneously identify and quantify hundreds of analytes. To date, comprehensive lipid studies exclusively rely on this technique. Here, we reviewed the use of MS in the study of lipids in various cancers and discuss its instrumental limitations and challenges.Expert opinion: MS and MS imaging have significantly contributed to revealing altered lipid metabolism in a variety of cancers. Currently, a single MS approach cannot profile the entire lipidome because of its lack of sensitivity and specificity for all lipid classes. For the metabolic pathway investigation, lipid study requires the integration of MS with other molecular approaches. Future developments regarding the high spatial resolution, mass resolution, and sensitivity of MS instruments are warranted.
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Affiliation(s)
- Md Mahamodun Nabi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Ganakbari, Savar, Dhaka, Bangladesh
| | - Md Al Mamun
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Ariful Islam
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Md Mahmudul Hasan
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - A S M Waliullah
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Zinat Tamannaa
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Tomohito Sato
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Tomoaki Kahyo
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu, Shizuoka, Japan
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17
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Huang Q, Garrett A, Bose S, Blocker S, Rios AC, Clevers H, Shen X. The frontier of live tissue imaging across space and time. Cell Stem Cell 2021; 28:603-622. [PMID: 33798422 PMCID: PMC8034393 DOI: 10.1016/j.stem.2021.02.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
What you see is what you get-imaging techniques have long been essential for visualization and understanding of tissue development, homeostasis, and regeneration, which are driven by stem cell self-renewal and differentiation. Advances in molecular and tissue modeling techniques in the last decade are providing new imaging modalities to explore tissue heterogeneity and plasticity. Here we describe current state-of-the-art imaging modalities for tissue research at multiple scales, with a focus on explaining key tradeoffs such as spatial resolution, penetration depth, capture time/frequency, and moieties. We explore emerging tissue modeling and molecular tools that improve resolution, specificity, and throughput.
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Affiliation(s)
- Qiang Huang
- Department of Pediatric Surgery, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004 Shaanxi, China; Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Aliesha Garrett
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Shree Bose
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Stephanie Blocker
- Center for In Vitro Microscopy, Duke University, Durham, NC 27708, USA
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584, the Netherlands; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht 3584, the Netherlands
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584, the Netherlands; Department of Cancer Research, Oncode Institute, Hubrecht Institute-KNAW Utrecht, Utrecht 3584, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht 3584, the Netherlands
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA.
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18
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Dueñas ME, Lee YJ. Single-Cell Metabolomics by Mass Spectrometry Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:69-82. [PMID: 33791975 DOI: 10.1007/978-3-030-51652-9_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multicellular organisms achieve their complex living activities through the highly organized metabolic interplay of individual cells and tissues. This complexity has driven the need to spatially resolve metabolomics down to the cellular and subcellular level. Recent technological advances have enabled mass spectrometry imaging (MSI), especially matrix-assisted laser desorption/ionization (MALDI), to become a powerful tool for the visualization of molecular species down to subcellular spatial resolution. In the present chapter, we summarize recent advances in the field of MALDI-MSI, with respect to single-cell level resolution metabolomics directly on tissue. In more detail, we focus on advancements in instrumentation for MSI at single-cell resolution, and the applications towards metabolomic scale imaging. Finally, we discuss new computational tools to aid in metabolite identification, future perspective, and the overall direction that the field of single-cell metabolomics directly on tissue may take in the years to come.
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Affiliation(s)
- Maria Emilia Dueñas
- Department of Chemistry, Iowa State University, Ames, IA, USA.
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, USA
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19
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Sekera ER, Saraswat D, Zemaitis KJ, Sim FJ, Wood TD. MALDI Mass Spectrometry Imaging in a Primary Demyelination Model of Murine Spinal Cord. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2462-2468. [PMID: 32926612 PMCID: PMC8628303 DOI: 10.1021/jasms.0c00187] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Destruction of myelin, or demyelination, is a characteristic of traumatic spinal cord injury and pathognomonic for primary demyelinating pathologies such as multiple sclerosis (MS). The regenerative process known as remyelination, which can occur following demyelination, fails as MS progresses. Models of focal demyelination by local injection of gliotoxins have provided important biological insights into the demyelination/remyelination process. Here, injection of lysolecithin to induce spinal cord demyelination is investigated using matrix-assisted laser desorption/ionization mass spectrometry imaging. A segmentation analysis revealed changes to the lipid composition during lysolecithin-induced demyelination at the lesion site and subsequent remyelination over time. The results of this study can be utilized to identify potential myelin-repair mechanisms and in the design of therapeutic strategies to enhance myelin repair.
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Affiliation(s)
- Emily R Sekera
- Department of Chemistry, Natural Sciences Complex, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Darpan Saraswat
- Department of Pharmacology & Toxicology, Jacobs School of Medicine and Biomedical Sciences, 955 Main Street, University at Buffalo State University of New York, Buffalo, New York 14203, United States
| | - Kevin J Zemaitis
- Department of Chemistry, Natural Sciences Complex, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Fraser J Sim
- Department of Pharmacology & Toxicology, Jacobs School of Medicine and Biomedical Sciences, 955 Main Street, University at Buffalo State University of New York, Buffalo, New York 14203, United States
| | - Troy D Wood
- Department of Chemistry, Natural Sciences Complex, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
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20
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Yan X, Zhao X, Zhou Z, McKay A, Brunet A, Zare RN. Cell-Type-Specific Metabolic Profiling Achieved by Combining Desorption Electrospray Ionization Mass Spectrometry Imaging and Immunofluorescence Staining. Anal Chem 2020; 92:13281-13289. [PMID: 32880432 PMCID: PMC8782277 DOI: 10.1021/acs.analchem.0c02519] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cell-type-specific metabolic profiling in tissue with heterogeneous composition has been of great interest across all mass spectrometry imaging (MSI) technologies. We report here a powerful new chemical imaging capability in desorption electrospray ionization (DESI) MSI, which enables cell-type-specific and in situ metabolic profiling in complex tissue samples. We accomplish this by combining DESI-MSI with immunofluorescence staining using specific cell-type markers. We take advantage of the variable frequency of each distinct cell type in the lateral septal nucleus (LSN) region of mouse forebrain. This allows computational deconvolution of the cell-type-specific metabolic profile in neurons and astrocytes by convex optimization-a machine learning method. Based on our approach, we observed 107 metabolites that show different distributions and intensities between astrocytes and neurons. We subsequently identified 23 metabolites using high-resolution mass spectrometry (MS) and tandem MS, which include small metabolites such as adenosine and N-acetylaspartate previously associated with astrocytes and neurons, respectively, as well as accumulation of several phospholipid species in neurons which have not been studied before. Overall, this method overcomes the relatively low spatial resolution of DESI-MSI and provides a new platform for in situ metabolic investigation at the cell-type level in complex tissue samples with heterogeneous cell-type composition.
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Affiliation(s)
- Xin Yan
- Department of Chemistry, Texas A&M University, College Station, TX 77843.; Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Xiaoai Zhao
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Zhenpeng Zhou
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Andrew McKay
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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21
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Tian J, Fu G, Xu Z, Chen X, Sun J, Jin B. Urinary exfoliated tumor single-cell metabolomics technology for establishing a drug resistance monitoring system for bladder cancer with intravesical chemotherapy. Med Hypotheses 2020; 143:110100. [DOI: 10.1016/j.mehy.2020.110100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022]
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22
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Flint LE, Hamm G, Ready JD, Ling S, Duckett CJ, Cross NA, Cole LM, Smith DP, Goodwin RJA, Clench MR. Characterization of an Aggregated Three-Dimensional Cell Culture Model by Multimodal Mass Spectrometry Imaging. Anal Chem 2020; 92:12538-12547. [PMID: 32786495 PMCID: PMC7497704 DOI: 10.1021/acs.analchem.0c02389] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Mass
spectrometry imaging (MSI) is an established analytical tool
capable of defining and understanding complex tissues by determining
the spatial distribution of biological molecules. Three-dimensional
(3D) cell culture models mimic the pathophysiological environment
of in vivo tumors and are rapidly emerging as a valuable
research tool. Here, multimodal MSI techniques were employed to characterize
a novel aggregated 3D lung adenocarcinoma model, developed by the
group to mimic the in vivo tissue. Regions of tumor
heterogeneity and the hypoxic microenvironment were observed based
on the spatial distribution of a variety of endogenous molecules.
Desorption electrospray ionization (DESI)-MSI defined regions of a
hypoxic core and a proliferative outer layer from metabolite distribution.
Targeted metabolites (e.g., lactate, glutamine, and citrate) were
mapped to pathways of glycolysis and the TCA cycle demonstrating tumor
metabolic behavior. The first application of imaging mass cytometry
(IMC) with 3D cell culture enabled single-cell phenotyping at 1 μm
spatial resolution. Protein markers of proliferation (Ki-67) and hypoxia (glucose transporter 1) defined metabolic
signaling in the aggregoid model, which complemented the metabolite
data. Laser ablation inductively coupled plasma (LA-ICP)-MSI analysis
localized endogenous elements including magnesium and copper, further
differentiating the hypoxia gradient and validating the protein expression.
Obtaining a large amount of molecular information on a complementary
nature enabled an in-depth understanding of the biological processes
within the novel tumor model. Combining powerful imaging techniques
to characterize the aggregated 3D culture highlighted a future methodology
with potential applications in cancer research and drug development.
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Affiliation(s)
- Lucy E Flint
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Gregory Hamm
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 0WG, United Kingdom
| | - Joseph D Ready
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Stephanie Ling
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 0WG, United Kingdom
| | - Catherine J Duckett
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Neil A Cross
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Laura M Cole
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - David P Smith
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Richard J A Goodwin
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 0WG, United Kingdom.,Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
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23
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Robison HM, Chini CE, Comi TJ, Ryu SW, Ognjanovski E, Perry RH. Identification of lipid biomarkers of metastatic potential and gene expression (HER2/p53) in human breast cancer cell cultures using ambient mass spectrometry. Anal Bioanal Chem 2020; 412:2949-2961. [PMID: 32322955 DOI: 10.1007/s00216-020-02537-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
In breast cancer, overexpression of human epidermal growth factor receptor 2 (HER2) correlates with overactivation of lipogenesis, mutation of tumor suppressor p53, and increased metastatic potential. The mechanisms through which lipids mediate p53, HER2, and metastatic potential are largely unknown. We have developed a desorption electrospray ionization mass spectrometry (DESI-MS) method to identify lipid biomarkers of HER2/p53 expression, metastatic potential, and disease state (viz. cancer vs. non-cancerous) in monolayer and suspension breast cancer cell cultures (metastatic potential: MCF-7, T-47D, MDA-MB-231; HER2/p53: HCC2218 (HER2+++/p53+), HCC1599 (HER2-/p53-), HCC202 (HER2++/p53-), HCC1419 (HER2+++/p53-) HCC70 (HER2-/p53+++); non-cancerous: MCF-10A). Unsupervised principal component analysis (PCA) of DESI-MS spectra enabled identification of twelve lipid biomarkers of metastatic potential and disease state, as well as ten lipids that distinguish cell lines based on HER2/p53 expression levels (> 200 lipids were identified per cell line). In addition, we developed a DESI-MS imaging (DESI-MSI) method for mapping the spatial distribution of lipids in metastatic spheroids (MDA-MB-231). Of the twelve lipids that correlate with changes in the metastatic potential of monolayer cell cultures, three were localized to the necrotic core of spheroids, indicating a potential role in promoting cancer cell survival in nutrient-deficient environments. One lipid species, which was not detected in monolayer MDA-MB-231 cultures, was spatially localized to the periphery of the spheroid, suggesting a potential role in invasion and/or proliferation. These results demonstrate that combining DESI-MS/PCA of monolayer and suspension cell cultures with DESI-MSI of spheroids is a promising approach for identifying lipid biomarkers of specific genotypes and phenotypes, as well as elucidating the potential function of these biomarkers in breast cancer. Graphical Absract.
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Affiliation(s)
- Heather M Robison
- Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA
| | - Corryn E Chini
- Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA
| | - Troy J Comi
- Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA
| | - Seung Woo Ryu
- Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA
| | - Elaine Ognjanovski
- Department of Chemistry and Physics, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Richard H Perry
- Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA. .,Department of Chemistry and Physics, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA.
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24
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Abstract
Metabolomics uses advanced analytical chemistry techniques to enable the high-throughput characterization of metabolites from cells, organs, tissues, or biofluids. The rapid growth in metabolomics is leading to a renewed interest in metabolism and the role that small molecule metabolites play in many biological processes. As a result, traditional views of metabolites as being simply the "bricks and mortar" of cells or just the fuel for cellular energetics are being upended. Indeed, metabolites appear to have much more varied and far more important roles as signaling molecules, immune modulators, endogenous toxins, and environmental sensors. This review explores how metabolomics is yielding important new insights into a number of important biological and physiological processes. In particular, a major focus is on illustrating how metabolomics and discoveries made through metabolomics are improving our understanding of both normal physiology and the pathophysiology of many diseases. These discoveries are yielding new insights into how metabolites influence organ function, immune function, nutrient sensing, and gut physiology. Collectively, this work is leading to a much more unified and system-wide perspective of biology wherein metabolites, proteins, and genes are understood to interact synergistically to modify the actions and functions of organelles, organs, and organisms.
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Affiliation(s)
- David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
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25
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Channaveerappa D, Ngounou Wetie AG, Darie CC. Bottlenecks in Proteomics: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:753-769. [PMID: 31347083 DOI: 10.1007/978-3-030-15950-4_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Mass spectrometry (MS) is the core for advanced methods in proteomic experiments. When effectively used, proteomics may provide extensive information about proteins and their post-translational modifications, as well as their interaction partners. However, there are also many problems that one can encounter during a proteomic experiment, including, but not limited to sample preparation, sample fractionation, sample analysis, data analysis & interpretation and biological significance. Here we discuss some of the problems that researchers should be aware of when performing a proteomic experiment.
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Affiliation(s)
- Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.
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26
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Precision pharmacology: Mass spectrometry imaging and pharmacokinetic drug resistance. Crit Rev Oncol Hematol 2019; 141:153-162. [PMID: 31302407 DOI: 10.1016/j.critrevonc.2019.06.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 12/27/2022] Open
Abstract
Failure of systemic cancer treatment can be, at least in part, due to the drug not being delivered to the tumour at sufficiently high concentration and/or sufficiently homogeneous distribution; this is termed as "pharmacokinetic drug resistance". To understand whether a drug is being adequately delivered to the tumour, "precision pharmacology" techniques are needed. Mass spectrometry imaging (MSI) is a relatively new and complex technique that allows imaging of drug distribution within tissues. In this review we address the applicability of MSI to the study of cancer drug distribution from the bench to the bedside. We address: (i) the role of MSI in pre-clinical studies to characterize anti-cancer drug distribution within the body and the tumour, (ii) the application of MSI in pre-clinical studies to define optimal drug dose or schedule, combinations or new drug delivery systems, and finally (iii) the emerging role of MSI in clinical research.
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Tucker LH, Hamm GR, Sargeant RJE, Goodwin RJA, Mackay CL, Campbell CJ, Clarke DJ. Untargeted Metabolite Mapping in 3D Cell Culture Models Using High Spectral Resolution FT-ICR Mass Spectrometry Imaging. Anal Chem 2019; 91:9522-9529. [DOI: 10.1021/acs.analchem.9b00661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lulu H. Tucker
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Gregory R. Hamm
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Rebecca J. E. Sargeant
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Richard J. A. Goodwin
- Pathology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - C. Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Colin J. Campbell
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - David J. Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
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Wang M, Dubiak K, Zhang Z, Huber PW, Chen DDY, Dovichi NJ. MALDI-imaging of early stage Xenopus laevis embryos. Talanta 2019; 204:138-144. [PMID: 31357275 DOI: 10.1016/j.talanta.2019.05.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/12/2019] [Accepted: 05/13/2019] [Indexed: 01/10/2023]
Abstract
Xenopus laevis is an important model organism for vertebrate development. An extensive literature has developed on changes in transcript expression during development of this organism, and there is a growing literature on the corresponding protein expression changes during development. In contrast, there is very little information on changes in metabolite expression during development. We present the first MALDI mass-spectrometry images of metabolites within the developing embryo. These images were generated for 142 metabolite ions. The images were subjected to an algorithm that revealed three spatially-resolved clusters of metabolites. One small cluster is localized near the outer membrane of the embryo. A large cluster of metabolites is found in cavities destined to form the neural tube and gut, and contains a number of ceramide species, which are associated with cellular signaling, including differentiation, proliferation, and programmed cell death. Another large cluster of metabolites is found in tissue and is dominated by phosphatidylcholines, which are common components of cell membranes. Surprisingly, no metabolites appear to be homogeneously distributed across the slices; metabolites are localized either within tissue or in cavities, but not both.
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Affiliation(s)
- Man Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Kyle Dubiak
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - David D Y Chen
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.
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‘What did I do wrong?’ An empirical evaluation of sample preparation methodologies in matrix-assisted laser desorption/ionization-mass spectrometry imaging. Future Sci OA 2019. [DOI: 10.4155/fsoa-2018-0095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: This guide aims to broaden the uptake of MALDI-MSI biomedical research by removing the initial ‘lag phase’ associated with empirical determination in sample preparation and data analysis. Methods: Samples from several tissue types were prepared for lipid, protein and peptide MSI analysis. Broadly, samples were cryo sectioned, mounted onto conductive MALDI slides and sublimed with an analyte specific matrix, recrystallised and analyzed in a Bruker UltrafleXtreme MALDI TOF/TOF. Results/conclusion: Here we present a general guide that serves as the first comprehensive, explanatory index for curation and verification of both sample preparation and data generation during the MALDI-MSI process.
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Xu J, Zhang Z, Liu R, Sun Y, Liu H, Nie Z, Zhao X, Pu X. Function of complement factor H and imaging of small molecules by MALDI-MSI in a methamphetamine behavioral sensitization model. Behav Brain Res 2019; 364:233-244. [PMID: 30731099 DOI: 10.1016/j.bbr.2019.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND At present, the harm of new-type drug, methamphetamine (METH), has gradually exceeded that of the traditional opioid drugs, and METH abuse has become a serious public health and social problem. In our previous study, complement factor H (CFH) was found to be upregulated in the sera of METH-addicted patients and rats and in certain brain regions in the rats. METHODS We used ELISA and immunofluorescence to confirm the changes in CFH in the serum and hippocampus of a METH behavioral sensitization mouse model, and C1q expression was also detected by immunofluorescence in the hippocampus. We aimed to elucidate the involvement of CFH and C1q in the mechanism of METH addiction. We also detected the distribution of various small molecules by matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) in select brain regions: the nucleus accumbens, the hippocampus and the ventral tegmental area. RESULTS The expression of CFH was upregulated in the serum and hippocampus of METH behavioral sensitization model mice, consistent with our previous research on conditioned place preference rats. In contrast, C1q decreased dramatically in the mossy fibers of the hippocampus. The results of small-molecule imaging by MALDI-MSI showed that the levels of K+, antioxidants, neurotransmitters, and ATP metabolism-related molecules were altered in different regions. CONCLUSIONS These results indicate the involvement of the complement system in the mechanism of METH addiction and validate the presence of oxidative stress, energy metabolism changes during addiction. This suggests the utility of further investigation into the above aspects.
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Affiliation(s)
- Jiamin Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhilin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Runzhe Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yi Sun
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Huihui Liu
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, China; Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
| | - Zongxiu Nie
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, China; Beijing National Laboratory for Molecular Sciences, Beijing 100190, China; Beijing Center for Mass Spectrometry, Beijing 100190, China
| | - Xin Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaoping Pu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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Andrews WT, Skube SB, Hummon AB. Magnetic bead-based peptide extraction methodology for tissue imaging. Analyst 2018; 143:133-140. [PMID: 29119981 DOI: 10.1039/c7an00757d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MALDI-TOF imaging mass spectrometry (IMS) is a common technique used for analyzing tissue samples, as it allows the user to detect multiple different analytes simultaneously. However, the detection and analysis of these analytes may sometimes be hampered due to the presence of contaminants in the tissue microenvironment, which leads to ion suppression. This challenge necessitates the development of an active extraction technique to selectively isolate analytes of interest without compromising their spatial localization within a tissue sample. This study proposes a magnetic bead-based active extraction approach to selectively sequester peptides of interest from tissue samples. The technique utilizes a heterobifunctional cross-linker to covalently bind peptides with free primary amine groups to functionalized magnetic beads. The cross-linked peptides can then be collected using a transfer magnet and imaged using MALDI-TOF IMS. We have established that this technique not only successfully isolates peptides both in-solution and on a solid surface, but also extracts peptides from a tissue section without significantly compromising their spatial localization. This novel method provides the means to detect a unique subset of peptides from tissue sections when compared to unextracted tryptically digested tissue, all while minimizing the presence of contaminants and maintaining spatial localization.
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Affiliation(s)
- William T Andrews
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA.
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Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
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Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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Liu X, Lukowski JK, Flinders C, Kim S, Georgiadis RA, Mumenthaler SM, Hummon AB. MALDI-MSI of Immunotherapy: Mapping the EGFR-Targeting Antibody Cetuximab in 3D Colon-Cancer Cell Cultures. Anal Chem 2018; 90:14156-14164. [PMID: 30479121 DOI: 10.1021/acs.analchem.8b02151] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Immunotherapies are treatments that use a patient's immune system to combat disease. One important type of immunotherapy employed in cancer treatments is the delivery of monoclonal antibodies to block growth receptors. In this manuscript, we develop a methodology that enables accurate and simple evaluation of antibody-type drug delivery using MALDI-MSI. To overcome the mass-range limitation that prevents the detection of large therapeutic antibodies, we used in situ reduction and alkylation to break disulfide bonds to generate smaller fragments. These smaller fragments are more readily ionized and detected by MALDI-MSI without loss of spatial information on the parent drug. As a proof of concept study, we evaluated the distribution of cetuximab in 3D colon cell cultures. Cetuximab is a monoclonal antibody that binds to the extracellular domain of epidermal-growth-factor receptor (EGFR), which is often overexpressed in colorectal cancer (CRC) and mediates cell differentiation, proliferation, migration, and angiogenesis. Cetuximab directly inhibits tumor growth and metastasis and induces apoptosis. By performing on-tissue reduction followed by MALDI-MSI analysis, we successfully mapped the time-dependent penetration and distribution of cetuximab in spheroids derived from two different colon-cancer cell lines (HT-29 and DLD-1). The localization patterns were further confirmed with IF staining of the drug. Changes in other biomolecules following drug treatment were also observed, including the elevation of ATP in spheroids. The developed method has also been applied to map cetuximab distribution in patient-derived colorectal-tumor organoids (CTOs). Overall, we believe this powerful label-free approach will be useful for visualizing the heterogeneous distribution of antibody drugs in tissues and tumors and will help to monitor and optimize their use in the clinic.
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Affiliation(s)
- Xin Liu
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute , University of Notre Dame , 152 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Jessica K Lukowski
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute , University of Notre Dame , 152 McCourtney Hall , Notre Dame , Indiana 46556 , United States.,Department of Chemistry and Biochemistry and Comprehensive Cancer Center , The Ohio State University , 414 Biomedical Research Tower , Columbus , Ohio 43210 , United States
| | - Colin Flinders
- Lawrence J. Ellison Institute for Transformative Medicine , University of Southern California , 2250 Alcazar Street, CSC 240 , Los Angeles , California 90033 , United States
| | - Seungil Kim
- Lawrence J. Ellison Institute for Transformative Medicine , University of Southern California , 2250 Alcazar Street, CSC 240 , Los Angeles , California 90033 , United States
| | - Rebecca A Georgiadis
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute , University of Notre Dame , 152 McCourtney Hall , Notre Dame , Indiana 46556 , United States
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine , University of Southern California , 2250 Alcazar Street, CSC 240 , Los Angeles , California 90033 , United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry and Comprehensive Cancer Center , The Ohio State University , 414 Biomedical Research Tower , Columbus , Ohio 43210 , United States
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Zink K, Dean M, Burdette JE, Sanchez LM. Imaging Mass Spectrometry Reveals Crosstalk between the Fallopian Tube and the Ovary that Drives Primary Metastasis of Ovarian Cancer. ACS CENTRAL SCIENCE 2018; 4:1360-1370. [PMID: 30410974 PMCID: PMC6202655 DOI: 10.1021/acscentsci.8b00405] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Indexed: 05/05/2023]
Abstract
High grade serous ovarian cancer (HGSOC) is the fifth leading cause of cancer deaths among women. New evidence suggests that HGSOC arises in the fallopian tube and then colonizes the ovary before spreading into the peritoneal space. Therefore, due to the proximity of this metastasis, an experimental design was optimized using imaging mass spectrometry to capture the spatial composition of small molecules uniquely expressed when fallopian-tube-derived tumor cells were grown in the microenvironment of the ovary as a model of primary metastasis. The observed mass-to-charge ratios (m/z's) that were induced specifically in coculture represent small molecules that may contribute to the metastasis of HGSOC selectively to the ovary. Human fallopian tube epithelial HGSOC and tumorigenic murine oviductal epithelial cells, but not normal cell types, repeatedly induced a signal from the ovary at m/z 170. This signal was identified as norepinephrine, which was confirmed to stimulate invasion of ovarian cancer cells lacking wild-type p53. These molecules may reveal pathways that contribute to metastasis and biological targets for therapeutic intervention to block ovarian metastasis of fallopian-tube-derived HGSOC. The developed mass spectrometry method can be adapted to other mammalian-based model systems for investigation of untargeted metabolomics that facilitate metastasis.
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35
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Proteomic-genomic adjustments and their confluence for elucidation of pathways and networks during liver fibrosis. Int J Biol Macromol 2018; 111:379-392. [DOI: 10.1016/j.ijbiomac.2017.12.168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/28/2017] [Accepted: 12/31/2017] [Indexed: 12/31/2022]
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Abstract
Drug metabolites have been monitored with various types of newly developed techniques and/or combination of common analytical methods, which could provide a great deal of information on metabolite profiling. Because it is not easy to analyze whole drug metabolites qualitatively and quantitatively, a single solution of analytical techniques is combined in a multilateral manner to cover the widest range of drug metabolites. Mass-based spectroscopic analysis of drug metabolites has been expanded with the help of other parameter-based methods. The current development of metabolism studies through contemporary pharmaceutical research are reviewed with an overview on conventionally used spectroscopic methods. Several technical approaches for conducting drug metabolic profiling through spectroscopic methods are discussed in depth.
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Affiliation(s)
- Jong-Jae Yi
- Department of Pharmacy, College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon-Si, Gyeonggi-do, 11160, Republic of Korea
| | - Kyeongsoon Park
- Department of Systems Biotechnology, College of Biotechnology and Natural Resources, Chung-Ang University, 4726 Seodong-daero, Anseong-Si, Gyeonggi-do, 17546, Republic of Korea
| | - Won-Je Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea.
| | - Woo Sung Son
- Department of Pharmacy, College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon-Si, Gyeonggi-do, 11160, Republic of Korea.
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37
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O'Rourke MB, Djordjevic SP, Padula MP. The quest for improved reproducibility in MALDI mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:217-228. [PMID: 27420733 DOI: 10.1002/mas.21515] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/19/2016] [Accepted: 06/16/2016] [Indexed: 05/18/2023]
Abstract
Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018.
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Affiliation(s)
- Matthew B O'Rourke
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
| | - Steven P Djordjevic
- The iThree Institute, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
| | - Matthew P Padula
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
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O'Rourke MB, Raymond BBA, Djordjevic SP, Padula MP. The Effect of Collimating Lens Focusing on Laser Beam Shape in Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:512-515. [PMID: 29313206 DOI: 10.1007/s13361-017-1867-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 06/07/2023]
Abstract
Tissue imaging using matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a well-established technique that, in recent years, has seen wider adoption and novel application. Applications such imaging mass spectrometry (IMS) and biotyping are beginning to gain greater exposure and use; however, with limitations in optimization methods, producing the best result often relies on the ability to customize the physical characteristics of the instrumentation, a task that is challenging for most mass spectrometry laboratories. With this in mind, we have described the effect of making simple adjustments to the laser optics at the final collimating lens area, to adjust the laser beam size and shape in order to allow greater customization of the instrument for improving techniques such as IMS. We have therefore been able to demonstrate that improvements can be made without requiring the help of an electrical engineer or external funding in a way that only costs a small amount of time. Graphical Abstract ᅟ.
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Affiliation(s)
- Matthew B O'Rourke
- Mass Spectrometry Core Facility, The University of Sydney, Office 4110, The Hub, Building D17, Sydney, NSW, 2006, Australia.
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, NSW, 2007, Australia.
| | - Benjamin B A Raymond
- The iThree Institute, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, NSW, 2007, Australia
| | - Steven P Djordjevic
- The iThree Institute, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, NSW, 2007, Australia
| | - Matthew P Padula
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, NSW, 2007, Australia
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39
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Liu X, Flinders C, Mumenthaler SM, Hummon AB. MALDI Mass Spectrometry Imaging for Evaluation of Therapeutics in Colorectal Tumor Organoids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:516-526. [PMID: 29209911 PMCID: PMC5839975 DOI: 10.1007/s13361-017-1851-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/16/2017] [Accepted: 11/13/2017] [Indexed: 05/03/2023]
Abstract
Patient-derived colorectal tumor organoids (CTOs) closely recapitulate the complex morphological, phenotypic, and genetic features observed in in vivo tumors. Therefore, evaluation of drug distribution and metabolism in this model system can provide valuable information to predict the clinical outcome of a therapeutic response in individual patients. In this report, we applied matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to examine the spatial distribution of the drug irinotecan and its metabolites in CTOs from two patients. Irinotecan is a prodrug and is often prescribed as part of therapeutic regimes for patients with advanced colorectal cancer. Irinotecan shows a time-dependent and concentration-dependent permeability and metabolism in the CTOs. More interestingly, the active metabolite SN-38 does not co-localize well with the parent drug irinotecan and the inactive metabolite SN-38G. The phenotypic effect of irinotecan metabolism was also confirmed by a viability study showing significantly reduced proliferation in the drug treated CTOs. MALDI-MSI can be used to investigate various pharmaceutical compounds in CTOs derived from different patients. By analyzing multiple CTOs from a patient, this method could be used to predict patient-specific drug responses and help to improve personalized dosing regimens. Graphical Abstract ᅟ.
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Affiliation(s)
- Xin Liu
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 140 McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Colin Flinders
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, 2250 Alcazar Street, CSC 240, Los Angeles, CA, 90033, USA
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, 2250 Alcazar Street, CSC 240, Los Angeles, CA, 90033, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 140 McCourtney Hall, Notre Dame, IN, 46556, USA.
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40
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Sans M, Feider CL, Eberlin LS. Advances in mass spectrometry imaging coupled to ion mobility spectrometry for enhanced imaging of biological tissues. Curr Opin Chem Biol 2018; 42:138-146. [PMID: 29275246 PMCID: PMC5828985 DOI: 10.1016/j.cbpa.2017.12.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 11/20/2022]
Abstract
Tissues present complex biochemical and morphological composition associated with their various cell types and physiological functions. Mass spectrometry (MS) imaging technologies are powerful tools to investigate the molecular information from biological tissue samples and visualize their complex spatial distributions. Coupling of gas-phase ion mobility spectrometry (IMS) technologies to MS imaging has been increasingly explored to improve performance for biological tissue imaging. This approach allows improved detection of low abundance ions and separation of isobaric molecular species, thus resulting in more accurate determination of the spatial distribution of molecular ions. In this review, we highlight recent advances in the field focusing on promising applications of these technologies for metabolite, lipid and protein tissue imaging.
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Affiliation(s)
- Marta Sans
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States
| | - Clara L Feider
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States
| | - Livia S Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States.
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41
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Desbenoit N, Walch A, Spengler B, Brunelle A, Römpp A. Correlative mass spectrometry imaging, applying time-of-flight secondary ion mass spectrometry and atmospheric pressure matrix-assisted laser desorption/ionization to a single tissue section. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:159-166. [PMID: 29105220 PMCID: PMC5838509 DOI: 10.1002/rcm.8022] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/20/2017] [Accepted: 10/20/2017] [Indexed: 05/02/2023]
Abstract
RATIONALE Mass spectrometry imaging (MSI) is a powerful tool for mapping the surface of a sample. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) offer complementary capabilities. Here, we present a workflow to apply both techniques to a single tissue section and combine the resulting data for the example of human colon cancer tissue. METHODS Following cryo-sectioning, images were acquired using the high spatial resolution (1 μm pixel size) provided by TOF-SIMS. The same section was then coated with a para-nitroaniline matrix and images were acquired using AP-MALDI coupled to an Orbitrap mass spectrometer, offering high mass resolution, high mass accuracy and tandem mass spectrometry (MS/MS) capabilities. Datasets provided by both mass spectrometers were converted into the open and vendor-independent imzML file format and processed with the open-source software MSiReader. RESULTS The TOF-SIMS and AP-MALDI mass spectra show strong signals of fatty acids, cholesterol, phosphatidylcholine and sphingomyelin. We showed a high correlation between the fatty acid ions detected with TOF-SIMS in negative ion mode and the phosphatidylcholine ions detected with AP-MALDI in positive ion mode using a similar setting for visualization. Histological staining on the same section allowed the identification of the anatomical structures and their correlation with the ion images. CONCLUSIONS This multimodal approach using two MSI platforms shows an excellent complementarity for the localization and identification of lipids. The spatial resolution of both systems is at or close to cellular dimensions, and thus spatial correlation can only be obtained if the same tissue section is analyzed sequentially. Data processing based on imzML allows a real correlation of the imaging datasets provided by these two technologies and opens the way for a more complete molecular view of the anatomical structures of biological tissues.
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Affiliation(s)
- N. Desbenoit
- Chair of Bioanalytical Sciences and Food AnalysisUniversity of BayreuthBayreuthGermany
- Institute of Inorganic and Analytical Chemistry, Justus Liebig UniversityGiessenGermany
| | - A. Walch
- Research Unit Analytical PathologyHelmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Germany
| | - B. Spengler
- Chair of Bioanalytical Sciences and Food AnalysisUniversity of BayreuthBayreuthGermany
| | - A. Brunelle
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris‐Sud, Université Paris‐SaclayAvenue de la TerrasseGif‐sur‐YvetteFrance
| | - A. Römpp
- Chair of Bioanalytical Sciences and Food AnalysisUniversity of BayreuthBayreuthGermany
- Institute of Inorganic and Analytical Chemistry, Justus Liebig UniversityGiessenGermany
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O'Rourke MB, Padula MP, Smith C, Youssef P, Cordwell S, Witting P, Sutherland G, Crossett B. Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows. J Vis Exp 2018. [PMID: 29364257 DOI: 10.3791/56778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The use of matrix-assisted laser desorption/ionization, mass spectrometry imaging (MALDI MSI) has rapidly expanded, since this technique analyzes a host of biomolecules from drugs and lipids to N-glycans. Although various sample preparation techniques exist, detecting peptides from formaldehyde preserved tissues remains one of the most difficult challenges for this type of mass spectrometric analysis. For this reason, we have created and optimized a robust methodology that preserves the spatial information contained within the sample, while eliciting the greatest number of ionizable peptides. We have also aimed to achieve this in a cost effective and simple way, thereby eliminating potential bias or preparation error, which can occur when using automated instrumentation. The end result is a reproducible and inexpensive protocol.
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Affiliation(s)
- Matthew B O'Rourke
- Mass Spectrometry Core Facility, University of Sydney; Proteomics Core Facility, University of Technology Sydney;
| | | | - Caine Smith
- Neuropathology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | - Priscilla Youssef
- Redox Biology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | | | - Paul Witting
- Redox Biology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | - Greg Sutherland
- Neuropathology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | - Ben Crossett
- Mass Spectrometry Core Facility, University of Sydney
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Ren JL, Zhang AH, Kong L, Wang XJ. Advances in mass spectrometry-based metabolomics for investigation of metabolites. RSC Adv 2018; 8:22335-22350. [PMID: 35539746 PMCID: PMC9081429 DOI: 10.1039/c8ra01574k] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022] Open
Abstract
Metabolomics is the systematic study of all the metabolites present within a biological system, which consists of a mass of molecules, having a variety of physical and chemical properties and existing over an extensive dynamic range in biological samples. Diverse analytical techniques are needed to achieve higher coverage of metabolites. The application of mass spectrometry (MS) in metabolomics has increased exponentially since the discovery and development of electrospray ionization and matrix-assisted laser desorption ionization techniques. Significant advances have also occurred in separation-based MS techniques (gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, capillary electrophoresis-mass spectrometry, and ion mobility-mass spectrometry), as well as separation-free MS techniques (direct infusion-mass spectrometry, matrix-assisted laser desorption ionization-mass spectrometry, mass spectrometry imaging, and direct analysis in real time mass spectrometry) in the past decades. This review presents a brief overview of the recent advanced MS techniques and their latest applications in metabolomics. The software/websites for MS result analyses are also reviewed. Metabolomics is the systematic study of all the metabolites present within a biological system, supply functional information and has received extensive attention in the field of life sciences.![]()
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Affiliation(s)
- Jun-Ling Ren
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Ai-Hua Zhang
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Ling Kong
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
| | - Xi-Jun Wang
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Chinmedomics Research Center of State Administration of TCM
- Laboratory of Metabolomics
- Department of Pharmaceutical Analysis
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Dueñas ME, Feenstra AD, Korte AR, Hinners P, Lee YJ. Cellular and Subcellular Level Localization of Maize Lipids and Metabolites Using High-Spatial Resolution MALDI Mass Spectrometry Imaging. Methods Mol Biol 2018; 1676:217-231. [PMID: 28986913 DOI: 10.1007/978-1-4939-7315-6_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent technological advances have pushed the achievable spatial resolution for mass spectrometry imaging (MSI) to cellular and subcellular levels. Direct visualization of maize tissues by this tool has provided key insights into the localization of metabolites and lipids. This chapter outlines methodology for sample preparation, data acquisition, and data analysis of maize tissue sections using high-spatial resolution matrix-assisted laser desorption ionization (MALDI)-MSI, as well as the incorporation of a multi-resolution optical system, which allows for simple inter-conversion between different resolution setups (5, 10, and 50 μm imaging).
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Affiliation(s)
- Maria Emilia Dueñas
- Department of Chemistry, Iowa State University of Science and Technology, 35A Carver Co-Lab, 1111 Woi Rd., Ames, IA, 50011, USA
- Ames Laboratory, U.S. Department of Energy, Ames, IA, 50011, USA
| | - Adam D Feenstra
- Department of Chemistry, Iowa State University of Science and Technology, 35A Carver Co-Lab, 1111 Woi Rd., Ames, IA, 50011, USA
- Ames Laboratory, U.S. Department of Energy, Ames, IA, 50011, USA
| | - Andrew R Korte
- Department of Chemistry, Iowa State University of Science and Technology, 35A Carver Co-Lab, 1111 Woi Rd., Ames, IA, 50011, USA
- Ames Laboratory, U.S. Department of Energy, Ames, IA, 50011, USA
| | - Paige Hinners
- Department of Chemistry, Iowa State University of Science and Technology, 35A Carver Co-Lab, 1111 Woi Rd., Ames, IA, 50011, USA
| | - Young Jin Lee
- Department of Chemistry, Iowa State University of Science and Technology, 35A Carver Co-Lab, 1111 Woi Rd., Ames, IA, 50011, USA.
- Ames Laboratory, U.S. Department of Energy, Ames, IA, 50011, USA.
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3D MALDI Mass Spectrometry Imaging of a Single Cell: Spatial Mapping of Lipids in the Embryonic Development of Zebrafish. Sci Rep 2017; 7:14946. [PMID: 29097697 PMCID: PMC5668422 DOI: 10.1038/s41598-017-14949-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022] Open
Abstract
The zebrafish (Danio rerio) has been widely used as a model vertebrate system to study lipid metabolism, the roles of lipids in diseases, and lipid dynamics in embryonic development. Here, we applied high-spatial resolution matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry imaging (MSI) to map and visualize the three-dimensional spatial distribution of phospholipid classes, phosphatidylcholine (PC), phosphatidylethanolamines (PE), and phosphatidylinositol (PI), in newly fertilized individual zebrafish embryos. This is the first time MALDI-MSI has been applied for three dimensional chemical imaging of a single cell. PC molecular species are present inside the yolk in addition to the blastodisc, while PE and PI species are mostly absent in the yolk. Two-dimensional MSI was also studied for embryos at different cell stages (1-, 2-, 4-, 8-, and 16-cell stage) to investigate the localization changes of some lipids at various cell developmental stages. Four different normalization approaches were compared to find reliable relative quantification in 2D- and 3D- MALDI MSI data sets.
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Hansen RL, Lee YJ. Overlapping MALDI-Mass Spectrometry Imaging for In-Parallel MS and MS/MS Data Acquisition without Sacrificing Spatial Resolution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1910-1918. [PMID: 28493035 DOI: 10.1007/s13361-017-1699-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/04/2017] [Accepted: 04/25/2017] [Indexed: 06/07/2023]
Abstract
Metabolomics experiments require chemical identifications, often through MS/MS analysis. In mass spectrometry imaging (MSI), this necessitates running several serial tissue sections or using a multiplex data acquisition method. We have previously developed a multiplex MSI method to obtain MS and MS/MS data in a single experiment to acquire more chemical information in less data acquisition time. In this method, each raster step is composed of several spiral steps and each spiral step is used for a separate scan event (e.g., MS or MS/MS). One main limitation of this method is the loss of spatial resolution as the number of spiral steps increases, limiting its applicability for high-spatial resolution MSI. In this work, we demonstrate multiplex MS imaging is possible without sacrificing spatial resolution by the use of overlapping spiral steps, instead of spatially separated spiral steps as used in the previous work. Significant amounts of matrix and analytes are still left after multiple spectral acquisitions, especially with nanoparticle matrices, so that high quality MS and MS/MS data can be obtained on virtually the same tissue spot. This method was then applied to visualize metabolites and acquire their MS/MS spectra in maize leaf cross-sections at 10 μm spatial resolution. Graphical Abstract ᅟ.
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Affiliation(s)
- Rebecca L Hansen
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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47
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Organic matrices, ionic liquids, and organic matrices@nanoparticles assisted laser desorption/ionization mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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48
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Feenstra AD, Dueñas ME, Lee YJ. Five Micron High Resolution MALDI Mass Spectrometry Imaging with Simple, Interchangeable, Multi-Resolution Optical System. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:434-442. [PMID: 28050871 DOI: 10.1007/s13361-016-1577-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/17/2016] [Accepted: 12/08/2016] [Indexed: 05/18/2023]
Abstract
High-spatial resolution mass spectrometry imaging (MSI) is crucial for the mapping of chemical distributions at the cellular and subcellular level. In this work, we improved our previous laser optical system for matrix-assisted laser desorption ionization (MALDI)-MSI, from ~9 μm practical laser spot size to a practical laser spot size of ~4 μm, thereby allowing for 5 μm resolution imaging without oversampling. This is accomplished through a combination of spatial filtering, beam expansion, and reduction of the final focal length. Most importantly, the new laser optics system allows for simple modification of the spot size solely through the interchanging of the beam expander component. Using 10×, 5×, and no beam expander, we could routinely change between ~4, ~7, and ~45 μm laser spot size, in less than 5 min. We applied this multi-resolution MALDI-MSI system to a single maize root tissue section with three different spatial resolutions of 5, 10, and 50 μm and compared the differences in imaging quality and signal sensitivity. We also demonstrated the difference in depth of focus between the optical systems with 10× and 5× beam expanders. Graphical Abstract ᅟ.
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Affiliation(s)
- Adam D Feenstra
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
- Ames Laboratory-US DOE, Ames, IA, 50011, USA
| | - Maria Emilia Dueñas
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
- Ames Laboratory-US DOE, Ames, IA, 50011, USA
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
- Ames Laboratory-US DOE, Ames, IA, 50011, USA.
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Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS DISCOVERY 2017; 22:213-237. [PMID: 28231035 DOI: 10.1177/2472555216682725] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.
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Affiliation(s)
- Albert Gough
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Andrew M Stern
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - John Maier
- 3 Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy Lezon
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Tong-Ying Shun
- 2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Chakra Chennubhotla
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E Schurdak
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Steven A Haney
- 5 Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - D Lansing Taylor
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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50
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O'Rourke MB, Padula MP. A new standard of visual data representation for imaging mass spectrometry. Proteomics Clin Appl 2016; 11. [PMID: 27730748 DOI: 10.1002/prca.201600098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/26/2016] [Accepted: 10/07/2016] [Indexed: 12/26/2022]
Abstract
PURPOSE MALDI imaging MS (IMS) is principally used for cancer diagnostics. In our own experience with publishing IMS data, we have been requested to modify our protocols with respect to the areas of the tissue that are imaged in order to comply with the wider literature. In light of this, we have determined that current methodologies lack effective controls and can potentially introduce bias by only imaging specific areas of the targeted tissue EXPERIMENTAL DESIGN: A previously imaged sample was selected and then cropped in different ways to show the potential effect of only imaging targeted areas. RESULTS By using a model sample, we were able to effectively show how selective imaging of samples can misinterpret tissue features and by changing the areas that are acquired, according to our new standard, an effective internal control can be introduced. CONCLUSIONS AND CLINICAL RELEVANCE Current IMS sampling convention relies on the assumption that sample preparation has been performed correctly. This prevents users from checking whether molecules have moved beyond borders of the tissue due to delocalization and consequentially products of improper sample preparation could be interpreted as biological features that are of critical importance when encountered in a visual diagnostic.
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Affiliation(s)
- Matthew B O'Rourke
- Proteomics Core Facility, University of Technology Sydney, Ultimo, NSW, Australia
| | - Matthew P Padula
- Proteomics Core Facility, University of Technology Sydney, Ultimo, NSW, Australia
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