State-of-the-Art of Profiling Immune Contexture in the Era of Multiplexed Staining and Digital Analysis to Study Paraffin Tumor Tissues
Abstract
:1. Introduction
2. Non-Fluorescence-Based Platforms
2.1. Multiplexed Immunohistochemical Consecutive Staining on Single Slide
2.2. Sequential Immunoperoxidase Labeling and Erasing
3. Fluorescence-Based Platforms
3.1. Bleaching Techniques without Signal Amplification System
3.2. Multi-Epitope-Ligand Cartography
3.3. MultiOmyxTM Staining or Hyperplexed Immunofluorescence Assay
4. Tissue-Based Cyclic Immunofluorescence (t-CyCIF) Method
Co-Detection by Indexing or Fluorescent Immunohisto-PCR
5. Amplification of the Epitope Detection
5.1. Multiplex Modified Hapten-Based Technology
5.2. Tyramide Signal Amplification and Fluorescent Multiplex Immunohistochemistry
5.3. Nanocrystal Quantum Dots
6. Fundamentals of Multiplexed Techniques Based on Mass Spectrometry
6.1. Imaging Mass Spectrometry
6.2. Secondary Ion Mass Spectrometry
6.3. Laser Desorption/Ionization
6.4. Matrix-Assisted Laser Desorption/Ionization
6.5. Multiplexed Ion Beam Imaging and Imaging Mass Cytometry: The Antibody-Based Tag-Mass IMS Strategy
6.6. Multiplexed Ion Beam Imaging
6.7. Imaging Mass Cytometry
7. Image Acquisition and Data Analysis
8. Clinical and Translational Use of Multiplexed Methodologies
9. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Multiplex Staining Method | Advantage | Disadvantage |
---|---|---|
Non-fluorescence based platform | ||
Multiplexed immunohistochemical consecutive staining on a single slide |
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Sequential immunoperoxidase labeling and erasing |
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Fluorescence based platform | ||
Bleaching techniques without signal amplification system | ||
Multi-epitope-ligand cartography |
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MultiOmyxTM staining or hyperplexed Immunofluorescence Assay |
|
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Tissue-based cyclic immunofluorescence method |
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Co-detection by indexing or fluorescent immunohisto-PCR |
|
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DNA exchange imaging |
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|
Amplification of the epitope detection | ||
Hapten-based modified multiplex |
|
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Tyramide signal amplification |
|
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Nanocrystal quantum dots |
|
|
Mass Spectrometry Imaging | ||
Secondary Ion Mass Spectrometry |
|
|
Laser Desorption/Ionization |
|
|
Matrix-assisted laser desorption/ionization |
|
|
Multiplexed ion beam imaging |
|
|
Imaging Mass Cytometry |
|
|
Vendor | Software Package | Capabilities | Data Visualization | Availability | Reference |
---|---|---|---|---|---|
Akoya/PerkinElmer | InForm | Color-Based Co-localization, Tissue Segmentation, Cell/Object Segmentation, Cell Phenotyping, Scoring and Automated Quantitation using Batch Analysis | Density Raw Data | Licensed | [6,96] |
Neo Genomics | MultiOmyx Quantification Program | Epithelial tissue reconstruction, Cellular and Subcellular Segmentation, Cell Phenotyping, Quantification Algorithms | Density Raw Data | Licensed | [3,20] |
Leica Biosystems | Aperio eSlide Manager Analysis | Pixel-Based Analysis, Cellular identification, Area Quantification and Positive Pixel Count IF Algorithm | Density Raw Data | Licensed | [82] |
Definiens | Tissue Studio/Image Developer | Imaging Segmentation, Marker Intensity Measurement, Cell Quantification, Batch Analysis, Statistical Analysis, and Algorithm Creator. | Histograms and Profile Plots | Licensed | [83] |
HistoRx | AQUAnalysis | Signal Intensity Quantification Per Unit Area and Per Layer | Density Raw Data | Licensed | [84] |
SlidePath | SlidePath’s Tissue Image Analysis | Membrane, Nuclear and Positive Pixel Quantification | Density Raw Data | Licensed | [85] |
Indica Labs | HALO | Membrane, Co-localization, Immune Cell Proximity, Spatial Analysis, Batch Analysis | Spatial Plot, Histogram | Licensed | [86] |
VISIOPHARM | Visimoph Tissuemorph | Signal Intensity, Area, Counting Objects, Spatial Analysis, Clustering Statistical Analysis, Batch Analysis and Algorithm Creator. | Phenotypic Matrix, t-SNE Plots | Licensed | [87] |
Media Cybernetics | Image-Pro | Color-Based, Nuclear segmentation, Cell quantification, Macro-enabled Advanced Image Processing Solution | Density Raw Data | Licensed | [97] |
CompuCyte | iCyte/iBroser/iNovator | Nucleus Segmentation or Phantom Contouring, Measures Associated Signals | Density Raw Data | Licensed | [98] |
TissueGnostics | HistoQuest/TissueQuest/StrataQuest | Nuclei-Based Segmentation of Tissues, Cell Phenotyping | Density Raw Data | Licensed | [99] |
NIH | Image J | Color-Based, User Interactive Segmentation | Histograms and Profile Plots | Open | [88] |
https://qupath.github.io | QuPath | View Measurements in Context by Color Coding Objects According to Their Features, Flexible Object Classification, Trainable Cell Classification and Quantification | Density Raw Data | Open | [89] |
http://icy.bioimageanalysis.org | Icy | Based and Color Object Identification, Size, Shape, Color Intensity, Texture, Spatial Analysis. | Plots, Histogram | Open | [90] |
https://cellprofiler.org/ | Cell Profiler/Cell Analyst | Based and Color Object Identification, Size, Shape, Color Intensity, Texture, and Number Neighbor Quantification. | Density Plot, Histogram | Open | [91,92,93] |
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Share and Cite
Parra, E.R.; Francisco-Cruz, A.; Wistuba, I.I. State-of-the-Art of Profiling Immune Contexture in the Era of Multiplexed Staining and Digital Analysis to Study Paraffin Tumor Tissues. Cancers 2019, 11, 247. https://doi.org/10.3390/cancers11020247
Parra ER, Francisco-Cruz A, Wistuba II. State-of-the-Art of Profiling Immune Contexture in the Era of Multiplexed Staining and Digital Analysis to Study Paraffin Tumor Tissues. Cancers. 2019; 11(2):247. https://doi.org/10.3390/cancers11020247
Chicago/Turabian StyleParra, Edwin Roger, Alejandro Francisco-Cruz, and Ignacio Ivan Wistuba. 2019. "State-of-the-Art of Profiling Immune Contexture in the Era of Multiplexed Staining and Digital Analysis to Study Paraffin Tumor Tissues" Cancers 11, no. 2: 247. https://doi.org/10.3390/cancers11020247