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Kiemen AL, Almagro-Pérez C, Matos V, Forjaz A, Braxton AM, Dequiedt L, Parksong J, Cannon CD, Yuan X, Shin SM, Babu JM, Thompson ED, Cornish TC, Ho WJ, Wood LD, Wu PH, Barrutia AM, Hruban RH, Wirtz D. 3D histology reveals that immune response to pancreatic precancers is heterogeneous and depends on global pancreas structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.03.606493. [PMID: 39149369 PMCID: PMC11326156 DOI: 10.1101/2024.08.03.606493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer for which few effective therapies exist. Immunotherapies specifically are ineffective in pancreatic cancer, in part due to its unique stromal and immune microenvironment. Pancreatic intraepithelial neoplasia, or PanIN, is the main precursor lesion to PDAC. Recently it was discovered that PanINs are remarkably abundant in the grossly normal pancreas, suggesting that the vast majority will never progress to cancer. Here, through construction of 48 samples of cm3-sized human pancreas tissue, we profiled the immune microenvironment of 1,476 PanINs in 3D and at single-cell resolution to better understand the early evolution of the pancreatic tumor microenvironment and to determine how inflammation may play a role in cancer progression. We found that bulk pancreatic inflammation strongly correlates to PanIN cell fraction. We found that the immune response around PanINs is highly heterogeneous, with distinct immune hotspots and cold spots that appear and disappear in a span of tens of microns. Immune hotspots generally mark locations of higher grade of dysplasia or locations near acinar atrophy. The immune composition at these hotspots is dominated by naïve, cytotoxic, and regulatory T cells, cancer associated fibroblasts, and tumor associated macrophages, with little similarity to the immune composition around less-inflamed PanINs. By mapping FOXP3+ cells in 3D, we found that regulatory T cells are present at higher density in larger PanIN lesions compared to smaller PanINs, suggesting that the early initiation of PanINs may not exhibit an immunosuppressive response. This analysis demonstrates that while PanINs are common in the pancreases of most individuals, inflammation may play a pivotal role, both at the bulk and the microscopic scale, in demarcating regions of significance in cancer progression.
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Affiliation(s)
- Ashley L. Kiemen
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- Institute for NanoBioTechnology, Johns Hopkins University
- Department of Functional Anatomy & Evolution, Johns Hopkins School of Medicine, Baltimore, MD
| | - Cristina Almagro-Pérez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, Leganés, Spain
| | - Valentina Matos
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, Leganés, Spain
| | - Andre Forjaz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Alicia M. Braxton
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Lucie Dequiedt
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Jeeun Parksong
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Courtney D. Cannon
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Xuan Yuan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Sarah M. Shin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Jaanvi Mahesh Babu
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Elizabeth D. Thompson
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Toby C. Cornish
- Department of Pathology and Data Science Institute, Medical College of Wisconsin, Milwaukee, WI
| | - Won Jin Ho
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Laura D. Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- Institute for NanoBioTechnology, Johns Hopkins University
| | - Arrate Muñoz Barrutia
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, Leganés, Spain
- Bioengineering Division, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Denis Wirtz
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
- Institute for NanoBioTechnology, Johns Hopkins University
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2
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Ma X, Fernández FM. Advances in mass spectrometry imaging for spatial cancer metabolomics. MASS SPECTROMETRY REVIEWS 2024; 43:235-268. [PMID: 36065601 PMCID: PMC9986357 DOI: 10.1002/mas.21804] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 05/09/2023]
Abstract
Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.
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Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
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3
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Krestensen KK, Heeren RMA, Balluff B. State-of-the-art mass spectrometry imaging applications in biomedical research. Analyst 2023; 148:6161-6187. [PMID: 37947390 DOI: 10.1039/d3an01495a] [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: 11/12/2023]
Abstract
Mass spectrometry imaging has advanced from a niche technique to a widely applied spatial biology tool operating at the forefront of numerous fields, most notably making a significant impact in biomedical pharmacological research. The growth of the field has gone hand in hand with an increase in publications and usage of the technique by new laboratories, and consequently this has led to a shift from general MSI reviews to topic-specific reviews. Given this development, we see the need to recapitulate the strengths of MSI by providing a more holistic overview of state-of-the-art MSI studies to provide the new generation of researchers with an up-to-date reference framework. Here we review scientific advances for the six largest biomedical fields of MSI application (oncology, pharmacology, neurology, cardiovascular diseases, endocrinology, and rheumatology). These publications thereby give examples for at least one of the following categories: they provide novel mechanistic insights, use an exceptionally large cohort size, establish a workflow that has the potential to become a high-impact methodology, or are highly cited in their field. We finally have a look into new emerging fields and trends in MSI (immunology, microbiology, infectious diseases, and aging), as applied MSI is continuously broadening as a result of technological breakthroughs.
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Affiliation(s)
- Kasper K Krestensen
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Ron M A Heeren
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Benjamin Balluff
- The Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, 6229 ER Maastricht, The Netherlands.
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4
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Lim MJ, Yagnik G, Henkel C, Frost SF, Bien T, Rothschild KJ. MALDI HiPLEX-IHC: multiomic and multimodal imaging of targeted intact proteins in tissues. Front Chem 2023; 11:1182404. [PMID: 37201132 PMCID: PMC10187789 DOI: 10.3389/fchem.2023.1182404] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/14/2023] [Indexed: 05/20/2023] Open
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is one of the most widely used methods for imaging the spatial distribution of unlabeled small molecules such as metabolites, lipids and drugs in tissues. Recent progress has enabled many improvements including the ability to achieve single cell spatial resolution, 3D-tissue image reconstruction, and the precise identification of different isomeric and isobaric molecules. However, MALDI-MSI of high molecular weight intact proteins in biospecimens has thus far been difficult to achieve. Conventional methods normally require in situ proteolysis and peptide mass fingerprinting, have low spatial resolution, and typically detect only the most highly abundant proteins in an untargeted manner. In addition, MSI-based multiomic and multimodal workflows are needed which can image both small molecules and intact proteins from the same tissue. Such a capability can provide a more comprehensive understanding of the vast complexity of biological systems at the organ, tissue, and cellular levels of both normal and pathological function. A recently introduced top-down spatial imaging approach known as MALDI HiPLEX-IHC (MALDI-IHC for short) provides a basis for achieving this high-information content imaging of tissues and even individual cells. Based on novel photocleavable mass-tags conjugated to antibody probes, high-plex, multimodal and multiomic MALDI-based workflows have been developed to image both small molecules and intact proteins on the same tissue sample. Dual-labeled antibody probes enable multimodal mass spectrometry and fluorescent imaging of targeted intact proteins. A similar approach using the same photocleavable mass-tags can be applied to lectin and other probes. We detail here several examples of MALDI-IHC workflows designed to enable high-plex, multiomic and multimodal imaging of tissues at a spatial resolution as low as 5 µm. This approach is compared to other existing high-plex methods such as imaging mass cytometry, MIBI-TOF, GeoMx and CODEX. Finally, future applications of MALDI-IHC are discussed.
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Affiliation(s)
- Mark J. Lim
- AmberGen, Inc., Billerica, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
| | | | | | | | - Tanja Bien
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Kenneth J. Rothschild
- AmberGen, Inc., Billerica, MA, United States
- Department of Physics and Photonics Center, Boston University, Boston, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
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5
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Kiemen AL, Braxton AM, Grahn MP, Han KS, Babu JM, Reichel R, Jiang AC, Kim B, Hsu J, Amoa F, Reddy S, Hong SM, Cornish TC, Thompson ED, Huang P, Wood LD, Hruban RH, Wirtz D, Wu PH. CODA: quantitative 3D reconstruction of large tissues at cellular resolution. Nat Methods 2022; 19:1490-1499. [PMID: 36280719 PMCID: PMC10500590 DOI: 10.1038/s41592-022-01650-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/14/2022] [Indexed: 12/15/2022]
Abstract
A central challenge in biology is obtaining high-content, high-resolution information while analyzing tissue samples at volumes relevant to disease progression. We address this here with CODA, a method to reconstruct exceptionally large (up to multicentimeter cubed) tissues at subcellular resolution using serially sectioned hematoxylin and eosin-stained tissue sections. Here we demonstrate CODA's ability to reconstruct three-dimensional (3D) distinct microanatomical structures in pancreas, skin, lung and liver tissues. CODA allows creation of readily quantifiable tissue volumes amenable to biological research. As a testbed, we assess the microanatomy of the human pancreas during tumorigenesis within the branching pancreatic ductal system, labeling ten distinct structures to examine heterogeneity and structural transformation during neoplastic progression. We show that pancreatic precancerous lesions develop into distinct 3D morphological phenotypes and that pancreatic cancer tends to spread far from the bulk tumor along collagen fibers that are highly aligned to the 3D curves of ductal, lobular, vascular and neural structures. Thus, CODA establishes a means to transform broadly the structural study of human diseases through exploration of exhaustively labeled 3D microarchitecture.
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Affiliation(s)
- Ashley L Kiemen
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alicia M Braxton
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mia P Grahn
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Kyu Sang Han
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Jaanvi Mahesh Babu
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Reichel
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ann C Jiang
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Bridgette Kim
- Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Jocelyn Hsu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Falone Amoa
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sashank Reddy
- Department of Plastic and Reconstructive Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Toby C Cornish
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Elizabeth D Thompson
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peng Huang
- Department of Biostatistics, The Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura D Wood
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Denis Wirtz
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Materials Science and Engineering, The Johns Hopkins University, Baltimore, MD, USA.
- Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD, USA.
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Pei-Hsun Wu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA.
- Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD, USA.
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6
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Balluff B, Heeren RM, Race AM. An overview of image registration for aligning mass spectrometry imaging with clinically relevant imaging modalities. J Mass Spectrom Adv Clin Lab 2022; 23:26-38. [PMID: 35156074 PMCID: PMC8821033 DOI: 10.1016/j.jmsacl.2021.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 01/25/2023] Open
Abstract
Mass spectrometry imaging (MSI) is a powerful molecular imaging technique. Integration with other imaging modalities is essential in clinical MSI. Image integration is performed by image registration techniques. Technical potential of image registration in MSI has not been fully exploited. Roadmap proposed to improve registration accuracy.
Mass spectrometry imaging (MSI) is used in many aspects of clinical research, including pharmacokinetics, toxicology, personalised medicine, and surgical decision-making. Maximising its potential requires the spatial integration of MSI images with imaging data from existing clinical imaging modalities, such as histology and MRI. To ensure that the information is properly integrated, all contributing images must be accurately aligned. This process is called image registration and is the focus of this review. In light of the ever-increasing spatial resolution of MSI instrumentation and a diversification of multi-modal MSI studies (e.g., spatial omics, 3D-MSI), the accuracy, versatility, and precision of image registration must increase accordingly. We review the application of image registration to align MSI data with different clinically relevant ex vivo and in vivo imaging techniques. Based on this, we identify steps in the current image registration processes where there is potential for improvement. Finally, we propose a roadmap for community efforts to address these challenges in order to increase registration quality and help MSI to fully exploit its multi-modal potential.
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7
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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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8
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Herrmann KH, Hoffmann F, Ernst G, Pertzborn D, Pelzel D, Geißler K, Guntinas-Lichius O, Reichenbach JR, von Eggeling F. High-resolution MRI of the human palatine tonsil and its schematic anatomic 3D reconstruction. J Anat 2021; 240:166-171. [PMID: 34342906 PMCID: PMC8655163 DOI: 10.1111/joa.13532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022] Open
Abstract
The palatine tonsils form an important part of the human immune system. Together with the other lymphoid tonsils of Waldeyer's tonsillar ring, they act as the first line of defense against ingested or inhaled pathogens. Although histologically stained sections of the palatine tonsil are widely available, they represent the tissue only in two dimensions and do not provide reference to three‐dimensional space. Such a representation of a tonsillar specimen based on imaging data as a 3D anatomical reconstruction is lacking both in scientific publications and especially in textbooks. As a first step in this direction, the objective of the present work was to image a resected tonsil specimen with high spatial resolution in a 9.4 T small‐bore pre‐clinical MRI and to combine these data with data from the completely sectioned and H&E stained same palatine tonsil. Based on the information from both image modalities, a 3D anatomical sketch was drawn by a scientific graphic artist. In perspective, such studies could help to overcome the difficulty of capturing the spatial extent and arrangement of anatomical structures from 2D images and to establish a link between three‐dimensional anatomical preparations and two‐dimensional sections or illustrations, as they have been found so far in common textbooks and anatomical atlases.
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Affiliation(s)
- Karl-Heinz Herrmann
- Medical Physics Group, Institute for Diagnostic and Interventional Radiology, Jena University Hospital, Jena, Germany
| | - Franziska Hoffmann
- Department of Otorhinolaryngology, MALDI Imaging and Innovative Biophotonics, Jena University Hospital, Jena, Germany
| | - Günther Ernst
- Department of Otorhinolaryngology, Head and Neck Surgery, Jena University Hospital, Jena, Germany
| | - David Pertzborn
- Department of Otorhinolaryngology, MALDI Imaging and Innovative Biophotonics, Jena University Hospital, Jena, Germany
| | - Daniela Pelzel
- Department of Otorhinolaryngology, MALDI Imaging and Innovative Biophotonics, Jena University Hospital, Jena, Germany
| | - Katharina Geißler
- Department of Otorhinolaryngology, Head and Neck Surgery, Jena University Hospital, Jena, Germany
| | - Orlando Guntinas-Lichius
- Department of Otorhinolaryngology, Head and Neck Surgery, Jena University Hospital, Jena, Germany
| | - Jürgen R Reichenbach
- Medical Physics Group, Institute for Diagnostic and Interventional Radiology, Jena University Hospital, Jena, Germany.,Michael-Stifel-Center for Data-Driven and Simulation Science Jena, Jena, Germany
| | - Ferdinand von Eggeling
- Michael-Stifel-Center for Data-Driven and Simulation Science Jena, Jena, Germany.,Department of Otorhinolaryngology, MALDI Imaging and Core Unit Proteome Analysis, DFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL), Jena University Hospital, Jena, Germany
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9
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Yamaguchi M, Yoshihara K, Yachida N, Suda K, Tamura R, Ishiguro T, Enomoto T. The New Era of Three-Dimensional Histoarchitecture of the Human Endometrium. J Pers Med 2021; 11:jpm11080713. [PMID: 34442357 PMCID: PMC8401133 DOI: 10.3390/jpm11080713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022] Open
Abstract
The histology of the endometrium has traditionally been established by observation of two-dimensional (2D) pathological sections. However, because human endometrial glands exhibit coiling and branching morphology, it is extremely difficult to obtain an entire image of the glands by 2D observation. In recent years, the development of three-dimensional (3D) reconstruction of serial pathological sections by computer and whole-mount imaging technology using tissue clearing methods with high-resolution fluorescence microscopy has enabled us to observe the 3D histoarchitecture of tissues. As a result, 3D imaging has revealed that human endometrial glands form a plexus network in the basalis, similar to the rhizome of grass, whereas mouse uterine glands are single branched tubular glands. This review summarizes the relevant literature on the 3D structure of mouse and human endometrium and discusses the significance of the rhizome structure in the human endometrium and the expected role of understanding the 3D tissue structure in future applications to systems biology.
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10
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Vos DRN, Ellis SR, Balluff B, Heeren RMA. Experimental and Data Analysis Considerations for Three-Dimensional Mass Spectrometry Imaging in Biomedical Research. Mol Imaging Biol 2021; 23:149-159. [PMID: 33025328 PMCID: PMC7910367 DOI: 10.1007/s11307-020-01541-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/12/2020] [Accepted: 09/10/2020] [Indexed: 10/26/2022]
Abstract
Mass spectrometry imaging (MSI) enables the visualization of molecular distributions on complex surfaces. It has been extensively used in the field of biomedical research to investigate healthy and diseased tissues. Most of the MSI studies are conducted in a 2D fashion where only a single slice of the full sample volume is investigated. However, biological processes occur within a tissue volume and would ideally be investigated as a whole to gain a more comprehensive understanding of the spatial and molecular complexity of biological samples such as tissues and cells. Mass spectrometry imaging has therefore been expanded to the 3D realm whereby molecular distributions within a 3D sample can be visualized. The benefit of investigating volumetric data has led to a quick rise in the application of single-sample 3D-MSI investigations. Several experimental and data analysis aspects need to be considered to perform successful 3D-MSI studies. In this review, we discuss these aspects as well as ongoing developments that enable 3D-MSI to be routinely applied to multi-sample studies.
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Affiliation(s)
- D R N Vos
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - S R Ellis
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - B Balluff
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - R M A Heeren
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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11
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Tuck M, Blanc L, Touti R, Patterson NH, Van Nuffel S, Villette S, Taveau JC, Römpp A, Brunelle A, Lecomte S, Desbenoit N. Multimodal Imaging Based on Vibrational Spectroscopies and Mass Spectrometry Imaging Applied to Biological Tissue: A Multiscale and Multiomics Review. Anal Chem 2020; 93:445-477. [PMID: 33253546 DOI: 10.1021/acs.analchem.0c04595] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tuck
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Landry Blanc
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Rita Touti
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-8575, United States
| | - Sebastiaan Van Nuffel
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sandrine Villette
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Jean-Christophe Taveau
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Andreas Römpp
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Alain Brunelle
- Laboratoire d'Archéologie Moléculaire et Structurale, LAMS UMR 8220, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Sophie Lecomte
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nicolas Desbenoit
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
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12
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Wang L, Sun J, Li T. Intelligent sports feature recognition system based on texture feature extraction and SVM parameter selection. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-179970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Feature extraction is the basis of texture analysis. How to obtain texture features with small feature dimension, simple calculation and comprehensive representation of images is a hot spot and a difficult point in feature extraction. The traditional image texture feature extraction method is to process the image in the spatial domain. However, due to its high computational complexity, its practical application is restricted. Based on this, this study studies the extraction method of texture features, and deeply analyzes the principle of non-subsampled Contourlet transform. Moreover, this study uses NSCT to transform the image from the spatial domain to the frequency domain and extracts the texture features of the decomposed low frequency sub-band, intermediate frequency sub-band and high frequency sub-band image respectively. In addition, this study selects the appropriate parameters to establish the support vector machine model and applies the extracted texture features into the support vector machine for recognition and applies it to the sports feature recognition. Finally, this study designed a controlled experiment to analyze the performance of the algorithm. The results show that the proposed method has certain effects.
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Affiliation(s)
- Lei Wang
- The School of Physical Education, Shandong University, Jinan, China
| | - Jinhai Sun
- The School of Physical Education, Shandong University, Jinan, China
| | - Tuojian Li
- The School of Physical Education, Shandong University, Jinan, China
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13
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Min J. Research on athlete training behavior based on improved support vector algorithm and target image detection. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-189050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In view of the defects and shortcomings of the traditional target detection and tracking algorithm in accurately detecting targets and targets in different scenarios, based on the current research status and technical level of target detection and tracking at home and abroad, this paper proposes a target detection algorithm and tracking method using neural network algorithm, and applies it to the athlete training model. Based on the Alex-Net network structure, this paper designs a three-layer convolutional layer and two layers of fully connected layers. The last layer is used as the input of the SVM classifier, and the target classification result is obtained by the SVM classifier. In addition, this article adds SPP-Layer between the convolutional layer and the fully connected layer, enabling the same dimension of the Feature Map to be obtained before the fully connected layer for different sized input images. The research results show that the proposed method has certain recognition effect and can be applied to athlete training.
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Affiliation(s)
- Jiang Min
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
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14
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Eggeling F, Hoffmann F. Microdissection—An Essential Prerequisite for Spatial Cancer Omics. Proteomics 2020; 20:e2000077. [DOI: 10.1002/pmic.202000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ferdinand Eggeling
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
| | - Franziska Hoffmann
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
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15
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Jones MA, Cho SH, Patterson NH, Van de Plas R, Spraggins JM, Boothby MR, Caprioli RM. Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry. Anal Chem 2020; 92:7079-7086. [PMID: 32298091 PMCID: PMC7456589 DOI: 10.1021/acs.analchem.0c00446] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Identifying the spatial distributions of biomolecules in tissue is crucial for understanding integrated function. Imaging mass spectrometry (IMS) allows simultaneous mapping of thousands of biosynthetic products such as lipids but has needed a means of identifying specific cell-types or functional states to correlate with molecular localization. We report, here, advances starting from identity marking with a genetically encoded fluorophore. The fluorescence emission data were integrated with IMS data through multimodal image processing with advanced registration techniques and data-driven image fusion. In an unbiased analysis of spleens, this integrated technology enabled identification of ether lipid species preferentially enriched in germinal centers. We propose that this use of genetic marking for microanatomical regions of interest can be paired with molecular information from IMS for any tissue, cell-type, or activity state for which fluorescence is driven by a gene-tracking allele and ultimately with outputs of other means of spatial mapping.
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Affiliation(s)
- Marissa A Jones
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
| | - Sung Hoon Cho
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN AA-4214B, MCN A-5301, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control (DCSC), Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Mark R Boothby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, MCN AA-4214B, MCN A-5301, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue South, MRB III Suite 9160, Nashville, Tennessee 37232, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
- Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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16
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Tobias F, McIntosh JC, LaBonia GJ, Boyce MW, Lockett MR, Hummon AB. Developing a Drug Screening Platform: MALDI-Mass Spectrometry Imaging of Paper-Based Cultures. Anal Chem 2019; 91:15370-15376. [PMID: 31755703 DOI: 10.1021/acs.analchem.9b03536] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many potential chemotherapeutics fail to reach patients. One of the key reasons is that compounds are tested during the drug discovery stage in two-dimensional (2D) cell cultures, which are often unable to accurately model in vivo outcomes. Three-dimensional (3D) in vitro tumor models are more predictive of chemotherapeutic effectiveness than 2D cultures, and thus, their implementation during the drug screening stage has the potential to more accurately evaluate compounds earlier, saving both time and money. Paper-based cultures (PBCs) are an emerging 3D culture platform in which cells suspended in Matrigel are seeded into paper scaffolds and cultured to generate a tissue-like environment. In this study, we demonstrate the potential of matrix-assisted laser desorption/ionization-mass spectrometry imaging with PBCs (MALDI-MSI-PBC) as a drug screening platform. This method discriminated regions of the PBCs with and without cells and/or drugs, indicating that coupling PBCs with MALDI-MSI has the potential to develop rapid, large-scale, and parallel mass spectrometric drug screens.
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Affiliation(s)
- Fernando Tobias
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center , The Ohio State University , Columbus , Ohio 43210-1132 , United States
| | - Julie C McIntosh
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Gabriel J LaBonia
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Matthew W Boyce
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Matthew R Lockett
- Department of Chemistry , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,Lineberger Comprehensive Cancer Center , The University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center , The Ohio State University , Columbus , Ohio 43210-1132 , United States
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17
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Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
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Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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18
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Hoffmann F, Umbreit C, Krüger T, Pelzel D, Ernst G, Kniemeyer O, Guntinas-Lichius O, Berndt A, von Eggeling F. Identification of Proteomic Markers in Head and Neck Cancer Using MALDI-MS Imaging, LC-MS/MS, and Immunohistochemistry. Proteomics Clin Appl 2018; 13:e1700173. [PMID: 30411850 DOI: 10.1002/prca.201700173] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 10/29/2018] [Indexed: 12/12/2022]
Abstract
PURPOSE The heterogeneity of squamous cell carcinoma tissue greatly complicates diagnosis and individualized therapy. Therefore, characterizing the heterogeneity of tissue spatially and identifying appropriate biomarkers is crucial. MALDI-MS imaging (MSI) is capable of analyzing spatially resolved tissue biopsies on a molecular level. EXPERIMENTAL DESIGN MALDI-MSI is used on snap frozen and formalin-fixed and paraffin-embedded (FFPE) tissue samples from patients with head and neck cancer (HNC) to analyze m/z values localized in tumor and nontumor regions. Peptide identification is performed using LC-MS/MS and immunohistochemistry (IHC). RESULTS In both FFPE and frozen tissue specimens, eight characteristic masses of the tumor's epithelial region are found. Using LC-MS/MS, the peaks are identified as vimentin, keratin type II, nucleolin, heat shock protein 90, prelamin-A/C, junction plakoglobin, and PGAM1. Lastly, vimentin, nucleolin, and PGAM1 are verified with IHC. CONCLUSIONS AND CLINICAL RELEVANCE The combination of MALDI-MSI, LC-MS/MS, and subsequent IHC furnishes a tool suitable for characterizing the molecular heterogeneity of tissue. It is also suited for use in identifying new representative biomarkers to enable a more individualized therapy.
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Affiliation(s)
- Franziska Hoffmann
- Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany
| | - Claudia Umbreit
- Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany.,Institute of Forensic Medicine, Section Pathology, Jena University Hospital, Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Daniela Pelzel
- Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany
| | - Günther Ernst
- Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | | | - Alexander Berndt
- Institute of Forensic Medicine, Section Pathology, Jena University Hospital, Jena, Germany
| | - Ferdinand von Eggeling
- Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University, Jena, Germany
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19
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Mallah K, Quanico J, Trede D, Kobeissy F, Zibara K, Salzet M, Fournier I. Lipid Changes Associated with Traumatic Brain Injury Revealed by 3D MALDI-MSI. Anal Chem 2018; 90:10568-10576. [DOI: 10.1021/acs.analchem.8b02682] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Khalil Mallah
- INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
- ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, 6573-14 Beirut, Lebanon
| | - Jusal Quanico
- INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | | | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, 1107 2020 Beirut, Lebanon
| | - Kazem Zibara
- ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, 6573-14 Beirut, Lebanon
| | - Michel Salzet
- INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Isabelle Fournier
- INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
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20
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Rabe JH, A Sammour D, Schulz S, Munteanu B, Ott M, Ochs K, Hohenberger P, Marx A, Platten M, Opitz CA, Ory DS, Hopf C. Fourier Transform Infrared Microscopy Enables Guidance of Automated Mass Spectrometry Imaging to Predefined Tissue Morphologies. Sci Rep 2018; 8:313. [PMID: 29321555 PMCID: PMC5762902 DOI: 10.1038/s41598-017-18477-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/12/2017] [Indexed: 12/27/2022] Open
Abstract
Multimodal imaging combines complementary platforms for spatially resolved tissue analysis that are poised for application in life science and personalized medicine. Unlike established clinical in vivo multimodality imaging, automated workflows for in-depth multimodal molecular ex vivo tissue analysis that combine the speed and ease of spectroscopic imaging with molecular details provided by mass spectrometry imaging (MSI) are lagging behind. Here, we present an integrated approach that utilizes non-destructive Fourier transform infrared (FTIR) microscopy and matrix assisted laser desorption/ionization (MALDI) MSI for analysing single-slide tissue specimen. We show that FTIR microscopy can automatically guide high-resolution MSI data acquisition and interpretation without requiring prior histopathological tissue annotation, thus circumventing potential human-annotation-bias while achieving >90% reductions of data load and acquisition time. We apply FTIR imaging as an upstream modality to improve accuracy of tissue-morphology detection and to retrieve diagnostic molecular signatures in an automated, unbiased and spatially aware manner. We show the general applicability of multimodal FTIR-guided MALDI-MSI by demonstrating precise tumor localization in mouse brain bearing glioma xenografts and in human primary gastrointestinal stromal tumors. Finally, the presented multimodal tissue analysis method allows for morphology-sensitive lipid signature retrieval from brains of mice suffering from lipidosis caused by Niemann-Pick type C disease.
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Affiliation(s)
- Jan-Hinrich Rabe
- Center for Applied Research in Applied Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
| | - Denis A Sammour
- Center for Applied Research in Applied Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
| | - Sandra Schulz
- Center for Applied Research in Applied Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
| | - Bogdan Munteanu
- Center for Applied Research in Applied Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany
| | - Martina Ott
- German Cancer Consortium (DKTK) CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katharina Ochs
- German Cancer Consortium (DKTK) CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and National Center of Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Hohenberger
- University Medical Center Mannheim of Heidelberg University, Mannheim, Germany
| | - Alexander Marx
- University Medical Center Mannheim of Heidelberg University, Mannheim, Germany
| | - Michael Platten
- German Cancer Consortium (DKTK) CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Medical Center Mannheim of Heidelberg University, Mannheim, Germany
| | - Christiane A Opitz
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and National Center of Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel S Ory
- Diabetic Cardiovascular Disease Center and Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Carsten Hopf
- Center for Applied Research in Applied Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany.
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, 68163, Mannheim, Germany.
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21
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Ucal Y, Durer ZA, Atak H, Kadioglu E, Sahin B, Coskun A, Baykal AT, Ozpinar A. Clinical applications of MALDI imaging technologies in cancer and neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:795-816. [PMID: 28087424 DOI: 10.1016/j.bbapap.2017.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/08/2016] [Accepted: 01/06/2017] [Indexed: 12/25/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) enables localization of analytes of interest along with histology. More specifically, MALDI-IMS identifies the distributions of proteins, peptides, small molecules, lipids, and drugs and their metabolites in tissues, with high spatial resolution. This unique capacity to directly analyze tissue samples without the need for lengthy sample preparation reduces technical variability and renders MALDI-IMS ideal for the identification of potential diagnostic and prognostic biomarkers and disease gradation. MALDI-IMS has evolved rapidly over the last decade and has been successfully used in both medical and basic research by scientists worldwide. In this review, we explore the clinical applications of MALDI-IMS, focusing on the major cancer types and neurodegenerative diseases. In particular, we re-emphasize the diagnostic potential of IMS and the challenges that must be confronted when conducting MALDI-IMS in clinical settings. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Yasemin Ucal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Zeynep Aslıhan Durer
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Hakan Atak
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Elif Kadioglu
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Abdurrahman Coskun
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Ahmet Tarık Baykal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Aysel Ozpinar
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey.
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22
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Prajapati S, Madrigal E, Friedman MT. Acquisition, Visualization and Potential Applications of 3D Data in Anatomic Pathology. Discoveries (Craiova) 2016; 4:e68. [PMID: 32309587 PMCID: PMC6941555 DOI: 10.15190/d.2016.15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Although human anatomy and histology are naturally three-dimensional (3D), commonly used diagnostic and educational tools are technologically restricted to providing two-dimensional representations (e.g. gross photography and glass slides). This limitation may be overcome by employing techniques to acquire and display 3D data, which refers to the digital information used to describe a 3D object mathematically. There are several established and experimental strategies to capture macroscopic and microscopic 3D data. In addition, recent hardware and software innovations have propelled the visualization of 3D models, including virtual and augmented reality. Accompanying these advances are novel clinical and non-clinical applications of 3D data in pathology. Medical education and research stand to benefit a great deal from utilizing 3D data as it can change our understanding of complex anatomical and histological structures. Although these technologies are yet to be adopted in routine surgical pathology, forensic pathology has embraced 3D scanning and model reconstruction. In this review, we intend to provide a general overview of the technologies and emerging applications involved with 3D data.
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Affiliation(s)
- Shyam Prajapati
- Mount Sinai Health System, Department of Diagnostic Pathology and Laboratory Medicine, New York, NY, USA
| | - Emilio Madrigal
- Mount Sinai Health System, Department of Diagnostic Pathology and Laboratory Medicine, New York, NY, USA
| | - Mark T Friedman
- Mount Sinai Health System, Department of Diagnostic Pathology and Laboratory Medicine, New York, NY, USA
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