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Hou JJ, Zhang ZJ, Wu WY, He QQ, Zhang TQ, Liu YW, Wang ZJ, Gao L, Long HL, Lei M, Wu WY, Guo DA. Mass spectrometry imaging: new eyes on natural products for drug research and development. Acta Pharmacol Sin 2022; 43:3096-3111. [PMID: 36229602 PMCID: PMC9712638 DOI: 10.1038/s41401-022-00990-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
Natural products (NPs) and their structural analogs represent a major source of novel drug development for disease prevention and treatment. The development of new drugs from NPs includes two crucial aspects. One is the discovery of NPs from medicinal plants/microorganisms, and the other is the evaluation of the NPs in vivo at various physiological and pathological states. The heterogeneous spatial distribution of NPs in medicinal plants/microorganisms or in vivo can provide valuable information for drug development. However, few molecular imaging technologies can detect thousands of compounds simultaneously on a label-free basis. Over the last two decades, mass spectrometry imaging (MSI) methods have progressively improved and diversified, thereby allowing for the development of various applications of NPs in plants/microorganisms and in vivo NP research. Because MSI allows for the spatial mapping of the production and distribution of numerous molecules in situ without labeling, it provides a visualization tool for NP research. Therefore, we have focused this mini-review on summarizing the applications of MSI technology in discovering NPs from medicinal plants and evaluating NPs in preclinical studies from the perspective of new drug research and development (R&D). Additionally, we briefly reviewed the factors that should be carefully considered to obtain the desired MSI results. Finally, the future development of MSI in new drug R&D is proposed.
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Affiliation(s)
- Jin-Jun Hou
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zi-Jia Zhang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Yong Wu
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Qing-Qing He
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Teng-Qian Zhang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Wen Liu
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhao-Jun Wang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Gao
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua-Li Long
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Lei
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan-Ying Wu
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - De-An Guo
- National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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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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3
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Hu Y, Wang Z, Liu L, Zhu J, Zhang D, Xu M, Zhang Y, Xu F, Chen Y. Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine. Chem Sci 2021; 12:7993-8009. [PMID: 34257858 PMCID: PMC8230026 DOI: 10.1039/d1sc00271f] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering "what", "where", "how many" and "whose" chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.
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Affiliation(s)
- Yechen Hu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Zhongcheng Wang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University Wuhan 430071 China
| | - Jianhua Zhu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Dongxue Zhang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Mengying Xu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Yuanyuan Zhang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- State Key Laboratory of Reproductive Medicine, Key Laboratory of Cardiovascular & Cerebrovascular Medicine Nanjing 210029 China
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4
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Ahmed AR, Candeo A, D'Abrantes S, Needham SR, Yadav RB, Botchway SW, Parker AW. Directly imaging the localisation and photosensitization properties of the pan-mTOR inhibitor, AZD2014, in living cancer cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2020; 213:112055. [PMID: 33142217 PMCID: PMC7762844 DOI: 10.1016/j.jphotobiol.2020.112055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/24/2020] [Accepted: 10/12/2020] [Indexed: 12/17/2022]
Abstract
The range of cellular functions the mechanistic target of rapamycin (mTOR) protein performs makes it an attractive drug target for cancer therapy. However, the cellular localisation and mode of action of second generation inhibitors of mTOR is poorly understood despite the level of attention there is in targeting the mTOR protein. We have therefore studied the properties of the pan-mTOR inhibitor AZD2014, an ideal candidate to study because it is naturally fluorescent, characterising its photochemical properties in solution phase (DMSO, PBS and BSA) and within living cells, where it localises within both the nucleus and the cytoplasm but with different excited state lifetimes of 4.8 (+/- 0.5) and 3.9 (+/- 0.4) ns respectively. We measure the uptake of the inhibitor AZD2014 (7 μM) in monolayer HEK293 cells occurring with a half-life of 1 min but observe complex behaviour for 3D spheroids with the core of the spheroid showing a slower uptake and a slow biphasic behaviour at longer times. From a cellular perspective using fluorescence lifetime imaging microscopy AZD2014 was found to interact directly with GFP-tagged mTORC1 proteins including the downstream target, S6K1. We observe light sensitive behaviour of the cells containing AZD2014 which leads to cell death, in both monolayer and spheroids cells, demonstrating the potential of AZD2014 to act as a possible photodynamic drug under both single photon and multiphoton excitation and discuss its use as a photosensitizer. We also briefly characterise another pan-mTOR inhibitor, INK128.
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Affiliation(s)
- Abdullah R Ahmed
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK; Larch House, Woodlands Business Park, Breckland, Linford Wood, Milton Keynes MK14 6FG, UK
| | - Alessia Candeo
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK
| | - Sofia D'Abrantes
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK; CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Gray Laboratories, ORCRB Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Sarah R Needham
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK
| | - Rahul B Yadav
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Stanley W Botchway
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK.
| | - Anthony W Parker
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, UK.
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5
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Mutuku SM, Trim PJ, Prabhala BK, Irani S, Bremert KL, Logan JM, Brooks DA, Stahl J, Centenera MM, Snel MF, Butler LM. Evaluation of Small Molecule Drug Uptake in Patient-Derived Prostate Cancer Explants by Mass Spectrometry. Sci Rep 2019; 9:15008. [PMID: 31628408 PMCID: PMC6802206 DOI: 10.1038/s41598-019-51549-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023] Open
Abstract
Patient-derived explant (PDE) culture of solid tumors is increasingly being applied to preclinical evaluation of novel therapeutics and for biomarker discovery. In this technique, treatments are added to culture medium and penetrate the tissue via a gelatin sponge scaffold. However, the penetration profile and final concentrations of small molecule drugs achieved have not been determined to date. Here, we determined the extent of absorption of the clinical androgen receptor antagonist, enzalutamide, into prostate PDEs, using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matrix-assisted laser/desorption ionisation (MALDI) mass spectrometry imaging (MSI). In a cohort of 11 PDE tissues from eight individual patients, LC-MS/MS quantification of PDE homogenates confirmed enzalutamide (10 µM) uptake by all PDEs, which reached maximal average tissue concentration of 0.24-0.50 ng/µg protein after 48 h culture. Time dependent uptake of enzalutamide (50 µM) in PDEs was visualized using MALDI MSI over 24-48 h, with complete penetration throughout tissues evident by 6 h of culture. Drug signal intensity was not homogeneous throughout the tissues but had areas of markedly high signal that corresponded to drug target (androgen receptor)-rich epithelial regions of tissue. In conclusion, application of MS-based drug quantification and visualization in PDEs, and potentially other 3-dimensional model systems, can provide a more robust basis for experimental study design and interpretation of pharmacodynamic data.
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Affiliation(s)
- Shadrack M Mutuku
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Paul J Trim
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Bala K Prabhala
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Department of Drug Design and Pharmacology, University of Copenhagen, København, Denmark
| | - Swati Irani
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Kayla L Bremert
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jessica M Logan
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Cancer Research Institute, University of South Australia, Adelaide, SA, 5000, Australia
| | - Douglas A Brooks
- Mechanisms in Cell Biology and Disease Research Group, School of Pharmacy and Medical Sciences, Cancer Research Institute, University of South Australia, Adelaide, SA, 5000, Australia
| | - Jürgen Stahl
- Clinpath Laboratories, Adelaide, SA, 5000, Australia
| | - Margaret M Centenera
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia.,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Marten F Snel
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Lisa M Butler
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5005, Australia. .,Prostate Cancer Research Group, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia. .,Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, 5005, Australia.
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6
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Satoh T, Kubo A, Hazama H. Matrix-Assisted Laser Desorption Ionization Imaging Mass Spectrometry of Drug Distribution in Mouse Brain Tissue by High-Resolution Time-of-Flight Mass Spectrometry. Methods Mol Biol 2018; 1810:133-139. [PMID: 29974425 DOI: 10.1007/978-1-4939-8579-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the opportunity to visualize the distributions of drugs and metabolites in tissue specimens without requiring radioisotopes, as are used for whole-body autoradiography. However, the analysis of low-molecular-weight compounds is often difficult using the common reflectron-type MALDI time-of-flight mass spectrometers. Insufficient mass resolving power causes overlapping of the target drug peak with matrix compound or surface contaminant peaks. To solve this issue, we describe the procedure for imaging mass spectrometry using a high-mass-resolution mass spectrometer that can separate isobaric peaks.
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7
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Dilillo M, Pellegrini D, Ait-Belkacem R, de Graaf EL, Caleo M, McDonnell LA. Mass Spectrometry Imaging, Laser Capture Microdissection, and LC-MS/MS of the Same Tissue Section. J Proteome Res 2017. [DOI: 10.1021/acs.jproteome.7b00284] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- Department of Chemistry
and Industrial Chemistry, University of Pisa, 56126 Pisa, Italy
| | - Davide Pellegrini
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- NEST, Scuola Normale Superiore di Pisa, 56127 Pisa, Italy
| | | | | | | | - Liam A. McDonnell
- Fondazione Pisana per la Scienza ONLUS, 56121 Pisa, Italy
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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8
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Electrospray deposition device used to precisely control the matrix crystal to improve the performance of MALDI MSI. Sci Rep 2016; 6:37903. [PMID: 27885266 PMCID: PMC5122855 DOI: 10.1038/srep37903] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/02/2016] [Indexed: 01/15/2023] Open
Abstract
MALDI MSI has been recently applied as an innovative tool for detection of molecular distribution within a specific tissue. MALDI MSI requires deposition of an organic compound, known as matrix, on the tissue of interest to assist analyte desorption and ionization, in which the matrix crystal homogeneity and size greatly influence the imaging reproducibility and spatial resolution in MALDI MSI. In this work, a homemade electrospray deposition device was developed for deposition of matrix in MALDI MSI. The device could be used to achieve 1 μm homogeneous matrix crystals in MALDI MSI analysis. Moreover, it was found, for the first time, that the electrospray deposition device could be used to precisely control the matrix crystal size, and the imaging spatial resolution was increased greatly as the matrix crystals size becoming smaller. In addition, the easily-built electrospray deposition device was durable for acid, base or organic solvent, and even could be used for deposition of nanoparticles matrix, which made it unparalleled for MALDI MSI analysis. The feasibility of the electrospray deposition device was investigated by combination with MALDI FTICR MSI to analyze the distributions of lipids in mouse brain and liver cancer tissue section.
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9
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Beine B, Diehl HC, Meyer HE, Henkel C. Tissue MALDI Mass Spectrometry Imaging (MALDI MSI) of Peptides. Methods Mol Biol 2016; 1394:129-150. [PMID: 26700046 DOI: 10.1007/978-1-4939-3341-9_10] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a technique to visualize molecular features of tissues based on mass detection. This chapter focuses on MALDI MSI of peptides and provides detailed operational instructions for sample preparation of cryoconserved and formalin-fixed paraffin-embedded (FFPE) tissue. Besides sample preparation we provide protocols for the MALDI measurement, tissue staining, and data analysis. On-tissue digestion and matrix application are described for two different commercially available and commonly used spraying devices: the SunCollect (SunChrom) and the ImagePrep (Bruker Daltonik GmbH).
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Affiliation(s)
- Birte Beine
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Hanna C Diehl
- Clinical Proteomics, Medizinisches Proteom-Center, Ruhr-University, Bochum, Germany
| | - Helmut E Meyer
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Corinna Henkel
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
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10
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Kell DB. The transporter-mediated cellular uptake of pharmaceutical drugs is based on their metabolite-likeness and not on their bulk biophysical properties: Towards a systems pharmacology. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pisc.2015.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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11
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Liu X, Hummon AB. Mass spectrometry imaging of therapeutics from animal models to three-dimensional cell cultures. Anal Chem 2015; 87:9508-19. [PMID: 26084404 PMCID: PMC4766864 DOI: 10.1021/acs.analchem.5b00419] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful label-free technique for the investigation of the spatial distribution of molecules at complex surfaces and has been widely used in the pharmaceutical sciences to understand the distribution of different drugs and their metabolites in various biological samples, ranging from cell-based models to tissues. Here, we review the current applications of MSI for drug studies in animal models, followed by a discussion of the novel advances of MSI in three-dimensional (3D) cell cultures for accurate, efficient, and high-throughput analyses to evaluate therapeutics.
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Affiliation(s)
- Xin Liu
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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Abstract
Advances in development of mass spectrometry (MS) are successfully utilized for spatial localization of pharmaceutical compounds in these tissue sections. Today MS instruments can be used in imaging mode when the datasets are generated from the surface of the tissue over an array of acquisition positions. This review is focused on the technological developments of matrix-assisted laser desorption/ionization MS imaging (MALDI-MSI) and related sample preparation procedures. MALDI-MSI provides a sensitive and label-free approach for imaging of drugs and their metabolites. Due to these features, MALDI-MSI is expected to become a standard technique in pharmaceutical development providing complementary information to current methods.
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Affiliation(s)
- Ákos Végvári
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, Sweden.,CREATE Health, Lund University, Sweden; Department of Pharmacology & Toxicology, University of Texas Medical Branch, Galveston, TX, USA
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13
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Ait-Belkacem R, Berenguer C, Villard C, Ouafik L, Figarella-Branger D, Beck A, Chinot O, Lafitte D. Monitoring therapeutic monoclonal antibodies in brain tumor. MAbs 2015; 6:1385-93. [PMID: 25484065 DOI: 10.4161/mabs.34405] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bevacizumab induces normalization of abnormal blood vessels, making them less leaky. By binding to vascular endothelial growth factor, it indirectly attacks the vascular tumor mass. The optimal delivery of targeted therapies including monoclonal antibodies or anti-angiogenesis drugs to the target tissue highly depends on the blood-brain barrier permeability. It is therefore critical to investigate how drugs effectively reach the tumor. In situ investigation of drug distribution could provide a better understanding of pharmacological agent action and optimize chemotherapies for solid tumors. We developed an imaging method coupled to protein identification using matrix-assisted laser desorption/ionization mass spectrometry. This approach monitored bevacizumab distribution within the brain structures, and especially within the tumor, without any labeling.
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Key Words
- 5 DAN, 1
- 5-diaminonaphtalene
- BBB, blood-brain barrier
- CRC, metastatic colorectal cancer
- CSF, cerebrospinal fluid; 1
- EMA, European Medicines Agency
- FDA, Food and Drug Administration
- GBM, glioblastoma multiforme
- IMS, imaging mass spectrometry
- ISD, in-source decay
- ITO, indium tin oxide
- LC-MS/MS, liquid chromatography coupled to tandem mass spectrometry
- MALDI imaging mass spectrometry
- MALDI, matrix-assisted laser desorption/ionization
- NSCLC, non-small cell lung cancer
- RMS, root mean square
- RP-HPLC, reversed phase high-performance liquid chromatography
- TOF, time of flight
- VEGF, vascular endothelial growth factor
- VEGFR, vascular endothelial growth factor receptor
- VH, variable domain of the heavy chain
- VL, variable domain of the light chain
- WHO, world health organization
- bevacizumab
- glioblastoma multiforme
- mAbs, monoclonal antibodies
- monoclonal antibodies
- pE, pyroglutamate
- palivizumab
- top down in source decay
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Affiliation(s)
- Rima Ait-Belkacem
- a Aix-Marseille Université Inserm ; CRO2 UMR S-911; Marseille , France
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14
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Galler K, Bräutigam K, Große C, Popp J, Neugebauer U. Making a big thing of a small cell--recent advances in single cell analysis. Analyst 2015; 139:1237-73. [PMID: 24495980 DOI: 10.1039/c3an01939j] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell analysis is an emerging field requiring a high level interdisciplinary collaboration to provide detailed insights into the complex organisation, function and heterogeneity of life. This review is addressed to life science researchers as well as researchers developing novel technologies. It covers all aspects of the characterisation of single cells (with a special focus on mammalian cells) from morphology to genetics and different omics-techniques to physiological, mechanical and electrical methods. In recent years, tremendous advances have been achieved in all fields of single cell analysis: (1) improved spatial and temporal resolution of imaging techniques to enable the tracking of single molecule dynamics within single cells; (2) increased throughput to reveal unexpected heterogeneity between different individual cells raising the question what characterizes a cell type and what is just natural biological variation; and (3) emerging multimodal approaches trying to bring together information from complementary techniques paving the way for a deeper understanding of the complexity of biological processes. This review also covers the first successful translations of single cell analysis methods to diagnostic applications in the field of tumour research (especially circulating tumour cells), regenerative medicine, drug discovery and immunology.
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Affiliation(s)
- Kerstin Galler
- Integrated Research and Treatment Center "Center for Sepsis Control and Care", Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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15
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Mainini V, Lalowski M, Gotsopoulos A, Bitsika V, Baumann M, Magni F. MALDI-imaging mass spectrometry on tissues. Methods Mol Biol 2015; 1243:139-64. [PMID: 25384744 DOI: 10.1007/978-1-4939-1872-0_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-profiling and imaging mass spectrometry (MSI) are promising technologies for measuring hundreds of different molecules directly on tissues. For instance, small molecules, drugs and their metabolites, endogenous lipids, carbohydrates and complex peptides/proteins can be measured at the same time. In the most advanced instruments, it is achieved without significant disruption of sample integrity. MSI is a unique approach for assessing the spatial distribution of molecules using graphical multidimensional maps of their constituent analytes, which may for instance be correlated with histopathological alterations in patient tissues. MALDI-TOF-MSI technology has been implemented in hospitals of several countries, where it is routinely used for quick pathogen(s) identification, a task formerly accomplished by laborious and expensive DNA/RNA-based PCR (polymerase chain reaction) screening.In this chapter, we describe how MSI is performed, what is required from the researcher, the instrument vendors and finally what can be achieved with MSI. We restrict our descriptions only to MALDI-MSI although several other MS techniques of ionization can easily be linked to MSI.
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Affiliation(s)
- Veronica Mainini
- Department of Health Sciences, University Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy
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16
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Kell DB, Oliver SG. How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol 2014; 5:231. [PMID: 25400580 PMCID: PMC4215795 DOI: 10.3389/fphar.2014.00231] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022] Open
Abstract
One approach to experimental science involves creating hypotheses, then testing them by varying one or more independent variables, and assessing the effects of this variation on the processes of interest. We use this strategy to compare the intellectual status and available evidence for two models or views of mechanisms of transmembrane drug transport into intact biological cells. One (BDII) asserts that lipoidal phospholipid Bilayer Diffusion Is Important, while a second (PBIN) proposes that in normal intact cells Phospholipid Bilayer diffusion Is Negligible (i.e., may be neglected quantitatively), because evolution selected against it, and with transmembrane drug transport being effected by genetically encoded proteinaceous carriers or pores, whose “natural” biological roles, and substrates are based in intermediary metabolism. Despite a recent review elsewhere, we can find no evidence able to support BDII as we can find no experiments in intact cells in which phospholipid bilayer diffusion was either varied independently or measured directly (although there are many papers where it was inferred by seeing a covariation of other dependent variables). By contrast, we find an abundance of evidence showing cases in which changes in the activities of named and genetically identified transporters led to measurable changes in the rate or extent of drug uptake. PBIN also has considerable predictive power, and accounts readily for the large differences in drug uptake between tissues, cells and species, in accounting for the metabolite-likeness of marketed drugs, in pharmacogenomics, and in providing a straightforward explanation for the late-stage appearance of toxicity and of lack of efficacy during drug discovery programmes despite macroscopically adequate pharmacokinetics. Consequently, the view that Phospholipid Bilayer diffusion Is Negligible (PBIN) provides a starting hypothesis for assessing cellular drug uptake that is much better supported by the available evidence, and is both more productive and more predictive.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester Manchester, UK ; Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge Cambridge, UK ; Cambridge Systems Biology Centre, University of Cambridge Cambridge, UK
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17
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Kumar R, Jain S, Kumari B, Kumar M. Protein sub-nuclear localization prediction using SVM and Pfam domain information. PLoS One 2014; 9:e98345. [PMID: 24897370 PMCID: PMC4045734 DOI: 10.1371/journal.pone.0098345] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 05/01/2014] [Indexed: 12/24/2022] Open
Abstract
The nucleus is the largest and the highly organized organelle of eukaryotic cells. Within nucleus exist a number of pseudo-compartments, which are not separated by any membrane, yet each of them contains only a specific set of proteins. Understanding protein sub-nuclear localization can hence be an important step towards understanding biological functions of the nucleus. Here we have described a method, SubNucPred developed by us for predicting the sub-nuclear localization of proteins. This method predicts protein localization for 10 different sub-nuclear locations sequentially by combining presence or absence of unique Pfam domain and amino acid composition based SVM model. The prediction accuracy during leave-one-out cross-validation for centromeric proteins was 85.05%, for chromosomal proteins 76.85%, for nuclear speckle proteins 81.27%, for nucleolar proteins 81.79%, for nuclear envelope proteins 79.37%, for nuclear matrix proteins 77.78%, for nucleoplasm proteins 76.98%, for nuclear pore complex proteins 88.89%, for PML body proteins 75.40% and for telomeric proteins it was 83.33%. Comparison with other reported methods showed that SubNucPred performs better than existing methods. A web-server for predicting protein sub-nuclear localization named SubNucPred has been established at http://14.139.227.92/mkumar/subnucpred/. Standalone version of SubNucPred can also be downloaded from the web-server.
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Affiliation(s)
- Ravindra Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Sohni Jain
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Bandana Kumari
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail:
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18
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Wang K, Huang C, Nice EC. Proteomics, genomics and transcriptomics: their emerging roles in the discovery and validation of colorectal cancer biomarkers. Expert Rev Proteomics 2014; 11:179-205. [PMID: 24611605 DOI: 10.1586/14789450.2014.894466] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is the second most common cancer in females and the third in males. Since CRC is often diagnosed at an advanced stage when prognosis is poor, identification of biomarkers for early diagnosis is urgently required. Recent advances in proteomics, genomics and transcriptomics have facilitated high-throughput profiling of data generated from CRC-related genes and proteins, providing a window of information for biomarker discovery and validation. However, transfer of candidate biomarkers from bench to bedside remains a dilemma. In this review, we will discuss emerging proteomic technologies and highlight various sample types utilized for proteomics-based identification of CRC biomarkers. Moreover, recent breakthroughs in genomics and transcriptomics for the identification of CRC biomarkers, with particular emphasis on the merits of emerging methylomic and miRNAomic strategies, will be discussed. Integration of proteomics, genomics and transcriptomics will facilitate the discovery and validation of CRC biomarkers leading to the emergence of personalized medicine.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, 610041 , P.R. China
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19
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Ait-Belkacem R, Berenguer C, Villard C, Ouafik L, Figarella-Branger D, Chinot O, Lafitte D. MALDI imaging and in-source decay for top-down characterization of glioblastoma. Proteomics 2014; 14:1290-301. [PMID: 24376047 DOI: 10.1002/pmic.201300329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/27/2013] [Accepted: 10/04/2013] [Indexed: 01/15/2023]
Abstract
Glioblastoma multiforme is one of the most common intracranial tumors encountered in adults. This tumor of very poor prognosis is associated with a median survival rate of approximately 14 months. One of the major issues to better understand the biology of these tumors and to optimize the therapy is to obtain the molecular structure of glioblastoma. MALDI molecular imaging enables location of molecules in tissues without labeling. However, molecular identification in situ is not an easy task. In this paper, we used MALDI imaging coupled to in-source decay to characterize markers of this pathology. We provided MALDI molecular images up to 30 μm spatial resolution of mouse brain tissue sections. MALDI images showed the heterogeneity of the glioblastoma. In the various zones and at various development stages of the tumor, using our top-down strategy, we identified several proteins. These proteins play key roles in tumorigenesis. Particular attention was given to the necrotic area with characterization of hemorrhage, one of the most important poor prognosis factors in glioblastoma.
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20
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Neubert P, Walch A. Current frontiers in clinical research application of MALDI imaging mass spectrometry. Expert Rev Proteomics 2014; 10:259-73. [DOI: 10.1586/epr.13.19] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Ibáñez C, García-Cañas V, Valdés A, Simó C. Direct Mass Spectrometry-Based Approaches in Metabolomics. FUNDAMENTALS OF ADVANCED OMICS TECHNOLOGIES: FROM GENES TO METABOLITES 2014. [DOI: 10.1016/b978-0-444-62651-6.00010-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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22
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Alexandrov T, Bartels A. Testing for presence of known and unknown molecules in imaging mass spectrometry. ACTA ACUST UNITED AC 2013; 29:2335-42. [PMID: 23873892 DOI: 10.1093/bioinformatics/btt388] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Imaging mass spectrometry has emerged in the past decade as a label-free, spatially resolved and multi-purpose bioanalytical technique for direct analysis of biological samples. However, solving two everyday data analysis problems still requires expert judgment: (i) the detection of unknown molecules and (ii) the testing for presence of known molecules. RESULTS We developed a measure of spatial chaos of a molecular image corresponding to a mass-to-charge value, which is a proxy for the molecular presence, and developed methods solving considered problems. The statistical evaluation was performed on a dataset from a rat brain section with test sets of molecular images selected by an expert. The measure of spatial chaos has shown high agreement with expert judges. The method for detection of unknown molecules allowed us to find structured molecular images corresponding to spectral peaks of any low intensity. The test for presence applied to a list of endogenous peptides ranked them according to the proposed measure of their presence in the sample. AVAILABILITY The source code and test sets of mass-to-charge images are available at http://www.math.uni-bremen.de/∼theodore. SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online. CONTACT theodore@uni-bremen.de.
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Affiliation(s)
- Theodore Alexandrov
- Center for Industrial Mathematics, University of Bremen, 28359 Bremen, Germany.
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23
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Gao Y, Lin Y, Zhang B, Zou D, He M, Dong B, Hang W, Huang B. Single-Cell Elemental Analysis via High Irradiance Femtosecond Laser Ionization Time-of-Flight Mass Spectrometry. Anal Chem 2013; 85:4268-72. [DOI: 10.1021/ac400317q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yao Gao
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yiming Lin
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bochao Zhang
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Dongxuan Zou
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Miaohong He
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bin Dong
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wei Hang
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Benli Huang
- Department of Chemistry, Key Laboratory
of Analytical
Sciences, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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24
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Suits F, Fehniger TE, Végvári A, Marko-Varga G, Horvatovich P. Correlation queries for mass spectrometry imaging. Anal Chem 2013; 85:4398-404. [PMID: 23537055 DOI: 10.1021/ac303658t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry imaging (MSI) generates large volumetric data sets consisting of mass to charge ratio (m/z), ion current, and x,y coordinate location. These data sets usually serve limited purposes centered on measuring the distribution of a small set of ions with known m/z. Such earmarked queries consider only a fraction of the full mass spectrum captured, and there are few tools to assist the exploration of the remaining volume of unknown data in terms of demonstrating similarity or discordance in tissue compartment distribution patterns. Here we present a novel, interactive approach to extract information from MSI data that relies on precalculated data structures to perform queries of large data sets with a typical laptop. We have devised methods to query the full volume to find new m/z values of potential interest based on similarity to biological structures or to the spatial distribution of known ions. We describe these query methods in detail and provide examples demonstrating the power of the methods to "discover" m/z values of ions that have such potentially interesting correlations. The "discovered" ions may be further correlated with either positional locations or the coincident distribution of other ions using successive queries. Finally, we show it is possible to gain insight to the fragmentation pattern of the parent molecule from such correlations. The ability to discover new ions of interest in the unknown bulk of an MSI data set offers the potential to further our understanding of biological and physiological processes related to health and disease.
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Affiliation(s)
- Frank Suits
- IBM T J Watson Research Center, Yorktown Heights, New York 10598, United States.
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25
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Prideaux B, Stoeckli M. Mass spectrometry imaging for drug distribution studies. J Proteomics 2012; 75:4999-5013. [DOI: 10.1016/j.jprot.2012.07.028] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/15/2012] [Accepted: 07/16/2012] [Indexed: 01/13/2023]
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