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Ma X, Fernández FM. Advances in mass spectrometry imaging for spatial cancer metabolomics. MASS SPECTROMETRY REVIEWS 2024; 43:235-268. [PMID: 36065601 PMCID: PMC9986357 DOI: 10.1002/mas.21804] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 05/09/2023]
Abstract
Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.
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Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
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2
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Croslow SW, Trinklein TJ, Sweedler JV. Advances in multimodal mass spectrometry for single-cell analysis and imaging enhancement. FEBS Lett 2024; 598:591-601. [PMID: 38243373 PMCID: PMC10963143 DOI: 10.1002/1873-3468.14798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]
Abstract
Multimodal mass spectrometry (MMS) incorporates an imaging modality with probe-based mass spectrometry (MS) to enable precise, targeted data acquisition and provide additional biological and chemical data not available by MS alone. Two categories of MMS are covered; in the first, an imaging modality guides the MS probe to target individual cells and to reduce acquisition time by automatically defining regions of interest. In the second category, imaging and MS data are coupled in the data analysis pipeline to increase the effective spatial resolution using a higher resolution imaging method, correct for tissue deformation, and incorporate fine morphological features in an MS imaging dataset. Recent methodological and computational developments are covered along with their application to single-cell and imaging analyses.
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Affiliation(s)
- Seth W. Croslow
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Timothy J. Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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3
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Rachman T, Bartlett D, LaFramboise W, Wagner P, Schwartz R, Carja O. Modeling the Effect of Spatial Structure on Solid Tumor Evolution and Circulating Tumor DNA Composition. Cancers (Basel) 2024; 16:844. [PMID: 38473206 PMCID: PMC10930890 DOI: 10.3390/cancers16050844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones are over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.
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Affiliation(s)
- Thomas Rachman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA 15213, USA
| | - David Bartlett
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - William LaFramboise
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Patrick Wagner
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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4
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Rachman T, Bartlett D, Laframboise W, Wagner P, Schwartz R, Carja O. Modeling the effect of spatial structure on solid tumor evolution and ctDNA composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566658. [PMID: 37986965 PMCID: PMC10659436 DOI: 10.1101/2023.11.10.566658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform on cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones end up over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases, but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.
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Affiliation(s)
- Thomas Rachman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology
| | - David Bartlett
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh PA
| | | | - Patrick Wagner
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh PA
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
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5
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Chen Y, Liu Y, Li X, He Y, Li W, Peng Y, Zheng J. Recent Advances in Mass Spectrometry-Based Spatially Resolved Molecular Imaging of Drug Disposition and Metabolomics. Drug Metab Dispos 2023; 51:1273-1283. [PMID: 37295949 DOI: 10.1124/dmd.122.001069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/04/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Mass spectrometric imaging is a nontargeted, tag-free, high-throughput, and highly responsive analytical approach. The highly accurate molecular visualization detection technology enables qualitative and quantitative analyses of biologic tissues or cells scanned by mass spectrometry in situ, extracting known and unknown multiple compounds, and simultaneously assessing relative contents of targeting molecules by monitoring their molecular ions and pinpointing the spatial locations of those molecules distributed. Five mass spectrometric imaging techniques and their characteristics are introduced in the review, including matrix-assisted laser desorption ionization mass spectrometry, secondary ion mass spectrometry, desorption electrospray ionization mass spectrometry, laser ablation electrospray ionization mass spectrometry, and laser ablation inductively coupled plasma mass spectrometry. The mass spectrometry-based techniques provide the possibility for spatial metabolomics with the capability of high throughput and precision detection. The approaches have been widely employed to spatially image not only metabolome of endogenous amino acids, peptides, proteins, neurotransmitters, and lipids but also the disposition of exogenous chemicals, such as pharmaceutical agents, environmental pollutants, toxicants, natural products, and heavy metals. The techniques also provide us with spatial distribution imaging of analytes in single cells, tissue microregions, organs, and whole animals. SIGNIFICANCE STATEMENT: The review article includes an overview of five commonly used mass spectrometers for spatial imaging and describes the advantages and disadvantages of each. Examples of the technology applications cover drug disposition, diseases, and omics. Technical aspects of relative and absolute quantification by mass spectrometric imaging and challenges for future new applications are discussed as well. The reviewed knowledge may benefit the development of new drugs and provide a better understanding of biochemical processes related to physiology and diseases.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ximei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Yan He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
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6
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Rafik ST, Vaidya JS, MacRobert AJ, Yaghini E. Organic Nanodelivery Systems as a New Platform in the Management of Breast Cancer: A Comprehensive Review from Preclinical to Clinical Studies. J Clin Med 2023; 12:jcm12072648. [PMID: 37048731 PMCID: PMC10095028 DOI: 10.3390/jcm12072648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/05/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Breast cancer accounts for approximately 25% of cancer cases and 16.5% of cancer deaths in women, and the World Health Organization predicts that the number of new cases will increase by almost 70% over the next two decades, mainly due to an ageing population. Effective diagnostic and treatment strategies are, therefore, urgently required for improving cure rates among patients since current therapeutic modalities have many limitations and side effects. Nanomedicine is evolving as a promising approach for cancer management, including breast cancer, and various types of organic and inorganic nanomaterials have been investigated for their role in breast cancer diagnosis and treatment. Following an overview on breast cancer characteristics and pathogenesis and challenges of the current treatment strategies, the therapeutic potential of biocompatible organic-based nanoparticles such as liposomes and polymeric micelles that have been tested in breast cancer models are reviewed. The efficacies of different drug delivery and targeting strategies are documented, ranging from synthetic to cell-derived nanoformulations together with a summary of the interaction of nanoparticles with externally applied energy such as radiotherapy. The clinical translation of nanoformulations for breast cancer treatment is summarized including those undergoing clinical trials.
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Affiliation(s)
- Salma T. Rafik
- Division of Surgery and Interventional Science, Faculty of Medical Sciences, University College London (UCL), London W1W 7TY, UK
- Department of Clinical Pharmacology, Faculty of Medicine, Alexandria University, Alexandria 21516, Egypt
| | - Jayant S. Vaidya
- Division of Surgery and Interventional Science, Faculty of Medical Sciences, University College London (UCL), London W1W 7TY, UK
| | - Alexander J. MacRobert
- Division of Surgery and Interventional Science, Faculty of Medical Sciences, University College London (UCL), London W1W 7TY, UK
| | - Elnaz Yaghini
- Division of Surgery and Interventional Science, Faculty of Medical Sciences, University College London (UCL), London W1W 7TY, UK
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7
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Bowman AP, Sawicki J, Talaty NN, Buck WR, Yang J, Wagner DS. Evaluation of Quantitative Platforms for Single Target Mass Spectrometry Imaging. Pharmaceuticals (Basel) 2022; 15:ph15101180. [PMID: 36297291 PMCID: PMC9609477 DOI: 10.3390/ph15101180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2022] Open
Abstract
(1) Imaging of pharmaceutical compounds in tissue is an increasingly important subsection of Mass Spectrometry Imaging (MSI). Identifying proper target engagement requires MS platforms with high sensitivity and spatial resolution. Three prominent categories of drugs are small molecule drugs, antibody-drug conjugate payloads, and protein degraders. (2) We tested six common MSI platforms for their limit of detection (LoD) on a representative compound for each category: a Matrix-Assisted Laser Desorption/Ionization (MALDI) Fourier Transform Ion Cyclotron, a MALDI-2 Time-of-Flight (ToF), a MALDI-2 Trapped Ion Mobility Spectrometry ToF, a Desorption Electrospray Ionization Orbitrap, and 2 Atmospheric Pressure-MALDI Triple Quadrupoles. Samples were homogenized tissue mimetic models of rat liver spiked with known concentrations of analytes. (3) We found that the AP-MALDI-QQQ platform outperformed all 4 competing platforms by a minimum of 2- to 52-fold increase in LoD for representative compounds from each category of pharmaceutical. (4) AP-MALDI-QQQ platforms are effective, cost-efficient mass spectrometers for the identification of targeted analytes of interest.
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Menetrey A, Legouffe R, Haouala A, Bonnel D, Rouits E, Bosq J, Stauber J. Tumor Distribution by Quantitative Mass Spectrometry Imaging of the Inhibitor of Apoptosis Protein Antagonist Xevinapant in Patients with Resectable Squamous Cell Carcinoma of the Head and Neck (EudraCT Number: 2014-004655-31). Anal Chem 2022; 94:12333-12341. [PMID: 36040476 DOI: 10.1021/acs.analchem.2c00943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As tumors are very heterogeneous, investigating the penetration and concentration of an anticancer drug in different histological regions of a tumor is key to evaluate the efficacy, to improve the pharmacokinetics/pharmacodynamics (PK/PD) relationship evaluation, and to confirm the adequacy of the dose regimen. Quantitative mass spectrometry imaging (QMSI) allows for the determination of the tissue distribution of drugs, metabolites, and biomarkers to support quick and precise evaluation of drug efficacy and safety in a single experiment. QMSI was applied in a preoperative window-of-opportunity (WoO) study of the inhibitor of apoptosis protein antagonist xevinapant (Debio 1143) in patients with resectable squamous cell carcinoma of the head and neck (SCCHN). Tumors were isolated, immediately snap-frozen, and sectioned, and then, the molecular distribution of the drug was generated by matrix-assisted laser desorption ionization (MALDI) imaging. Additionally, the different histological regions (tumor, epithelium, salivary glands, muscle, nerve, and blood vessels) were identified on stained sections adjacent to the ones used for QMSI, leading to a specific quantification integrating the biological characterization of the tumor heterogeneity. This innovative approach allowed one to highlight the high affinity of xevinapant for the tumor tissues.
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Affiliation(s)
- Annick Menetrey
- Debiopharm International SA, Chemin Messidor 5-7, 1002 Lausanne, Switzerland
| | - Raphael Legouffe
- ImaBiotech, Parc Eurasanté, 152 rue du Docteur Yersin, 59120 Loos, France
| | - Amina Haouala
- Medicines for Malaria Venture, Route de Pré-Bois 20, 1215 Meyrin, Switzerland
| | - David Bonnel
- ImaBiotech, Parc Eurasanté, 152 rue du Docteur Yersin, 59120 Loos, France
| | - Elisabeth Rouits
- Debiopharm International SA, Chemin Messidor 5-7, 1002 Lausanne, Switzerland
| | - Jacques Bosq
- Sciempath Labo, 7, rue de la Gratiole, 37270 Larcay, France
| | - Jonathan Stauber
- ImaBiotech, Parc Eurasanté, 152 rue du Docteur Yersin, 59120 Loos, France
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Baquer G, Sementé L, Mahamdi T, Correig X, Ràfols P, García-Altares M. What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022:e21794. [PMID: 35822576 DOI: 10.1002/mas.21794] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) has become a widespread analytical technique to perform nonlabeled spatial molecular identification. The Achilles' heel of MSI is the annotation and identification of molecular species due to intrinsic limitations of the technique (lack of chromatographic separation and the difficulty to apply tandem MS). Successful strategies to perform annotation and identification combine extra analytical steps, like using orthogonal analytical techniques to identify compounds; with algorithms that integrate the spectral and spatial information. In this review, we discuss different experimental strategies and bioinformatics tools to annotate and identify compounds in MSI experiments. We target strategies and tools for small molecule applications, such as lipidomics and metabolomics. First, we explain how sample preparation and the acquisition process influences annotation and identification, from sample preservation to the use of orthogonal techniques. Then, we review twelve software tools for annotation and identification in MSI. Finally, we offer perspectives on two current needs of the MSI community: the adaptation of guidelines for communicating confidence levels in identifications; and the creation of a standard format to store and exchange annotations and identifications in MSI.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Toufik Mahamdi
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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10
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Analytical Performance Evaluation of New DESI Enhancements for Targeted Drug Quantification in Tissue Sections. Pharmaceuticals (Basel) 2022; 15:ph15060694. [PMID: 35745613 PMCID: PMC9228120 DOI: 10.3390/ph15060694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 02/05/2023] Open
Abstract
Desorption/ionization (DI)-mass spectrometric (MS) methods offer considerable advantages of rapidity and low-sample input for the analysis of solid biological matrices such as tissue sections. The concept of desorption electrospray ionization (DESI) offers the possibility to ionize compounds from solid surfaces at atmospheric pressure, without the addition of organic compounds to initiate desorption. However, severe drawbacks from former DESI hardware stability made the development of assays for drug quantification difficult. In the present study, the potential of new prototype source setups (High Performance DESI Sprayer and Heated Transfer Line) for the development of drug quantification assays in tissue sections was evaluated. It was demonstrated that following dedicated optimization, new DESI XS enhancements present promising options regarding targeted quantitative analyses. As a model compound for these developments, ulixertinib, an inhibitor of extracellular signal-regulated kinase (ERK) 1 and 2 was used.
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11
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Onoda N, Kawabata A, Hasegawa K, Sakakura M, Urakawa I, Seki M, Zenkoh J, Suzuki A, Suzuki Y. Spatial and single-cell transcriptome analysis reveals changes in gene expression in response to drug perturbation in rat kidney. DNA Res 2022; 29:dsac007. [PMID: 35325072 PMCID: PMC9014450 DOI: 10.1093/dnares/dsac007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/22/2022] [Indexed: 12/25/2022] Open
Abstract
The kidney is a complex organ that consists of various types of cells. It is occasionally difficult to resolve molecular alterations and possible perturbations that the kidney experiences due to drug-induced damage. In this study, we performed spatial and single-cell transcriptome analysis of rat kidneys and constructed a precise rat renal cell atlas with spatial information. Using the constructed catalogue, we were able to characterize cells of several minor populations, such as macula densa or juxtaglomerular cells. Further inspection of the spatial gene expression data allowed us to identify the upregulation of genes involved in the renin regulating pathway in losartan-treated populations. Losartan is an angiotensin II receptor antagonist drug, and the observed upregulation of the renin pathway-related genes could be due to feedback from the hypotensive action of the drug. Furthermore, we found spatial heterogeneity in the response to losartan among the glomeruli. These results collectively indicate that integrated single-cell and spatial gene expression analysis is a powerful approach to reveal the detailed associations between the different cell types spanning the complicated renal compartments.
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Affiliation(s)
- Naoki Onoda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba 277-0882, Japan
- Research Core Function Laboratories, Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo 194-8533, Japan
| | - Ayako Kawabata
- Research Core Function Laboratories, Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo 194-8533, Japan
| | - Kumi Hasegawa
- Biomedical Science Research Laboratories 1, Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo 194-8533, Japan
| | - Megumi Sakakura
- Research Core Function Laboratories, Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo 194-8533, Japan
| | - Itaru Urakawa
- Research Core Function Laboratories, Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo 194-8533, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba 277-0882, Japan
| | - Junko Zenkoh
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba 277-0882, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba 277-0882, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba 277-0882, Japan
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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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Pathmasiri KC, Nguyen TTA, Khamidova N, Cologna SM. Mass spectrometry-based lipid analysis and imaging. CURRENT TOPICS IN MEMBRANES 2021; 88:315-357. [PMID: 34862030 DOI: 10.1016/bs.ctm.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for in situ mapping of analytes across a sample. With growing interest in lipid biochemistry, the ability to perform such mapping without antibodies has opened many opportunities for MSI and lipid analysis. Herein, we discuss the basics of MSI with particular emphasis on MALDI mass spectrometry and lipid analysis. A discussion of critical advancements as well as protocol details are provided to the reader. In addition, strategies for improving the detection of lipids, as well as applications in biomedical research, are presented.
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Affiliation(s)
- Koralege C Pathmasiri
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Thu T A Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Nigina Khamidova
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States; Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, United States.
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14
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Lee PY, Yeoh Y, Omar N, Pung YF, Lim LC, Low TY. Molecular tissue profiling by MALDI imaging: recent progress and applications in cancer research. Crit Rev Clin Lab Sci 2021; 58:513-529. [PMID: 34615421 DOI: 10.1080/10408363.2021.1942781] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) imaging is an emergent technology that has been increasingly adopted in cancer research. MALDI imaging is capable of providing global molecular mapping of the abundance and spatial information of biomolecules directly in the tissues without labeling. It enables the characterization of a wide spectrum of analytes, including proteins, peptides, glycans, lipids, drugs, and metabolites and is well suited for both discovery and targeted analysis. An advantage of MALDI imaging is that it maintains tissue integrity, which allows correlation with histological features. It has proven to be a valuable tool for probing tumor heterogeneity and has been increasingly applied to interrogate molecular events associated with cancer. It provides unique insights into both the molecular content and spatial details that are not accessible by other techniques, and it has allowed considerable progress in the field of cancer research. In this review, we first provide an overview of the MALDI imaging workflow and approach. We then highlight some useful applications in various niches of cancer research, followed by a discussion of the challenges, recent developments and future prospect of this technique in the field.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Yeelon Yeoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, University of Nottingham Malaysia, Selangor, Malaysia
| | - Lay Cheng Lim
- Department of Life Sciences, School of Pharmacy, International Medical University (IMU), Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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15
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Morosi L, Meroni M, Ubezio P, Fuso Nerini I, Minoli L, Porcu L, Panini N, Colombo M, Blouw B, Kang DW, Davoli E, Zucchetti M, D'Incalci M, Frapolli R. PEGylated recombinant human hyaluronidase (PEGPH20) pre-treatment improves intra-tumour distribution and efficacy of paclitaxel in preclinical models. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:286. [PMID: 34507591 PMCID: PMC8434701 DOI: 10.1186/s13046-021-02070-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Scarce drug penetration in solid tumours is one of the possible causes of the limited efficacy of chemotherapy and is related to the altered tumour microenvironment. The abnormal tumour extracellular matrix (ECM) together with abnormal blood and lymphatic vessels, reactive stroma and inflammation all affect the uptake, distribution and efficacy of anticancer drugs. METHODS We investigated the effect of PEGylated recombinant human hyaluronidase PH20 (PEGPH20) pre-treatment in degrading hyaluronan (hyaluronic acid; HA), one of the main components of the ECM, to improve the delivery of antitumor drugs and increase their therapeutic efficacy. The antitumor activity of paclitaxel (PTX) in HA synthase 3-overexpressing and wild-type SKOV3 ovarian cancer model and in the BxPC3 pancreas xenograft tumour model, was evaluated by monitoring tumour growth with or without PEGPH20 pre-treatment. Pharmacokinetics and tumour penetration of PTX were assessed by HPLC and mass spectrometry imaging analysis in the same tumour models. Tumour tissue architecture and HA deposition were analysed by histochemistry. RESULTS Pre-treatment with PEGPH20 modified tumour tissue architecture and improved the antitumor activity of paclitaxel in the SKOV3/HAS3 tumour model, favouring its accumulation and more homogeneous intra-tumour distribution, as assessed by quantitative and qualitative analysis. PEGPH20 also reduced HA content influencing, though less markedly, PTX distribution and antitumor activity in the BxPC3 tumour model. CONCLUSION Remodelling the stroma of HA-rich tumours by depletion of HA with PEGPH20 pre-treatment, is a potentially successful strategy to improve the intra-tumour distribution of anticancer drugs, increasing their therapeutic efficacy, without increasing toxicity.
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Affiliation(s)
- Lavinia Morosi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy.,Present address: IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Marina Meroni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy
| | - Paolo Ubezio
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy
| | - Ilaria Fuso Nerini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy.,Present address: IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Lucia Minoli
- Department of Veterinary Medicine, University of Milan, Lodi, Italy.,Mouse and Animal Pathology Laboratory (MAPLab), Fondazione UniMi, Milan, Italy
| | - Luca Porcu
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy
| | - Nicolò Panini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy
| | - Marika Colombo
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy
| | | | - David W Kang
- Halozyme Therapeutics, San Diego, California, USA
| | - Enrico Davoli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Laboratory of Mass Spectrometry, Milan, Italy
| | - Massimo Zucchetti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy
| | - Maurizio D'Incalci
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy.,Present address: IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy.,Present address: Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090, Pieve Emanuele, Milan, Italy
| | - Roberta Frapolli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Oncology, via M. Negri 2, 20156, Milan, Italy.
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16
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Hasan MM, Mimi MA, Mamun MA, Islam A, Waliullah ASM, Nabi MM, Tamannaa Z, Kahyo T, Setou M. Mass Spectrometry Imaging for Glycome in the Brain. Front Neuroanat 2021; 15:711955. [PMID: 34393728 PMCID: PMC8358800 DOI: 10.3389/fnana.2021.711955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Glycans are diverse structured biomolecules that play crucial roles in various biological processes. Glycosylation, an enzymatic system through which various glycans are bound to proteins and lipids, is the most common and functionally crucial post-translational modification process. It is known to be associated with brain development, signal transduction, molecular trafficking, neurodegenerative disorders, psychopathologies, and brain cancers. Glycans in glycoproteins and glycolipids expressed in brain cells are involved in neuronal development, biological processes, and central nervous system maintenance. The composition and expression of glycans are known to change during those physiological processes. Therefore, imaging of glycans and the glycoconjugates in the brain regions has become a “hot” topic nowadays. Imaging techniques using lectins, antibodies, and chemical reporters are traditionally used for glycan detection. However, those techniques offer limited glycome detection. Mass spectrometry imaging (MSI) is an evolving field that combines mass spectrometry with histology allowing spatial and label-free visualization of molecules in the brain. In the last decades, several studies have employed MSI for glycome imaging in brain tissues. The current state of MSI uses on-tissue enzymatic digestion or chemical reaction to facilitate successful glycome imaging. Here, we reviewed the available literature that applied MSI techniques for glycome visualization and characterization in the brain. We also described the general methodologies for glycome MSI and discussed its potential use in the three-dimensional MSI in the brain.
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Affiliation(s)
- Md Mahmudul Hasan
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mst Afsana Mimi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Al Mamun
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ariful Islam
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - A S M Waliullah
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Mahamodun Nabi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Zinat Tamannaa
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomoaki Kahyo
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu, Japan
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17
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Abstract
Mass spectrometry imaging (MSI) is a powerful, label-free technique that provides detailed maps of hundreds of molecules in complex samples with high sensitivity and subcellular spatial resolution. Accurate quantification in MSI relies on a detailed understanding of matrix effects associated with the ionization process along with evaluation of the extraction efficiency and mass-dependent ion losses occurring in the analysis step. We present a critical summary of approaches developed for quantitative MSI of metabolites, lipids, and proteins in biological tissues and discuss their current and future applications.
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Affiliation(s)
- Daisy Unsihuay
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA; , ,
| | - Daniela Mesa Sanchez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA; , ,
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA; , ,
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18
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Vos DRN, Ellis SR, Balluff B, Heeren RMA. Experimental and Data Analysis Considerations for Three-Dimensional Mass Spectrometry Imaging in Biomedical Research. Mol Imaging Biol 2021; 23:149-159. [PMID: 33025328 PMCID: PMC7910367 DOI: 10.1007/s11307-020-01541-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/12/2020] [Accepted: 09/10/2020] [Indexed: 10/26/2022]
Abstract
Mass spectrometry imaging (MSI) enables the visualization of molecular distributions on complex surfaces. It has been extensively used in the field of biomedical research to investigate healthy and diseased tissues. Most of the MSI studies are conducted in a 2D fashion where only a single slice of the full sample volume is investigated. However, biological processes occur within a tissue volume and would ideally be investigated as a whole to gain a more comprehensive understanding of the spatial and molecular complexity of biological samples such as tissues and cells. Mass spectrometry imaging has therefore been expanded to the 3D realm whereby molecular distributions within a 3D sample can be visualized. The benefit of investigating volumetric data has led to a quick rise in the application of single-sample 3D-MSI investigations. Several experimental and data analysis aspects need to be considered to perform successful 3D-MSI studies. In this review, we discuss these aspects as well as ongoing developments that enable 3D-MSI to be routinely applied to multi-sample studies.
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Affiliation(s)
- D R N Vos
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - S R Ellis
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - B Balluff
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - R M A Heeren
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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19
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Flinders B, Morrell J, Marshall PS, Ranshaw LE, Heeren RMA, Clench MR. Monitoring the three-dimensional distribution of endogenous species in the lungs by matrix-assisted laser desorption/ionization mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8957. [PMID: 32990347 DOI: 10.1002/rcm.8957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is routinely employed to monitor the distribution of compounds in tissue sections and generate two-dimensional (2D) images. Whilst informative the images do not represent the distribution of the analyte of interest through the entire organ. The generation of 3D images is an exciting field that can provide a deeper view of the analyte of interest throughout an entire organ. METHODS Serial sections of mouse and rat lung tissue were obtained at 120 μm depth intervals and imaged individually. Homogenate registration markers were incorporated in order to aid the final 3D image construction. Using freely available software packages, the images were stacked together to generate a 3D image that showed the distribution of endogenous species throughout the lungs. RESULTS Preliminary tests were performed on 16 serial tissue sections of mouse lungs. A 3D model showing the distribution of phosphocholine at m/z 184.09 was constructed, which defined the external structure of the lungs and trachea. Later, a second experiment was performed using 24 serial tissue sections of the left lung of a rat. Two molecular markers, identified as [PC (32:1) + K]+ at m/z 770.51 and [PC (36:4) + K]+ at m/z 820.52, were used to generate 3D models of the parenchyma and airways, respectively. CONCLUSIONS A straightforward method to generate 3D MALDI-MS images of selected molecules in lung tissue has been presented. Using freely available imaging software, the 3D distributions of molecules related to different anatomical features were determined.
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Affiliation(s)
- Bryn Flinders
- Centre for Mass Spectrometry Imaging, Biomedical Research Centre, City Campus, Sheffield Hallam University, Sheffield, S1 1WB, UK
- Hair Diagnostix, Dutch Screening Group, Gaetano Martinolaan 63A, Maastricht, 6229 GS, The Netherlands
- Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, Maastricht, 6229 ER, The Netherlands
| | - Josie Morrell
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | | | - Lisa E Ranshaw
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, Maastricht, 6229 ER, The Netherlands
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomedical Research Centre, City Campus, Sheffield Hallam University, Sheffield, S1 1WB, UK
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20
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Zhang J, Hong Y, Xie P, Chen Y, Jiang L, Yang Z, Cao G, Chen Z, Liu X, Chen Y, Wu Y, Cai Z. Spatial Lipidomics Reveals Anticancer Mechanisms of Bufalin in Combination with Cinobufagin in Tumor-Bearing Mice. Front Pharmacol 2021; 11:593815. [PMID: 33597874 PMCID: PMC7883642 DOI: 10.3389/fphar.2020.593815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/30/2020] [Indexed: 01/31/2023] Open
Abstract
Bufalin (BFL) and cinobufagin (CBF) are the principal bioactive constituents of Chansu, a widely used traditional Chinese medicine (TCM). The synergistic effects of potential active components are responsible for the bioactivities of TCM. Our results showed that the cotreatment with BFL and CBF confers superior anticancer efficacy compared to monotreatment. To reveal the underlying mechanisms of their cotreatment, an integrated method composed of mass spectrometry-based lipidomics and matrix-assisted laser desorption/ionization mass spectrometry imaging was used to delineate the responses of tumor-bearing mice treated with BFL and CBF individually or in combination. The cotreatment with BFL and CBF modulated the sphingolipid metabolism and glycerophospholipid metabolism, and subsequently led to mitochondria-driven apoptosis and systemic disruption of biomembranes in tumor cells. Furthermore, we found that the disturbed lipid markers were mainly located in the non-necrotic tumor areas, the essential parts for the formation of solid tumor framework. Together, our findings revealed what occurred in tumor in response to the treatment of BFL and CBF, from lipids to enzymes, and thus provide insights into the critical role of lipid reprogramming in the satisfactory anticancer effect of BFL in combination with CBF.
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Affiliation(s)
- Jinghui Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yanjun Hong
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.,Shenzhen Research Institute and Continuing Education, Hong Kong Baptist University, Shenzhen, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Peisi Xie
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Yang Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lilong Jiang
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.,Shenzhen Research Institute and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Zhiyi Yang
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Guodong Cao
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Zhongjian Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, China
| | - Xuesong Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yongjiang Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zongwei Cai
- Department of Chemistry, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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21
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Bai H, Linder KE, Muddiman DC. Three-dimensional (3D) imaging of lipids in skin tissues with infrared matrix-assisted laser desorption electrospray ionization (MALDESI) mass spectrometry. Anal Bioanal Chem 2021; 413:2793-2801. [PMID: 33388847 DOI: 10.1007/s00216-020-03105-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]
Abstract
Three-dimensional (3D) mass spectrometry imaging (MSI) has become a growing frontier as it has the potential to provide a 3D representation of analytes in a label-free, untargeted, and chemically specific manner. The most common 3D MSI is accomplished by the reconstruction of 2D MSI from serial cryosections; however, this presents significant challenges in image alignment and registration. An alternative method would be to sequentially image a sample by consecutive ablation events to create a 3D image. In this study, we describe the use of infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) in ablation-based 3D MSI for analyses of lipids within fresh frozen skin tissue. Depth resolution using different laser energy levels was explored with a confocal laser scanning microscope to establish the imaging parameters for skin. The lowest and highest laser energy level resulted in a depth resolution of 7 μm and 18 μm, respectively. A total of 594 lipids were putatively detected and detailed lipid profiles across different skin layers were revealed in a 56-layer 3D imaging experiment. Correlated with histological information, the skin structure was characterized with differential lipid distributions with a lateral resolution of 50 μm and a z resolution of 7 μm.
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Affiliation(s)
- Hongxia Bai
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Keith E Linder
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA. .,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA. .,Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, 27695, USA.
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22
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Saigusa D, Matsukawa N, Hishinuma E, Koshiba S. Identification of biomarkers to diagnose diseases and find adverse drug reactions by metabolomics. Drug Metab Pharmacokinet 2020; 37:100373. [PMID: 33631535 DOI: 10.1016/j.dmpk.2020.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Metabolomics has been widely used for investigating the biological functions of disease expression and has the potential to discover biomarkers in circulating biofluids or tissue extracts that reflect in phenotypic changes. Metabolic profiling has advantages because of the use of unbiased techniques, including multivariate analysis, and has been applied in pharmacological studies to predict therapeutic and adverse reactions of drugs, which is called pharmacometabolomics (PMx). Nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics has contributed to the discovery of recent disease biomarkers; however, the optimal strategy for the study purpose must be selected from many established protocols, methodologies and analytical platforms. Additionally, information on molecular localization in tissue is essential for further functional analyses related to therapeutic and adverse effects of drugs in the process of drug development. MS imaging (MSI) is a promising technology that can visualize molecules on tissue surfaces without labeling and thus provide localized information. This review summarizes recent uses of MS-based global and wide-targeted metabolomics technologies and the advantages of the MSI approach for PMx and highlights the PMx technique for the biomarker discovery of adverse drug effects.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Eiji Hishinuma
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
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Prasad M, Postma G, Franceschi P, Morosi L, Giordano S, Falcetta F, Giavazzi R, Davoli E, Buydens LMC, Jansen J. A methodological approach to correlate tumor heterogeneity with drug distribution profile in mass spectrometry imaging data. Gigascience 2020; 9:6006351. [PMID: 33241286 PMCID: PMC7688471 DOI: 10.1093/gigascience/giaa131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/28/2020] [Accepted: 11/01/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Drug mass spectrometry imaging (MSI) data contain knowledge about drug and several other molecular ions present in a biological sample. However, a proper approach to fully explore the potential of such type of data is still missing. Therefore, a computational pipeline that combines different spatial and non-spatial methods is proposed to link the observed drug distribution profile with tumor heterogeneity in solid tumor. Our data analysis steps include pre-processing of MSI data, cluster analysis, drug local indicators of spatial association (LISA) map, and ions selection. RESULTS The number of clusters identified from different tumor tissues. The spatial homogeneity of the individual cluster was measured using a modified version of our drug homogeneity method. The clustered image and drug LISA map were simultaneously analyzed to link identified clusters with observed drug distribution profile. Finally, ions selection was performed using the spatially aware method. CONCLUSIONS In this paper, we have shown an approach to correlate the drug distribution with spatial heterogeneity in untargeted MSI data. Our approach is freely available in an R package 'CorrDrugTumorMSI'.
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Affiliation(s)
- Mridula Prasad
- IMM/ Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ Nijmegen, Netherlands.,Unit of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, 38010 San Michele all' Adige, Italy
| | - Geert Postma
- IMM/ Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ Nijmegen, Netherlands
| | - Pietro Franceschi
- Unit of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, 38010 San Michele all' Adige, Italy
| | - Lavinia Morosi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19-20156 Milan, Italy
| | - Silvia Giordano
- Mass Spectrometry Laboratory, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19-20156 Milan, Italy
| | - Francesca Falcetta
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19-20156 Milan, Italy
| | - Raffaella Giavazzi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19-20156 Milan, Italy
| | - Enrico Davoli
- Mass Spectrometry Laboratory, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19-20156 Milan, Italy
| | - Lutgarde M C Buydens
- IMM/ Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ Nijmegen, Netherlands
| | - Jeroen Jansen
- IMM/ Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ Nijmegen, Netherlands
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24
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Henderson F, Jones E, Denbigh J, Christie L, Chapman R, Hoyes E, Claude E, Williams KJ, Roncaroli F, McMahon A. 3D DESI-MS lipid imaging in a xenograft model of glioblastoma: a proof of principle. Sci Rep 2020; 10:16512. [PMID: 33020565 PMCID: PMC7536442 DOI: 10.1038/s41598-020-73518-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022] Open
Abstract
Desorption electrospray ionisation mass spectrometry (DESI-MS) can image hundreds of molecules in a 2D tissue section, making it an ideal tool for mapping tumour heterogeneity. Tumour lipid metabolism has gained increasing attention over the past decade; and here, lipid heterogeneity has been visualised in a glioblastoma xenograft tumour using 3D DESI-MS imaging. The use of an automatic slide loader automates 3D imaging for high sample-throughput. Glioblastomas are highly aggressive primary brain tumours, which display heterogeneous characteristics and are resistant to chemotherapy and radiotherapy. It is therefore important to understand biochemical contributions to their heterogeneity, which may be contributing to treatment resistance. Adjacent sections to those used for DESI-MS imaging were used for H&E staining and immunofluorescence to identify different histological regions, and areas of hypoxia. Comparing DESI-MS imaging with biological staining allowed association of different lipid species with hypoxic and viable tissue within the tumour, and hence mapping of molecularly different tumour regions in 3D space. This work highlights that lipids are playing an important role in the heterogeneity of this xenograft tumour model, and DESI-MS imaging can be used for lipid 3D imaging in an automated fashion to reveal heterogeneity, which is not apparent in H&E stains alone.
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Affiliation(s)
- Fiona Henderson
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Stopford Building, Manchester, M13 9PT, UK
| | | | | | - Lidan Christie
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK
| | | | - Emmy Hoyes
- Waters Corporation, Wilmslow, SK9 4AX, UK
| | | | - Kaye J Williams
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Stopford Building, Manchester, M13 9PT, UK
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester and Manchester Centre for Clinical Neuroscience, Salford, UK
| | - Adam McMahon
- Wolfson Molecular Imaging Centre, Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M20 3LJ, UK.
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25
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Tobias F, Hummon AB. Considerations for MALDI-Based Quantitative Mass Spectrometry Imaging Studies. J Proteome Res 2020; 19:3620-3630. [PMID: 32786684 DOI: 10.1021/acs.jproteome.0c00443] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significant advances in mass spectrometry imaging (MSI) have pushed the boundaries in obtaining spatial information and quantification in biological samples. Quantitative MSI (qMSI) has typically been challenging to achieve because of matrix and tissue heterogeneity, inefficient analyte extraction, and ion suppression effects, but recent studies have demonstrated approaches to obtain highly robust methods and reproducible results. In this perspective, we share our insights into sample preparation, how the choice of matrix influences sensitivity, construction of calibration curves, signal normalization, and visualization of MSI data. We hope that by articulating these guidelines that qMSI can be routinely conducted while retaining the analytical merits of other mass spectrometry modalities.
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26
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Van de Sande L, Rahimi‐Gorji M, Giordano S, Davoli E, Matteo C, Detlefsen S, D'Herde K, Braet H, Shariati M, Remaut K, Xie F, Debbaut C, Ghorbaniasl G, Cosyns S, Willaert W, Ceelen W. Electrostatic Intraperitoneal Aerosol Delivery of Nanoparticles: Proof of Concept and Preclinical Validation. Adv Healthc Mater 2020; 9:e2000655. [PMID: 32548967 DOI: 10.1002/adhm.202000655] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/13/2020] [Indexed: 12/21/2022]
Abstract
There is an increasing interest in intraperitoneal delivery of chemotherapy as an aerosol in patients with peritoneal metastasis. The currently used technology is hampered by inhomogenous drug delivery throughout the peritoneal cavity because of gravity, drag, and inertial impaction. Addition of an electrical force to aerosol particles, exerted by an electrostatic field, can improve spatial aerosol homogeneity and enhance tissue penetration. A computational fluid dynamics model shows that electrostatic precipitation (EP) results in a significantly improved aerosol distribution. Fluorescent nanoparticles (NPs) remain stable after nebulization in vitro, while EP significantly improves spatial homogeneity of NP distribution. Next, pressurized intraperitoneal chemotherapy with and without EP using NP albumin bound paclitaxel (Nab-PTX) in a novel rat model is examined. EP does not worsen the effects of CO2 insufflation and intraperitoneal Nab-PTX on mesothelial structural integrity or the severity of peritoneal inflammation. Importantly, EP significantly enhances tissue penetration of Nab-PTX in the anatomical regions not facing the nozzle of the nebulizer. Also, the addition of EP leads to more homogenous peritoneal tissue concentrations of Nab-PTX, in parallel with higher plasma concentrations. In conclusion, EP enhances spatial homogeneity and tissue uptake after intraperitoneal nebulization of anticancer NPs.
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Affiliation(s)
- Leen Van de Sande
- Department of Human Structure and RepairGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
| | - Mohammad Rahimi‐Gorji
- Department of Human Structure and RepairGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- IBiTech – bioMMedaGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
| | - Silvia Giordano
- Mass Spectrometry LaboratoryIstituto di Ricerche Farmacologiche Mario Negri IRCCS Via Mario Negri 2 Milan 20156 Italy
| | - Enrico Davoli
- Mass Spectrometry LaboratoryIstituto di Ricerche Farmacologiche Mario Negri IRCCS Via Mario Negri 2 Milan 20156 Italy
| | - Cristina Matteo
- Cancer Pharmacology LaboratoryIstituto di Ricerche Farmacologiche Mario Negri IRCCS Via Mario Negri 2 Milan 20156 Italy
| | - Sönke Detlefsen
- Department of PathologyOdense University Hospital J.B. Winsløws Vej 4 Odense 5000 Denmark
- Department of Clinical ResearchUniversity of Southern Denmark Winsløwsparken 19 Odense 5000 Denmark
| | - Katharina D'Herde
- Department of Human Structure and RepairGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
| | - Helena Braet
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Laboratory of General Biochemistry and Physical PharmacyFaculty of Pharmaceutical SciencesGhent University Ottergemsesteenweg 460 Ghent 9000 Belgium
| | - Molood Shariati
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Laboratory of General Biochemistry and Physical PharmacyFaculty of Pharmaceutical SciencesGhent University Ottergemsesteenweg 460 Ghent 9000 Belgium
| | - Katrien Remaut
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Laboratory of General Biochemistry and Physical PharmacyFaculty of Pharmaceutical SciencesGhent University Ottergemsesteenweg 460 Ghent 9000 Belgium
| | - Feifan Xie
- Laboratory of Medical Biochemistry and Clinical AnalysisFaculty of Pharmaceutical SciencesGhent University Ottergemsesteenweg 460 Ghent 9000 Belgium
| | - Charlotte Debbaut
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- IBiTech – bioMMedaGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
| | - Ghader Ghorbaniasl
- Department of Mechanical EngineeringVrije Universiteit Brussel (VUB) Pleinlaan 2 Brussels 1050 Belgium
| | - Sarah Cosyns
- Department of Human Structure and RepairGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
| | - Wouter Willaert
- Department of Human Structure and RepairGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
| | - Wim Ceelen
- Department of Human Structure and RepairGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Cancer Research Institute Ghent (CRIG)Ghent University Corneel Heymanslaan 10 Ghent 9000 Belgium
- Department of Human Structure and RepairGhent University Corneel Heymanslaan 10 Ghent 9000 Belgium
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27
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Abbott DM, Bortolotto C, Benvenuti S, Lancia A, Filippi AR, Stella GM. Malignant Pleural Mesothelioma: Genetic and Microenviromental Heterogeneity as an Unexpected Reading Frame and Therapeutic Challenge. Cancers (Basel) 2020; 12:cancers12051186. [PMID: 32392897 PMCID: PMC7281319 DOI: 10.3390/cancers12051186] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Mesothelioma is a malignancy of serosal membranes including the peritoneum, pleura, pericardium and the tunica vaginalis of the testes. Malignant mesothelioma (MM) is a rare disease with a global incidence in countries like Italy of about 1.15 per 100,000 inhabitants. Malignant Pleural Mesothelioma (MPM) is the most common form of mesothelioma, accounting for approximately 80% of disease. Although rare in the global population, mesothelioma is linked to industrial pollutants and mineral fiber exposure, with approximately 80% of cases linked to asbestos. Due to the persistent asbestos exposure in many countries, a worldwide progressive increase in MPM incidence is expected for the current and coming years. The tumor grows in a loco-regional pattern, spreading from the parietal to the visceral pleura and invading the surrounding structures that induce the clinical picture of pleural effusion, pain and dyspnea. Distant spreading and metastasis are rarely observed, and most patients die from the burden of the primary tumor. Currently, there are no effective treatments for MPM, and the prognosis is invariably poor. Some studies average the prognosis to be roughly one-year after diagnosis. The uniquely poor mutational landscape which characterizes MPM appears to derive from a selective pressure operated by the environment; thus, inflammation and immune response emerge as key players in driving MPM progression and represent promising therapeutic targets. Here we recapitulate current knowledge on MPM with focus on the emerging network between genetic asset and inflammatory microenvironment which characterize the disease as amenable target for novel therapeutic approaches.
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Affiliation(s)
- David Michael Abbott
- Department of Medical Sciences and Infective Diseases, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy;
| | - Chandra Bortolotto
- Unit of Radiology, Department of Intensive Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy;
| | - Silvia Benvenuti
- Candiolo Cancer Institute, FPO—IRCCS—Str. Prov.le 142, km. 3,95—10060 Candiolo (TO), Italy;
| | - Andrea Lancia
- Unit of Radiation Therapy, Department of Medical Sciences and Infective Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy; (A.L.); (A.R.F.)
| | - Andrea Riccardo Filippi
- Unit of Radiation Therapy, Department of Medical Sciences and Infective Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy; (A.L.); (A.R.F.)
| | - Giulia Maria Stella
- Department of Medical Sciences and Infective Diseases, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy;
- Correspondence:
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28
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Alexandrov T. Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence. Annu Rev Biomed Data Sci 2020; 3:61-87. [PMID: 34056560 DOI: 10.1146/annurev-biodatasci-011420-031537] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spatial metabolomics is an emerging field of omics research that has enabled localizing metabolites, lipids, and drugs in tissue sections, a feat considered impossible just two decades ago. Spatial metabolomics and its enabling technology-imaging mass spectrometry-generate big hyper-spectral imaging data that have motivated the development of tailored computational methods at the intersection of computational metabolomics and image analysis. Experimental and computational developments have recently opened doors to applications of spatial metabolomics in life sciences and biomedicine. At the same time, these advances have coincided with a rapid evolution in machine learning, deep learning, and artificial intelligence, which are transforming our everyday life and promise to revolutionize biology and healthcare. Here, we introduce spatial metabolomics through the eyes of a computational scientist, review the outstanding challenges, provide a look into the future, and discuss opportunities granted by the ongoing convergence of human and artificial intelligence.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA
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29
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Zink KE, Tarnowski DA, Mandel MJ, Sanchez LM. Optimization of a minimal sample preparation protocol for imaging mass spectrometry of unsectioned juvenile invertebrates. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4458. [PMID: 31693273 PMCID: PMC7145758 DOI: 10.1002/jms.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/02/2019] [Accepted: 10/17/2019] [Indexed: 05/03/2023]
Abstract
Tissue sections have long been the subject matter for the application of imaging mass spectrometry, but recently the technique has been adapted for many other purposes including bacterial colonies and 3D cell culture. Here, we present a simple preparation method for unsectioned invertebrate tissue without the need for fixing, embedding, or slicing. The protocol was used to successfully prepare a Hawaiian bobtail squid hatchling for analysis, and the resulting data detected ions that correspond to compounds present in the host only during its symbiotic colonization by Vibrio fischeri.
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Affiliation(s)
- Katherine E Zink
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612
| | - Denise A Tarnowski
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI 53706
- Department of Microbiology & Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior Street, Chicago, IL 60611
| | - Mark J Mandel
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, 1550 Linden Dr, Madison, WI 53706
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612
- Corresponding author: Phone: 312-996-0842
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30
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de Maar JS, Sofias AM, Porta Siegel T, Vreeken RJ, Moonen C, Bos C, Deckers R. Spatial heterogeneity of nanomedicine investigated by multiscale imaging of the drug, the nanoparticle and the tumour environment. Am J Cancer Res 2020; 10:1884-1909. [PMID: 32042343 PMCID: PMC6993242 DOI: 10.7150/thno.38625] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic and phenotypic tumour heterogeneity is an important cause of therapy resistance. Moreover, non-uniform spatial drug distribution in cancer treatment may cause pseudo-resistance, meaning that a treatment is ineffective because the drug does not reach its target at sufficient concentrations. Together with tumour heterogeneity, non-uniform drug distribution causes “therapy heterogeneity”: a spatially heterogeneous treatment effect. Spatial heterogeneity in drug distribution occurs on all scales ranging from interpatient differences to intratumour differences on tissue or cellular scale. Nanomedicine aims to improve the balance between efficacy and safety of drugs by targeting drug-loaded nanoparticles specifically to tumours. Spatial heterogeneity in nanoparticle and payload distribution could be an important factor that limits their efficacy in patients. Therefore, imaging spatial nanoparticle distribution and imaging the tumour environment giving rise to this distribution could help understand (lack of) clinical success of nanomedicine. Imaging the nanoparticle, drug and tumour environment can lead to improvements of new nanotherapies, increase understanding of underlying mechanisms of heterogeneous distribution, facilitate patient selection for nanotherapies and help assess the effect of treatments that aim to reduce heterogeneity in nanoparticle distribution. In this review, we discuss three groups of imaging modalities applied in nanomedicine research: non-invasive clinical imaging methods (nuclear imaging, MRI, CT, ultrasound), optical imaging and mass spectrometry imaging. Because each imaging modality provides information at a different scale and has its own strengths and weaknesses, choosing wisely and combining modalities will lead to a wealth of information that will help bring nanomedicine forward.
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31
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Melnyk T, Đorđević S, Conejos-Sánchez I, Vicent MJ. Therapeutic potential of polypeptide-based conjugates: Rational design and analytical tools that can boost clinical translation. Adv Drug Deliv Rev 2020; 160:136-169. [PMID: 33091502 DOI: 10.1016/j.addr.2020.10.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022]
Abstract
The clinical success of polypeptides as polymeric drugs, covered by the umbrella term "polymer therapeutics," combined with related scientific and technological breakthroughs, explain their exponential growth in the development of polypeptide-drug conjugates as therapeutic agents. A deeper understanding of the biology at relevant pathological sites and the critical biological barriers faced, combined with advances regarding controlled polymerization techniques, material bioresponsiveness, analytical methods, and scale up-manufacture processes, have fostered the development of these nature-mimicking entities. Now, engineered polypeptides have the potential to combat current challenges in the advanced drug delivery field. In this review, we will discuss examples of polypeptide-drug conjugates as single or combination therapies in both preclinical and clinical studies as therapeutics and molecular imaging tools. Importantly, we will critically discuss relevant examples to highlight those parameters relevant to their rational design, such as linking chemistry, the analytical strategies employed, and their physicochemical and biological characterization, that will foster their rapid clinical translation.
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Affiliation(s)
- Tetiana Melnyk
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Snežana Đorđević
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inmaculada Conejos-Sánchez
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - María J Vicent
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Lab, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
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32
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Kishimoto S, Brender JR, Crooks DR, Matsumoto S, Seki T, Oshima N, Merkle H, Lin P, Reed G, Chen AP, Ardenkjaer-Larsen JH, Munasinghe J, Saito K, Yamamoto K, Choyke PL, Mitchell J, Lane AN, Fan TWM, Linehan WM, Krishna MC. Imaging of glucose metabolism by 13C-MRI distinguishes pancreatic cancer subtypes in mice. eLife 2019; 8:e46312. [PMID: 31408004 PMCID: PMC6706239 DOI: 10.7554/elife.46312] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022] Open
Abstract
Metabolic differences among and within tumors can be an important determinant in cancer treatment outcome. However, methods for determining these differences non-invasively in vivo is lacking. Using pancreatic ductal adenocarcinoma as a model, we demonstrate that tumor xenografts with a similar genetic background can be distinguished by their differing rates of the metabolism of 13C labeled glucose tracers, which can be imaged without hyperpolarization by using newly developed techniques for noise suppression. Using this method, cancer subtypes that appeared to have similar metabolic profiles based on steady state metabolic measurement can be distinguished from each other. The metabolic maps from 13C-glucose imaging localized lactate production and overall glucose metabolism to different regions of some tumors. Such tumor heterogeneity would not be not detectable in FDG-PET.
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Affiliation(s)
- Shun Kishimoto
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Jeffrey R Brender
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, NCI, NIHBethesdaUnited States
| | - Shingo Matsumoto
- Graduate School of Information Science and Technology, Division of Bioengineering and BioinformaticsHokkaido UniversitySapporoJapan
- JST, PRESTSaitamaJapan
| | - Tomohiro Seki
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Nobu Oshima
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | | | - Penghui Lin
- Center for Environmental and Systems BiochemistryUniversity of KentuckyLexingtonUnited States
| | | | | | - Jan Henrik Ardenkjaer-Larsen
- GE HealthCareChicagoUnited States
- Department of Electrical EngineeringTechnical University of DenmarkKongens LyngbyDenmark
| | | | - Keita Saito
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Kazutoshi Yamamoto
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Peter L Choyke
- Molecular Imaging Program, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - James Mitchell
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
| | - Andrew N Lane
- Center for Environmental and Systems BiochemistryUniversity of KentuckyLexingtonUnited States
- Markey Cancer CenterUniversity of KentuckyLexingtonUnited States
| | - Teresa WM Fan
- Center for Environmental and Systems BiochemistryUniversity of KentuckyLexingtonUnited States
- Markey Cancer CenterUniversity of KentuckyLexingtonUnited States
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, NCI, NIHBethesdaUnited States
| | - Murali C Krishna
- Radiation Biology Branch, Center for Cancer ResearchNCI, NIHBethesdaUnited States
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33
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Applications of MALDI mass spectrometry imaging for pharmacokinetic studies during drug development. Drug Metab Pharmacokinet 2019; 34:209-216. [DOI: 10.1016/j.dmpk.2019.04.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/14/2019] [Accepted: 04/19/2019] [Indexed: 12/23/2022]
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34
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Quantitative Mass Spectrometry Imaging Reveals Mutation Status-independent Lack of Imatinib in Liver Metastases of Gastrointestinal Stromal Tumors. Sci Rep 2019; 9:10698. [PMID: 31337874 PMCID: PMC6650609 DOI: 10.1038/s41598-019-47089-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry imaging (MSI) is an enabling technology for label-free drug disposition studies at high spatial resolution in life science- and pharmaceutical research. We present the first extensive clinical matrix-assisted laser desorption/ionization (MALDI) quantitative mass spectrometry imaging (qMSI) study of drug uptake and distribution in clinical specimen, analyzing 56 specimens of tumor and corresponding non-tumor tissues from 27 imatinib-treated patients with the biopsy-proven rare disease gastrointestinal stromal tumors (GIST). For validation, we compared MALDI-TOF-qMSI with conventional UPLC-ESI-QTOF-MS-based quantification from tissue extracts and with ultra-high resolution MALDI-FTICR-qMSI. We introduced a novel generalized nonlinear calibration model of drug quantities based on computational evaluation of drug-containing areas that enabled better data fitting and assessment of the inherent method nonlinearities. Imatinib tissue spatial maps revealed striking inefficiency in drug penetration into GIST liver metastases even though the corresponding healthy liver tissues in the vicinity showed abundant imatinib levels beyond the limit of quantification (LOQ), thus providing evidence for secondary drug resistance independent of mutation status. Taken together, these findings underscore the important application of MALDI-qMSI in studying the spatial distribution of molecularly targeted therapeutics in oncology, namely to serve as orthogonal post-surgical approach to evaluate the contribution of anticancer drug disposition to resistance against treatment.
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Song X, He J, Li C, Sun C, Pang X, Zhang J, Zang Q, Luo Z, Li X, Zhang R, Abliz Z. Fabrication of homogenous three-dimensional biomimetic tissue for mass spectrometry imaging. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:378-388. [PMID: 30742348 DOI: 10.1002/jms.4342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/26/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Reference samples are essential for mass spectrometric method optimization, data quality control, and target analyte quantitation. However, it is highly challenging to prepare an ideal homogeneous, standard-spiked tissue sample for mass spectrometry imaging (MSI) research. Herein, we present a standard-spiked 3D biomimetic tissue model fabricated with native cells, homogenate matrix, and biocompatible polymer. Unlike traditional homogenized tissue surrogates or those constructed with "on-tissue" or "under-tissue" micropipetting strategies, this simulated tissue shares both structural integrity of cells and homogeneous properties of matrix. As a result, analyte standards could undergo more in-depth incorporation and has a more comparable native status with a real tissue. Series of tissue sections made from the 3D tissue model were proven to be feasible and useful for the parameter optimization, analyte quantitation, and calibration curve fitting for the air-flow assisted desorption electrospray ionization MSI. Additionally, by analyzing the quality control model sections, we proposed a median principal component score calibration and demonstrated that this method can normalize instrumental fluctuations to stable levels in a large-scale untargeted MSI experiments for the reliable metabolomic biomarker discovery. Thus, these results indicated that the standard-spiked 3D biomimetic tissue has convincing significance in MSI analysis.
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Affiliation(s)
- Xiaowei Song
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Chao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Chenglong Sun
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xuechao Pang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jin Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zhigang Luo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xin Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- Centre for Imaging and Systems Biology, School of Pharmacy, Minzu University of China, Beijing, 100081, China
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Garattini S, Fuso Nerini I, D'Incalci M. Not only tumor but also therapy heterogeneity. Ann Oncol 2019; 29:13-19. [PMID: 29045538 DOI: 10.1093/annonc/mdx646] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- S Garattini
- Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - I Fuso Nerini
- Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - M D'Incalci
- Department of Oncology, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
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37
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Han J, Permentier H, Bischoff R, Groothuis G, Casini A, Horvatovich P. Imaging of protein distribution in tissues using mass spectrometry: An interdisciplinary challenge. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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38
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Schulz S, Becker M, Groseclose MR, Schadt S, Hopf C. Advanced MALDI mass spectrometry imaging in pharmaceutical research and drug development. Curr Opin Biotechnol 2019; 55:51-59. [DOI: 10.1016/j.copbio.2018.08.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/21/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
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39
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Nishida-Aoki N, Gujral TS. Emerging approaches to study cell-cell interactions in tumor microenvironment. Oncotarget 2019; 10:785-797. [PMID: 30774780 PMCID: PMC6366828 DOI: 10.18632/oncotarget.26585] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/27/2018] [Indexed: 01/19/2023] Open
Abstract
Cell-cell interactions are of crucial importance for tissue formation, homeostasis, regeneration processes, and immune response. Recent studies underlined contribution of cell-cell interaction in tumor microenvironment (TME) for tumor progression and metastasis. Cancer cells modify the host cells to tumor-supportive traits, and the modified host cells contribute to tumor progression by interacting with cancer cells and further modifying other normal cells. However, the complex interaction networks of cancer cells and host cells remained largely unknown. Recent advances in high throughput microscopy and single cells-based molecular analyses have unlocked a new era for studying cell-cell interactions in the complex tissue microenvironment at the resolution of a single cell. Here, we review various model systems and emerging experimental approaches that are used to study cell-cell interactions focusing on the studies of TME. We discuss strengths and weaknesses of each model system and each experimental approach, and how upcoming approaches can solve current fundamental questions of cell-cell interactions in TME.
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Affiliation(s)
- Nao Nishida-Aoki
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Taranjit S. Gujral
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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40
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Xu G, Li J. Recent advances in mass spectrometry imaging for multiomics application in neurology. J Comp Neurol 2018; 527:2158-2169. [DOI: 10.1002/cne.24571] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/14/2018] [Accepted: 10/24/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Guang Xu
- Hubei Education Cloud Service Engineering Technology Research CenterHubei University of Education Wuhan China
| | - Jianjun Li
- Human Health TherapeuticsNational Research Council Canada Ottawa Ontario
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41
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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: 136] [Impact Index Per Article: 22.7] [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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Lagast N, Carlier C, Ceelen WP. Pharmacokinetics and Tissue Transport of Intraperitoneal Chemotherapy. Surg Oncol Clin N Am 2018; 27:477-494. [PMID: 29935684 DOI: 10.1016/j.soc.2018.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The presence of a peritoneal barrier results in a pharmacokinetic advantage associated with intraperitoneal (IP) delivery of anticancer drugs. The anticancer efficacy of IP chemotherapy depends, however, on its ability to penetrate the tumor stroma. Tumor tissue transport is governed by diffusion and convection and is affected by numerous physical, biological, and pharmaceutical variables. From preclinical and clinical studies, it appears that tissue penetration after IP chemotherapy delivery is very limited. Several approaches are studied in order to improve tissue penetration of small molecular and macromolecular anticancer drugs after IP instillation.
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Affiliation(s)
- Nick Lagast
- Department of Surgery, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent B-9000, Belgium
| | - Charlotte Carlier
- Department of Surgery, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent B-9000, Belgium
| | - Wim P Ceelen
- Department of Surgery, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent B-9000, Belgium.
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43
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Restriction of drug transport by the tumor environment. Histochem Cell Biol 2018; 150:631-648. [DOI: 10.1007/s00418-018-1744-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/31/2022]
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44
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Smith PJ, Darzynkiewicz Z, Errington RJ. Nuclear cytometry and chromatin organization. Cytometry A 2018; 93:771-784. [PMID: 30144297 DOI: 10.1002/cyto.a.23521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022]
Abstract
The nuclear-targeting chemical probe, for the detection and quantification of DNA within cells, has been a mainstay of cytometry-from the colorimetric Feulgen stain to smart fluorescent agents with tuned functionality. The level of nuclear structure and function at which the probe aims to readout, or indeed at which a DNA-targeted drug acts, is shadowed by a wide range of detection modalities and analytical methods. These methods are invariably limited in terms of the resolution attainable versus the volume occupied by targeted chromatin structures. The scalar challenge arises from the need to understand the extent and different levels of compaction of genomic DNA and how such structures can be re-modeled, reported, or even perturbed by both probes and drugs. Nuclear cytometry can report on the complex levels of chromatin order, disorder, disassembly, and even active disruption by probes and drugs. Nuclear probes can report defining features of clinical and therapeutic interest as in NETosis and other cell death processes. New cytometric approaches continue to bridge the scalar challenges of analyzing chromatin organization. Advances in super-resolution microscopy address the resolution and depth of analysis issues in cellular systems. Typical of recent insights into chromatin organization enabled by exploiting a DNA interacting probe is ChromEM tomography (ChromEMT). ChromEMT uses the unique properties of the anthraquinone-based cytometric dye DRAQ5™ to reveal that local and global 3D chromatin structures effect differences in compaction. The focus of this review is nuclear and chromatin cytometry, with linked reference to DNA targeting probes and drugs as exemplified by the anthracenediones.
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Affiliation(s)
- Paul J Smith
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Zbigniew Darzynkiewicz
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, Valhalla, New York, 10595
| | - Rachel J Errington
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
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Falcetta F, Morosi L, Ubezio P, Giordano S, Decio A, Giavazzi R, Frapolli R, Prasad M, Franceschi P, D'Incalci M, Davoli E. Past-in-the-Future. Peak detection improves targeted mass spectrometry imaging. Anal Chim Acta 2018; 1042:1-10. [PMID: 30428975 DOI: 10.1016/j.aca.2018.06.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/19/2018] [Accepted: 06/24/2018] [Indexed: 11/30/2022]
Abstract
Mass spectrometry imaging is a valuable tool for visualizing the localization of drugs in tissues, a critical issue especially in cancer pharmacology where treatment failure may depend on poor drug distribution within the tumours. Proper preprocessing procedures are mandatory to obtain quantitative data of drug distribution in tumours, even at low intensity, through reliable ion peak identification and integration. We propose a simple preprocessing and quantification pipeline. This pipeline was designed starting from classical peak integration methods, developed when "microcomputers" became available for chromatography, now applied to MSI. This pre-processing approach is based on a novel method using the fixed mass difference between the analyte and its 5 d derivatives to set up a mass range gate. We demonstrate the use of this pipeline for the evaluating the distribution of the anticancer drug paclitaxel in tumour sections. The procedure takes advantage of a simple peak analysis and allows to quantify the drug concentration in each pixel with a limit of detection below 0.1 pmol mm-2 or 10 μg g-1. Quantitative images of paclitaxel distribution in different tumour models were obtained and average paclitaxel concentrations were compared with HPLC measures in the same specimens, showing <20% difference. The scripts are developed in Python and available through GitHub, at github.com/FrancescaFalcetta/Imaging_of_drugs_distribution_and_quantifications.git.
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Affiliation(s)
- Francesca Falcetta
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Lavinia Morosi
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Paolo Ubezio
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Silvia Giordano
- Mass Spectrometry Laboratory, Department of Environmental Health Sciences, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Alessandra Decio
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Raffaella Giavazzi
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Roberta Frapolli
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Mridula Prasad
- IMM/Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ, Nijmegen, Netherlands; Biostatistics and Data Management Group, Fondazione Edmund Mach, 38010, San Michele all' Adige, Italy; Nanotechnology in Medicinal Chemistry, Department of Molecular Biotechnology and Health Sciences, Università di Torino, 10126, Torino, Italy
| | - Pietro Franceschi
- Biostatistics and Data Management Group, Fondazione Edmund Mach, 38010, San Michele all' Adige, Italy
| | - Maurizio D'Incalci
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Enrico Davoli
- Mass Spectrometry Laboratory, Department of Environmental Health Sciences, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy.
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Prideaux B, Lenaerts A, Dartois V. Imaging and spatially resolved quantification of drug distribution in tissues by mass spectrometry. Curr Opin Chem Biol 2018; 44:93-100. [PMID: 29957376 DOI: 10.1016/j.cbpa.2018.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/03/2018] [Indexed: 12/14/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful label-free technique for visualizing drug and metabolite distributions in biological tissues. In this review, we discuss recent developments in MSI and spatial profiling technologies to visualize and quantify drug distributions in tissues. We also present recent examples of applications of these technologies for assessing drug distribution within tissues and individual cells. Finally, we focus on an emerging technique coupling laser capture microdissection (LCM) to quantitative mass spectrometry, which combines the respective advantages of imaging and conventional liquid chromatography mass spectrometry, and thus enables spatially resolved drug quantification.
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Affiliation(s)
- Brendan Prideaux
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA.
| | - Anne Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Véronique Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA; Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
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Abdelmoula WM, Pezzotti N, Hölt T, Dijkstra J, Vilanova A, McDonnell LA, Lelieveldt BPF. Interactive Visual Exploration of 3D Mass Spectrometry Imaging Data Using Hierarchical Stochastic Neighbor Embedding Reveals Spatiomolecular Structures at Full Data Resolution. J Proteome Res 2018; 17:1054-1064. [PMID: 29430923 PMCID: PMC5838640 DOI: 10.1021/acs.jproteome.7b00725] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Technological
advances in mass spectrometry imaging (MSI) have
contributed to growing interest in 3D MSI. However, the large size
of 3D MSI data sets has made their efficient analysis and visualization
and the identification of informative molecular patterns computationally
challenging. Hierarchical stochastic neighbor embedding (HSNE), a
nonlinear dimensionality reduction technique that aims at finding
hierarchical and multiscale representations of large data sets, is
a recent development that enables the analysis of millions of data
points, with manageable time and memory complexities. We demonstrate
that HSNE can be used to analyze large 3D MSI data sets at full mass
spectral and spatial resolution. To benchmark the technique as well
as demonstrate its broad applicability, we have analyzed a number
of publicly available 3D MSI data sets, recorded from various biological
systems and spanning different mass-spectrometry ionization techniques.
We demonstrate that HSNE is able to rapidly identify regions of interest
within these large high-dimensionality data sets as well as aid the
identification of molecular ions that characterize these regions of
interest; furthermore, through clearly separating measurement artifacts,
the HSNE analysis exhibits a degree of robustness to measurement batch
effects, spatially correlated noise, and mass spectral misalignment.
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Affiliation(s)
- Walid M Abdelmoula
- Division of Image Processing, Department of Radiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands.,Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Nicola Pezzotti
- Computer Graphics and Visualization Group, Faculty of EEMCS, Delft University of Technology , 2628 CN Delft, The Netherlands
| | - Thomas Hölt
- Computer Graphics and Visualization Group, Faculty of EEMCS, Delft University of Technology , 2628 CN Delft, The Netherlands
| | - Jouke Dijkstra
- Division of Image Processing, Department of Radiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Anna Vilanova
- Computer Graphics and Visualization Group, Faculty of EEMCS, Delft University of Technology , 2628 CN Delft, The Netherlands
| | | | - Boudewijn P F Lelieveldt
- Division of Image Processing, Department of Radiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands.,Computer Graphics and Visualization Group, Faculty of EEMCS, Delft University of Technology , 2628 CN Delft, The Netherlands
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Barbero N, Coletti M, Catalano F, Visentin S. Exploring gold nanoparticles interaction with mucins: A spectroscopic-based study. Int J Pharm 2018; 535:438-443. [DOI: 10.1016/j.ijpharm.2017.11.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/09/2017] [Accepted: 11/12/2017] [Indexed: 01/26/2023]
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49
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Matrix-Assisted Laser Desorption/Ionisation Mass Spectrometry Imaging in the Study of Gastric Cancer: A Mini Review. Int J Mol Sci 2017; 18:ijms18122588. [PMID: 29194417 PMCID: PMC5751191 DOI: 10.3390/ijms18122588] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide and the disease outcome commonly depends upon the tumour stage at the time of diagnosis. However, this cancer can often be asymptomatic during the early stages and remain undetected until the later stages of tumour development, having a significant impact on patient prognosis. However, our comprehension of the mechanisms underlying the development of gastric malignancies is still lacking. For these reasons, the search for new diagnostic and prognostic markers for gastric cancer is an ongoing pursuit. Modern mass spectrometry imaging (MSI) techniques, in particular matrix-assisted laser desorption/ionisation (MALDI), have emerged as a plausible tool in clinical pathology as a whole. More specifically, MALDI-MSI is being increasingly employed in the study of gastric cancer and has already elucidated some important disease checkpoints that may help us to better understand the molecular mechanisms underpinning this aggressive cancer. Here we report the state of the art of MALDI-MSI approaches, ranging from sample preparation to statistical analysis, and provide a complete review of the key findings that have been reported in the literature thus far.
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50
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Wang H, Wang Y, Wang G, Hong L. Matrix-assisted laser-desorption/ionization mass spectrometric imaging of olanzapine in a single hair using esculetin as a matrix. J Pharm Biomed Anal 2017; 141:123-131. [DOI: 10.1016/j.jpba.2017.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/04/2017] [Accepted: 04/14/2017] [Indexed: 12/11/2022]
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