1
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Dannhorn A, Kazanc E, Flint L, Guo F, Carter A, Hall AR, Jones SA, Poulogiannis G, Barry ST, Sansom OJ, Bunch J, Takats Z, Goodwin RJA. Morphological and molecular preservation through universal preparation of fresh-frozen tissue samples for multimodal imaging workflows. Nat Protoc 2024:10.1038/s41596-024-00987-z. [PMID: 38806741 DOI: 10.1038/s41596-024-00987-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 05/30/2024]
Abstract
The landscape of tissue-based imaging modalities is constantly and rapidly evolving. While formalin-fixed, paraffin-embedded material is still useful for histological imaging, the fixation process irreversibly changes the molecular composition of the sample. Therefore, many imaging approaches require fresh-frozen material to get meaningful results. This is particularly true for molecular imaging techniques such as mass spectrometry imaging, which are widely used to probe the spatial arrangement of the tissue metabolome. As high-quality fresh-frozen tissues are limited in their availability, any sample preparation workflow they are subjected to needs to ensure morphological and molecular preservation of the tissues and be compatible with as many of the established and emerging imaging techniques as possible to obtain the maximum possible insights from the tissues. Here we describe a universal sample preparation workflow, from the initial step of freezing the tissues to the cold embedding in a new hydroxypropyl methylcellulose/polyvinylpyrrolidone-enriched hydrogel and the generation of thin tissue sections for analysis. Moreover, we highlight the optimized storage conditions that limit molecular and morphological degradation of the sections. The protocol is compatible with human and plant tissues and can be easily adapted for the preparation of alternative sample formats (e.g., three-dimensional cell cultures). The integrated workflow is universally compatible with histological tissue analysis, mass spectrometry imaging and imaging mass cytometry, as well as spatial proteomic, genomic and transcriptomic tissue analysis. The protocol can be completed within 4 h and requires minimal prior experience in the preparation of tissue samples for multimodal imaging experiments.
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Affiliation(s)
- Andreas Dannhorn
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Emine Kazanc
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Lucy Flint
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Fei Guo
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Alfie Carter
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Andrew R Hall
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Stewart A Jones
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Simon T Barry
- Bioscience, Discovery, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington, UK
| | - Zoltan Takats
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Richard J A Goodwin
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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2
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Zhou Y, Li C, Chen Y, Yu Y, Diao X, Chiu R, Fang J, Shen Y, Wang J, Zhu L, Zhou J, Cai Z. Human Airway Organoids and Multimodal Imaging-Based Toxicity Evaluation of 1-Nitropyrene. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6083-6092. [PMID: 38547129 PMCID: PMC11008236 DOI: 10.1021/acs.est.3c07195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/10/2024]
Abstract
Despite significant advances in understanding the general health impacts of air pollution, the toxic effects of air pollution on cells in the human respiratory tract are still elusive. A robust, biologically relevant in vitro model for recapitulating the physiological response of the human airway is needed to obtain a thorough understanding of the molecular mechanisms of air pollutants. In this study, by using 1-nitropyrene (1-NP) as a proof-of-concept, we demonstrate the effectiveness and reliability of evaluating environmental pollutants in physiologically active human airway organoids. Multimodal imaging tools, including live cell imaging, fluorescence microscopy, and MALDI-mass spectrometry imaging (MSI), were implemented to evaluate the cytotoxicity of 1-NP for airway organoids. In addition, lipidomic alterations upon 1-NP treatment were quantitatively analyzed by nontargeted lipidomics. 1-NP exposure was found to be associated with the overproduction of reactive oxygen species (ROS), and dysregulation of lipid pathways, including the SM-Cer conversion, as well as cardiolipin in our organoids. Compared with that of cell lines, a higher tolerance of 1-NP toxicity was observed in the human airway organoids, which might reflect a more physiologically relevant response in the native airway epithelium. Collectively, we have established a novel system for evaluating and investigating molecular mechanisms of environmental pollutants in the human airways via the combinatory use of human airway organoids, multimodal imaging analysis, and MS-based analyses.
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Affiliation(s)
- Yingyan Zhou
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Cun Li
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Yanyan Chen
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Yifei Yu
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Xin Diao
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Raymond Chiu
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jiacheng Fang
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Yuting Shen
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Jianing Wang
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Lin Zhu
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Jie Zhou
- Department
of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty
of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Zongwei Cai
- State
Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
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3
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Liu W, Ma J, Zhang J, Cao J, Hu X, Huang Y, Wang R, Wu J, Di W, Qian K, Yin X. Identification and validation of serum metabolite biomarkers for endometrial cancer diagnosis. EMBO Mol Med 2024; 16:988-1003. [PMID: 38355748 PMCID: PMC11018850 DOI: 10.1038/s44321-024-00033-1] [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: 09/23/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Endometrial cancer (EC) stands as the most prevalent gynecological tumor in women worldwide. Notably, differentiation diagnosis of abnormity detected by ultrasound findings (e.g., thickened endometrium or mass in the uterine cavity) is essential and remains challenging in clinical practice. Herein, we identified a metabolic biomarker panel for differentiation diagnosis of EC using machine learning of high-performance serum metabolic fingerprints (SMFs) and validated the biological function. We first recorded the high-performance SMFs of 191 EC and 204 Non-EC subjects via particle-enhanced laser desorption/ionization mass spectrometry (PELDI-MS). Then, we achieved an area-under-the-curve (AUC) of 0.957-0.968 for EC diagnosis through machine learning of high-performance SMFs, outperforming the clinical biomarker of cancer antigen 125 (CA-125, AUC of 0.610-0.684, p < 0.05). Finally, we identified a metabolic biomarker panel of glutamine, glucose, and cholesterol linoleate with an AUC of 0.901-0.902 and validated the biological function in vitro. Therefore, our work would facilitate the development of novel diagnostic biomarkers for EC in clinics.
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Affiliation(s)
- Wanshan Liu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Jinglan Ma
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
| | - Juxiang Zhang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Jing Cao
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Xiaoxiao Hu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
| | - Yida Huang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Ruimin Wang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Jiao Wu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Wen Di
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China.
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China.
| | - Kun Qian
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China.
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China.
- School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China.
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China.
| | - Xia Yin
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China.
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, 200127, P. R. China.
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4
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Sekera ER, Akkaya-Colak KB, Lopez A, Mihaylova MM, Hummon AB. Mass Spectrometry Imaging and Histology for the Analysis of Budding Intestinal Organoids. Anal Chem 2024; 96:4251-4258. [PMID: 38427328 PMCID: PMC10955551 DOI: 10.1021/acs.analchem.3c05725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Three-dimensional (3D) organoids have been at the forefront of regenerative medicine and cancer biology fields for the past decade. However, the fragile nature of organoids makes their spatial analysis challenging due to their budding structures and composition of single layer of cells. The standard sample preparation approaches can collapse the organoid morphology. Therefore, in this study, we evaluated several approaches to optimize a method compatible with both mass spectrometry imaging (MSI) and immunohistological techniques. Murine intestinal organoids were used to evaluate embedding in gelatin, carboxymethylcellulose (CMC)-gelatin-CMC-sucrose, or hydroxypropyl methylcellulose (HPMC) and polyvinylpyrrolidone (PVP) solutions. Organoids were assessed with and without aldehyde fixation and analyzed for lipid distributions by MSI coupled with hematoxylin and eosin (H&E) staining and immunofluorescence (IF) in consecutive sections from the same sample. While chemical fixation preserves morphology for better histological outcomes, it can lead to suppression of the matrix-assisted laser desorption/ionization (MALDI) lipid signal. By contrast, leaving organoid samples unfixed enhanced MALDI lipid signal. The method that performed best for both MALDI and histological analysis was embedding unfixed samples in HPMC and PVP. This approach allowed assessment of cell proliferation by Ki67 while also identifying putative phosphatidylethanolamine (PE(18:0/18:1)), which was confirmed further by tandem MS approaches. Overall, these protocols will be amenable to multiplexing imaging mass spectrometry analysis with several histological assessments and help advance our understanding of the biological processes that take place in district subsets of cells in budding organoid structures.
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Affiliation(s)
- Emily R Sekera
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, Ohio 43210, United States
| | - Kubra B Akkaya-Colak
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd, Columbus, Ohio 43210, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, 410 W 12th Ave, Columbus, Ohio 43210, United States
| | - Arbil Lopez
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, Ohio 43210, United States
| | - Maria M Mihaylova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd, Columbus, Ohio 43210, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, 410 W 12th Ave, Columbus, Ohio 43210, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, 410 W 12th Ave, Columbus, Ohio 43210, United States
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5
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Holbrook JH, Kemper GE, Hummon AB. Quantitative mass spectrometry imaging: therapeutics & biomolecules. Chem Commun (Camb) 2024; 60:2137-2151. [PMID: 38284765 PMCID: PMC10878071 DOI: 10.1039/d3cc05988j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/22/2024] [Indexed: 01/30/2024]
Abstract
Mass spectrometry imaging (MSI) has become increasingly utilized in the analysis of biological molecules. MSI grants the ability to spatially map thousands of molecules within one experimental run in a label-free manner. While MSI is considered by most to be a qualitative method, recent advancements in instrumentation, sample preparation, and development of standards has made quantitative MSI (qMSI) more common. In this feature article, we present a tailored review of recent advancements in qMSI of therapeutics and biomolecules such as lipids and peptides/proteins. We also provide detailed experimental considerations for conducting qMSI studies on biological samples, aiming to advance the methodology.
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Affiliation(s)
- Joseph H Holbrook
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Gabrielle E Kemper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amanda B Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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6
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Duivenvoorden AM, Claes BSR, van der Vloet L, Lubbers T, Glunde K, Olde Damink SWM, Heeren RMA, Lenaerts K. Lipidomic Phenotyping Of Human Small Intestinal Organoids Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Anal Chem 2023; 95:18443-18450. [PMID: 38060464 PMCID: PMC10733903 DOI: 10.1021/acs.analchem.3c03543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023]
Abstract
In the past decade, interest in organoids for biomedical research has surged, resulting in a higher demand for advanced imaging techniques. Traditional specimen embedding methods pose challenges, such as analyte delocalization and histological assessment. Here, we present an optimized sample preparation approach utilizing an Epredia M-1 cellulose-based embedding matrix, which preserves the structural integrity of fragile small intestinal organoids (SIOs). Additionally, background interference (delocalization of analytes, nonspecific (histological) staining, matrix ion clusters) was minimized, and we demonstrate the compatibility with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). With our approach, we can conduct label-free lipid imaging at the single-cell level, thereby yielding insights into the spatial distribution of lipids in both positive and negative ion modes. Moreover, M-1 embedding allows for an improved coregistration with histological and immunohistochemical (IHC) stainings, including MALDI-IHC, facilitating combined untargeted and targeted spatial information. Applying this approach, we successfully phenotyped crypt-like (CL) and villus-like (VL) SIOs, revealing that PE 36:2 [M - H]- (m/z 742.5) and PI 38:4 [M - H]- (m/z 885.5) display higher abundance in CL organoids, whereas PI 36:1 [M - H]- (m/z 863.6) was more prevalent in VL organoids. Our findings demonstrate the utility of M-1 embedding for advancing organoid research and unraveling intricate biological processes within these in vitro models.
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Affiliation(s)
- Annet
A. M. Duivenvoorden
- Department
of Surgery, NUTRIM School of Nutrition and Translational Research
in Metabolism, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Britt S. R. Claes
- The
Maastricht MultiModal Molecular Imaging (M4i) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Laura van der Vloet
- The
Maastricht MultiModal Molecular Imaging (M4i) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Tim Lubbers
- Department
of Surgery, Maastricht University Medical
Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
- GROW
– School for Oncology and Developmental Biology, Maastricht University Medical Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
| | - Kristine Glunde
- The
Russell H. Morgan Department of Radiology and Radiological Science,
Division of Cancer Imaging Research, The
Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The
Sidney
Kimmel Comprehensive Cancer Center, The
Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Department
of Biological Chemistry, The Johns Hopkins
School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven W. M. Olde Damink
- Department
of Surgery, NUTRIM School of Nutrition and Translational Research
in Metabolism, Maastricht University, 6229 ER Maastricht, The Netherlands
- Department
of Surgery, Maastricht University Medical
Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
- Department
of General, Gastrointestinal, Hepatobiliary and Transplant Surgery, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Ron M. A. Heeren
- The
Maastricht MultiModal Molecular Imaging (M4i) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department
of Surgery, NUTRIM School of Nutrition and Translational Research
in Metabolism, Maastricht University, 6229 ER Maastricht, The Netherlands
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7
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Bourceau P, Geier B, Suerdieck V, Bien T, Soltwisch J, Dreisewerd K, Liebeke M. Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling. Nat Protoc 2023; 18:3050-3079. [PMID: 37674095 DOI: 10.1038/s41596-023-00864-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/31/2023] [Indexed: 09/08/2023]
Abstract
Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.
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Affiliation(s)
- Patric Bourceau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tanja Bien
- Institute of Hygiene, University of Münster, Münster, Germany
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Institute of Human Nutrition and Food Sciences, University of Kiel, Kiel, Germany.
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8
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Fangma Y, Liu M, Liao J, Chen Z, Zheng Y. Dissecting the brain with spatially resolved multi-omics. J Pharm Anal 2023; 13:694-710. [PMID: 37577383 PMCID: PMC10422112 DOI: 10.1016/j.jpha.2023.04.003] [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: 10/31/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 08/15/2023] Open
Abstract
Recent studies have highlighted spatially resolved multi-omics technologies, including spatial genomics, transcriptomics, proteomics, and metabolomics, as powerful tools to decipher the spatial heterogeneity of the brain. Here, we focus on two major approaches in spatial transcriptomics (next-generation sequencing-based technologies and image-based technologies), and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics. Furthermore, we discuss their applications in neuroscience, including building the brain atlas, uncovering gene expression patterns of neurons for special behaviors, deciphering the molecular basis of neuronal communication, and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders. However, further efforts are still needed toward the integrative application of multi-omics technologies, including the real-time spatial multi-omics analysis in living cells, the detailed gene profile in a whole-brain view, and the combination of functional verification.
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Affiliation(s)
- Yijia Fangma
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Mengting Liu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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9
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Cappuccio G, Khalil SM, Osenberg S, Li F, Maletic-Savatic M. Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids. Front Mol Biosci 2023; 10:1181965. [PMID: 37304070 PMCID: PMC10251497 DOI: 10.3389/fmolb.2023.1181965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Human brain organoids are emerging models to study human brain development and pathology as they recapitulate the development and characteristics of major neural cell types, and enable manipulation through an in vitro system. Over the past decade, with the advent of spatial technologies, mass spectrometry imaging (MSI) has become a prominent tool for metabolic microscopy, providing label-free, non-targeted molecular and spatial distribution information of the metabolites within tissue, including lipids. This technology has never been used for studies of brain organoids and here, we set out to develop a standardized protocol for preparation and mass spectrometry imaging of human brain organoids. We present an optimized and validated sample preparation protocol, including sample fixation, optimal embedding solution, homogenous deposition of matrices, data acquisition and processing to maximize the molecular information derived from mass spectrometry imaging. We focus on lipids in organoids, as they play critical roles during cellular and brain development. Using high spatial and mass resolution in positive- and negative-ion modes, we detected 260 lipids in the organoids. Seven of them were uniquely localized within the neurogenic niches or rosettes as confirmed by histology, suggesting their importance for neuroprogenitor proliferation. We observed a particularly striking distribution of ceramide-phosphoethanolamine CerPE 36:1; O2 which was restricted within rosettes and of phosphatidyl-ethanolamine PE 38:3, which was distributed throughout the organoid tissue but not in rosettes. This suggests that ceramide in this particular lipid species might be important for neuroprogenitor biology, while its removal may be important for terminal differentiation of their progeny. Overall, our study establishes the first optimized experimental pipeline and data processing strategy for mass spectrometry imaging of human brain organoids, allowing direct comparison of lipid signal intensities and distributions in these tissues. Further, our data shed new light on the complex processes that govern brain development by identifying specific lipid signatures that may play a role in cell fate trajectories. Mass spectrometry imaging thus has great potential in advancing our understanding of early brain development as well as disease modeling and drug discovery.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Saleh M. Khalil
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Sivan Osenberg
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Feng Li
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, United States
| | - Mirjana Maletic-Savatic
- Department of Pediatrics–Neurology, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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Loewa A, Feng JJ, Hedtrich S. Human disease models in drug development. NATURE REVIEWS BIOENGINEERING 2023; 1:1-15. [PMID: 37359774 PMCID: PMC10173243 DOI: 10.1038/s44222-023-00063-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 06/20/2023]
Abstract
Biomedical research is undergoing a paradigm shift towards approaches centred on human disease models owing to the notoriously high failure rates of the current drug development process. Major drivers for this transition are the limitations of animal models, which, despite remaining the gold standard in basic and preclinical research, suffer from interspecies differences and poor prediction of human physiological and pathological conditions. To bridge this translational gap, bioengineered human disease models with high clinical mimicry are being developed. In this Review, we discuss preclinical and clinical studies that benefited from these models, focusing on organoids, bioengineered tissue models and organs-on-chips. Furthermore, we provide a high-level design framework to facilitate clinical translation and accelerate drug development using bioengineered human disease models.
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Affiliation(s)
- Anna Loewa
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - James J. Feng
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC Canada
| | - Sarah Hedtrich
- Department of Infectious Diseases and Respiratory Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Center of Biological Design, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC Canada
- Max-Delbrück Center for Molecular Medicine (MCD), Helmholtz Association, Berlin, Germany
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Kogler S, Kømurcu KS, Olsen C, Shoji JY, Skottvoll FS, Krauss S, Wilson SR, Røberg-Larsen H. Organoids, organ-on-a-chip, separation science and mass spectrometry: An update. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Murphy SE, Sweedler JV. Metabolomics-based mass spectrometry methods to analyze the chemical content of 3D organoid models. Analyst 2022; 147:2918-2929. [PMID: 35660810 PMCID: PMC9533735 DOI: 10.1039/d2an00599a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Metabolomics, the study of metabolites present in biological samples, can provide a global view of sample state as well as insights into biological changes caused by disease or environmental interactions. Mass spectrometry (MS) is commonly used for metabolomics analysis given its high-throughput capabilities, high sensitivity, and capacity to identify multiple compounds in complex samples simultaneously. MS can be coupled to separation methods that can handle small volumes, making it well suited for analyzing the metabolome of organoids, miniaturized three-dimensional aggregates of stem cells that model in vivo organs. Organoids are being used in research efforts to study human disease and development, and in the design of personalized drug treatments. For organoid models to be useful, they need to recapitulate morphological and chemical aspects, such as the metabolome, of the parent tissue. This review highlights the separation- and imaging-based MS-based metabolomics methods that have been used to analyze the chemical contents of organoids. Future perspectives on how MS techniques can be optimized to determine the accuracy of organoid models and expand the field of organoid research are also discussed.
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Affiliation(s)
- Shannon E Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801, USA.
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801, USA.
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