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Shi D, Grey AC, Guo G. An isotopically-labelled temporal mass spectrometry imaging data analysis workflow to reveal glucose spatial metabolism patterns in bovine lens tissue. Sci Rep 2024; 14:18843. [PMID: 39138264 PMCID: PMC11322647 DOI: 10.1038/s41598-024-69507-z] [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: 03/05/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Application of stable isotopically labelled (SIL) molecules in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) over a series of time points allows the temporal and spatial dynamics of biochemical reactions to be tracked in a biological system. However, these large kinetic MSI datasets and the inherent variability of biological replicates presents significant challenges to the rapid analysis of the data. In addition, manual annotation of downstream SIL metabolites involves human input to carefully analyse the data based on prior knowledge and personal expertise. To overcome these challenges to the analysis of spatiotemporal MALDI-MSI data and improve the efficiency of SIL metabolite identification, a bioinformatics pipeline has been developed and demonstrated by analysing normal bovine lens glucose metabolism as a model system. The pipeline consists of spatial alignment to mitigate the impact of sample variability and ensure spatial comparability of the temporal data, dimensionality reduction to rapidly map regional metabolic distinctions within the tissue, and metabolite annotation coupled with pathway enrichment modules to summarise and display the metabolic pathways induced by the treatment. This pipeline will be valuable for the spatial metabolomics community to analyse kinetic MALDI-MSI datasets, enabling rapid characterisation of spatio-temporal metabolic patterns from tissues of interest.
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Affiliation(s)
- Dingchang Shi
- Department of Physiology, School of Medical Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Angus C Grey
- Department of Physiology, School of Medical Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.
| | - George Guo
- Department of Physiology, School of Medical Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
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2
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Iwama T, Kano K, Kawana H, Shindou H, Shimizu T, Kono N, Aoki J. Visualization of Phospholipid Synthesis on Tissue Sections Using Functional Mass Spectrometry Imaging. Anal Chem 2024; 96:11771-11779. [PMID: 38995673 DOI: 10.1021/acs.analchem.4c01219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Functional mass spectrometry imaging (fMSI) is a potent tool for elucidating the spatial distribution of enzyme activities in tissues at high resolution. In this study, we applied fMSI to probe the intricate biosynthesis of phospholipids, which exist as thousands of molecular species in tissues and exhibit a unique distribution specific to cell type. By using deuterium- and 13C-labeled substrates, we visualized the activities of key enzymes involved in phospholipid synthesis, including glycerol 3-phosphate acyltransferase (GPAT), lysophosphatidic acid acyltransferases (LPAAT), lysophospholipid acyltransferases (LPLAT), and long-chain acyl-CoA synthetase (ACSL). Additionally, we were able to visualize a two-step sequential enzyme reaction involving ACSL and LPLAT. This novel approach unveiled significant variations in enzyme activity distribution depending on the type of fatty acids used as substrates. It will also help to reveal the mechanisms underlying the formation of numerous phospholipid species.
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Affiliation(s)
- Taiga Iwama
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroki Kawana
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology. Nara 630-0192, Japan
| | - Hideo Shindou
- Department of Lipid Life Science, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
- Department of Medical Lipid Science, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takao Shimizu
- Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
- Institute of Microbial Chemistry, Tokyo 141-0021, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
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3
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Fan X, Sun AR, Young RSE, Afara IO, Hamilton BR, Ong LJY, Crawford R, Prasadam I. Spatial analysis of the osteoarthritis microenvironment: techniques, insights, and applications. Bone Res 2024; 12:7. [PMID: 38311627 PMCID: PMC10838951 DOI: 10.1038/s41413-023-00304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 02/06/2024] Open
Abstract
Osteoarthritis (OA) is a debilitating degenerative disease affecting multiple joint tissues, including cartilage, bone, synovium, and adipose tissues. OA presents diverse clinical phenotypes and distinct molecular endotypes, including inflammatory, metabolic, mechanical, genetic, and synovial variants. Consequently, innovative technologies are needed to support the development of effective diagnostic and precision therapeutic approaches. Traditional analysis of bulk OA tissue extracts has limitations due to technical constraints, causing challenges in the differentiation between various physiological and pathological phenotypes in joint tissues. This issue has led to standardization difficulties and hindered the success of clinical trials. Gaining insights into the spatial variations of the cellular and molecular structures in OA tissues, encompassing DNA, RNA, metabolites, and proteins, as well as their chemical properties, elemental composition, and mechanical attributes, can contribute to a more comprehensive understanding of the disease subtypes. Spatially resolved biology enables biologists to investigate cells within the context of their tissue microenvironment, providing a more holistic view of cellular function. Recent advances in innovative spatial biology techniques now allow intact tissue sections to be examined using various -omics lenses, such as genomics, transcriptomics, proteomics, and metabolomics, with spatial data. This fusion of approaches provides researchers with critical insights into the molecular composition and functions of the cells and tissues at precise spatial coordinates. Furthermore, advanced imaging techniques, including high-resolution microscopy, hyperspectral imaging, and mass spectrometry imaging, enable the visualization and analysis of the spatial distribution of biomolecules, cells, and tissues. Linking these molecular imaging outputs to conventional tissue histology can facilitate a more comprehensive characterization of disease phenotypes. This review summarizes the recent advancements in the molecular imaging modalities and methodologies for in-depth spatial analysis. It explores their applications, challenges, and potential opportunities in the field of OA. Additionally, this review provides a perspective on the potential research directions for these contemporary approaches that can meet the requirements of clinical diagnoses and the establishment of therapeutic targets for OA.
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Affiliation(s)
- Xiwei Fan
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Antonia Rujia Sun
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Reuben S E Young
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Isaac O Afara
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, QLD, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD, Australia
| | - Louis Jun Ye Ong
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Ross Crawford
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Indira Prasadam
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia.
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia.
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4
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Chen Y, Yang S, Yu K, Zhang J, Wu M, Zheng Y, Zhu Y, Dai J, Wang C, Zhu X, Dai Y, Sun Y, Wu T, Wang S. Spatial omics: An innovative frontier in aging research. Ageing Res Rev 2024; 93:102158. [PMID: 38056503 DOI: 10.1016/j.arr.2023.102158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Disentangling the impact of aging on health and disease has become critical as population aging progresses rapidly. Studying aging at the molecular level is complicated by the diverse aging profiles and dynamics. However, the examination of cellular states within aging tissues in situ is hampered by the lack of high-resolution spatial data. Emerging spatial omics technologies facilitate molecular and spatial analysis of tissues, providing direct access to precise information on various functional regions and serving as a favorable tool for unraveling the heterogeneity of aging. In this review, we summarize the recent advances in spatial omics application in multi-organ aging research, which has enhanced the understanding of aging mechanisms from multiple standpoints. We also discuss the main challenges in spatial omics research to date, the opportunities for further developing the technology, and the potential applications of spatial omics in aging and aging-related diseases.
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Affiliation(s)
- Ying Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Shuhao Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Kaixu Yu
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinjin Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yongqiang Zheng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Centre, Sun Yat-sen University, Guangzhou, China
| | - Yun Zhu
- Department of Internal Medicine, Southern Illinois University School of Medicine, 801 N. Rutledge, P.O. Box 19628, Springfield, IL 62702, USA
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Chunyan Wang
- College of Science & Engineering Jinan University, Guangzhou, China
| | - Xiaoran Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yunhong Sun
- Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tong Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
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5
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Kumar BS. Recent developments and applications of ambient mass spectrometry imaging in pharmaceutical research: an overview. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 16:8-32. [PMID: 38088775 DOI: 10.1039/d3ay01267k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The application of ambient mass spectrometry imaging "MSI" is expanding in the areas of fundamental research on drug delivery and multiple phases of the process of identifying and developing drugs. Precise monitoring of a drug's pharmacological workflows, such as intake, distribution, metabolism, and discharge, is made easier by MSI's ability to determine the concentrations of the initiating drug and its metabolites across dosed samples without losing spatial data. Lipids, glycans, and proteins are just a few of the many phenotypes that MSI may be used to concurrently examine. Each of these substances has a particular distribution pattern and biological function throughout the body. MSI offers the perfect analytical tool for examining a drug's pharmacological features, especially in vitro and in vivo effectiveness, security, probable toxic effects, and putative molecular pathways, because of its high responsiveness in chemical and physical environments. The utilization of MSI in the field of pharmacy has further extended from the traditional tissue examination to the early stages of drug discovery and development, including examining the structure-function connection, high-throughput capabilities in vitro examination, and ex vivo research on individual cells or tumor spheroids. Additionally, an enormous array of endogenous substances that may function as tissue diagnostics can be scanned simultaneously, giving the specimen a highly thorough characterization. Ambient MSI techniques are soft enough to allow for easy examination of the native sample to gather data on exterior chemical compositions. This paper provides a scientific and methodological overview of ambient MSI utilization in research on pharmaceuticals.
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Affiliation(s)
- Bharath Sampath Kumar
- Independent researcher, 21, B2, 27th Street, Lakshmi Flats, Nanganallur, Chennai 600061, India.
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6
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Hartmann S, Botha SM, Gray CM, Valdes DS, Tong S, Kaitu'u-Lino TJ, Herse F, Bergman L, Cluver CA, Dechend R, Nonn O. Can single-cell and spatial omics unravel the pathophysiology of pre-eclampsia? J Reprod Immunol 2023; 159:104136. [PMID: 37634318 DOI: 10.1016/j.jri.2023.104136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
Pre-eclampsia is a leading cause of maternal and fetal morbidity and mortality. Characterised by the onset of hypertension and proteinuria in the second half of pregnancy, it can lead to maternal end-organ injury such as cerebral ischemia and oedema, pulmonary oedema and renal failure, and potentially fatal outcomes for both mother and fetus. The causes of the different maternal end-organ phenotypes of pre-eclampsia and why some women develop pre-eclampsia condition early in pregnancy have yet to be elucidated. Omics methods include proteomics, genomics, metabolomics, transcriptomics. These omics techniques, previously mostly used on bulk tissue and individually, are increasingly available at a single cellular level and can be combined with each other. Multi-omics techniques on a single-cell or spatial level provide us with a powerful tool to understand the pathophysiology of pre-eclampsia. This review will explore the status of omics methods and how they can and could contribute to understanding the pathophysiology of pre-eclampsia.
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Affiliation(s)
- Sunhild Hartmann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany; Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria 3084, Australia; Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, Heidelberg, Victoria 3084, Australia; Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Center for Cardiovascular Research), partner site Berlin, Germany
| | - Stefan Marc Botha
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany; Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria 3084, Australia; Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, Heidelberg, Victoria 3084, Australia; Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Clive M Gray
- Division of Molecular Biology and Human Genetics, Biomedical Research Institute, Stellenbosch University, Cape Town 7505, South Africa
| | - Daniela S Valdes
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany; Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Stephen Tong
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria 3084, Australia; Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Tu'uhevaha J Kaitu'u-Lino
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria 3084, Australia; Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Florian Herse
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany; Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Lina Bergman
- Department of Obstetrics and Gynaecology, Stellenbosch University, Cape Town 7505, South Africa; Department of Women's and Children's Health, Uppsala University, Uppsala 751 85, Sweden,; Department of Obstetrics and Gynaecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Catherine A Cluver
- Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria 3084, Australia; Translational Obstetrics Group, The Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, Heidelberg, Victoria 3084, Australia; Department of Obstetrics and Gynaecology, Stellenbosch University, Cape Town 7505, South Africa
| | - Ralf Dechend
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany; Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Center for Cardiovascular Research), partner site Berlin, Germany; HELIOS Clinic, Department of Cardiology and Nephrology, Berlin, Germany
| | - Olivia Nonn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany; Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Center for Cardiovascular Research), partner site Berlin, Germany; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.
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7
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He MJ, Pu W, Wang X, Zhang W, Tang D, Dai Y. Comparing DESI-MSI and MALDI-MSI Mediated Spatial Metabolomics and Their Applications in Cancer Studies. Front Oncol 2022; 12:891018. [PMID: 35924152 PMCID: PMC9340374 DOI: 10.3389/fonc.2022.891018] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/20/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolic heterogeneity of cancer contributes significantly to its poor treatment outcomes and prognosis. As a result, studies continue to focus on identifying new biomarkers and metabolic vulnerabilities, both of which depend on the understanding of altered metabolism in cancer. In the recent decades, the rise of mass spectrometry imaging (MSI) enables the in situ detection of large numbers of small molecules in tissues. Therefore, researchers look to using MSI-mediated spatial metabolomics to further study the altered metabolites in cancer patients. In this review, we examined the two most commonly used spatial metabolomics techniques, MALDI-MSI and DESI-MSI, and some recent highlights of their applications in cancer studies. We also described AFADESI-MSI as a recent variation from the DESI-MSI and compare it with the two major techniques. Specifically, we discussed spatial metabolomics results in four types of heterogeneous malignancies, including breast cancer, esophageal cancer, glioblastoma and lung cancer. Multiple studies have effectively classified cancer tissue subtypes using altered metabolites information. In addition, distribution trends of key metabolites such as fatty acids, high-energy phosphate compounds, and antioxidants were identified. Therefore, while the visualization of finer distribution details requires further improvement of MSI techniques, past studies have suggested spatial metabolomics to be a promising direction to study the complexity of cancer pathophysiology.
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Affiliation(s)
- Michelle Junyi He
- Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Wenjun Pu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Xi Wang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Wei Zhang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin, 924st Hospital, Guilin, China
- *Correspondence: Yong Dai,
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8
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Dong Y, Aharoni A. Image to insight: exploring natural products through mass spectrometry imaging. Nat Prod Rep 2022; 39:1510-1530. [PMID: 35735199 DOI: 10.1039/d2np00011c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2017 to 2022Mass spectrometry imaging (MSI) has become a mature molecular imaging technique that is well-matched for natural product (NP) discovery. Here we present a brief overview of MSI, followed by a thorough discussion of different MSI applications in NP research. This review will mainly focus on the recent progress of MSI in plants and microorganisms as they are the main producers of NPs. Specifically, the opportunity and potential of combining MSI with other imaging modalities and stable isotope labeling are discussed. Throughout, we focus on both the strengths and weaknesses of MSI, with an eye on future improvements that are necessary for the progression of MSI toward routine NP studies. Finally, we discuss new areas of research, future perspectives, and the overall direction that the field may take in the years to come.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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9
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Probing altered enzyme activity in the biochemical characterization of cancer. Biosci Rep 2022; 42:230680. [PMID: 35048115 PMCID: PMC8819661 DOI: 10.1042/bsr20212002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
Abstract
Enzymes have evolved to catalyze their precise reactions at the necessary rates, locations, and time to facilitate our development, to respond to a variety of insults and challenges, and to maintain a healthy, balanced state. Enzymes achieve this extraordinary feat through their unique kinetic parameters, myriad regulatory strategies, and their sensitivity to their surroundings, including substrate concentration and pH. The Cancer Genome Atlas (TCGA) highlights the extraordinary number of ways in which the finely tuned activities of enzymes can be disrupted, contributing to cancer development and progression often due to somatic and/or inherited genetic alterations. Rather than being limited to the domain of enzymologists, kinetic constants such as kcat, Km, and kcat/Km are highly informative parameters that can impact a cancer patient in tangible ways—these parameters can be used to sort tumor driver mutations from passenger mutations, to establish the pathways that cancer cells rely on to drive patients’ tumors, to evaluate the selectivity and efficacy of anti-cancer drugs, to identify mechanisms of resistance to treatment, and more. In this review, we will discuss how changes in enzyme activity, primarily through somatic mutation, can lead to altered kinetic parameters, new activities, or changes in conformation and oligomerization. We will also address how changes in the tumor microenvironment can affect enzymatic activity, and briefly describe how enzymology, when combined with additional powerful tools, and can provide us with tremendous insight into the chemical and molecular mechanisms of cancer.
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10
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Takeo E, Sugiura Y, Ohnishi Y, Kishima H, Fukusaki E, Shimma S. Mass Spectrometric Enzyme Histochemistry for Choline Acetyltransferase Reveals De Novo Acetylcholine Synthesis in Rodent Brain and Spinal Cord. ACS Chem Neurosci 2021; 12:2079-2087. [PMID: 34078081 DOI: 10.1021/acschemneuro.0c00720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Choline acetyltransferase (ChAT), responsible for the synthesis of acetylcholine, plays an important role in neurotransmission. However, no method to visualize the ChAT activity in tissues has been reported to date. In this study, mass spectrometry imaging (MSI) was used to visualize ChAT activity in situ, which is difficult with conventional enzyme histochemistry. By using choline chloride-trimethyl-d9 (choline-d9) as a substrate and simultaneously supplying an inhibitor of cholinesterase to tissues, we succeeded in directly visualizing the ChAT activity in the rodent brain and spinal cord. The findings revealed heterogeneous ChAT activity in the striatum of the mouse brain and in the spinal lower motor neurons that connect the anterior horn to the ventral root. Furthermore, extending the developed method to spinal cord injury (SCI) model mice revealed the site-specific effect of primary and secondary injury on ChAT activity. This study shows that the MSI-based enzyme histochemistry of ChAT could be a useful tool for studying cholinergic neurons.
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Affiliation(s)
- Emi Takeo
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuichiro Ohnishi
- Department of Neurosurgery, Graduate school of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Graduate school of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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