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A Simple Open-source Method For Highly Multiplexed Imaging Of Single Cells In Tissues And Tumours
Jia-Ren Lin, Benjamin Izar, Shaolin Mei, S. Wang, Parin Shah, P. Sorger
Published 2017 · Biology
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Intratumoural heterogeneity strongly influences the development and progression of cancer as well as responsiveness and resistance to therapy. To improve our ability to measure and analyze such heterogeneity we have developed an open source method for fluorescence imaging of up to 60 protein antigens at subcellular resolution using formalin-fixed, paraffin-embedded (FFPE) tissue samples mounted on glass slides, the most widely used specimens for the diagnosis of cancer and other diseases. As described here, tissue-based cyclic immunofluorescence (t-CyCIF) creates high-dimensional imaging data through successive acquisition of four-color images and requires no specialized instruments or reagents. We apply t-CyCIF to 14 cancer and healthy tissue types and quantify the extent of cell to cell variability in signal transduction cascades, tumor antigens and stromal markers. By imaging immune cell lineage markers we enumerate classes of tumour-infiltrating lymphocytes (TILs) and their spatial relationships to the tumor microenvironment (TME). The simplicity and adaptability of t-CyCIF makes it a powerful method for pre-clinical and clinical research and a natural complement to single-cell genomics.
This paper references
What brown cannot do for you
D. Rimm (2006)
Hallmarks of Cancer: The Next Generation
D. Hanahan (2011)
Using the molecular classification of glioblastoma to inform personalized treatment
Adriana Olar (2014)
Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
S. Jones (2008)
Highly Multiplexed Subcellular RNA Sequencing in Situ
J. H. Lee (2014)
Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications.
B. Bodenmiller (2016)
Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue
M. Gerdes (2013)
Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits
K. Micheva (2007)
Prognostic and predictive markers for the new immunotherapies.
K. Mahoney (2014)
Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method
Jia-Ren Lin (2015)
Fast live simultaneous multiwavelength four-dimensional optical microscopy
P. Carlton (2010)
F. Chen (2015)
What's wrong with correlative experiments?
M. Vilela (2011)
Genetic heterogeneity and cancer drug resistance.
N. Turner (2012)
A BaSiC tool for background and shading correction of optical microscopy images
T. Peng (2017)
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
A. Carpenter (2006)
Determination of three-dimensional imaging properties of a light microscope system. Partial confocal behavior in epifluorescence microscopy.
Y. Hiraoka (1990)
Cancer of unknown primary site.
G. Varadhachary (2014)
RSPO2 Enhances Canonical Wnt Signaling to Confer Stemness-Associated Traits to Susceptible Pancreatic Cancer Cells.
Matthias Ilmer (2015)
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
Anoop P. Patel (2014)
Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis.
E. Stack (2014)
In-depth tissue profiling using multiplexed immunohistochemical consecutive staining on single slide
R. Remark (2016)
COMPARATIVE ANALYSIS OF DIRECT FLUORESCENCE, ZENON LABELING, AND QUANTUM DOT NANOCRYSTAL TECHNOLOGY IN IMMUNOFLUORESCENCE STAINING
X. Tang (2010)
Hyperlog—A flexible log‐like transform for negative, zero, and positive valued data
C. Bagwell (2005)
Cancer Genome Landscapes
B. Vogelstein (2013)
The future of immune checkpoint therapy
P. Sharma (2015)
Improved survival with vemurafenib in melanoma with BRAF V600E mutation.
P. Chapman (2011)
Histo-cytometry: a method for highly multiplex quantitative tissue imaging analysis applied to dendritic cell subset microanatomy in lymph nodes.
Michael Y Gerner (2012)
Deep profiling of mouse splenic architecture with CODEX multiplexed imaging
Y. Goltsev (2017)
KRAS Mutant Pancreatic Cancer: No Lone Path to an Effective Treatment
Daniel Zeitouni (2016)
Antigen Retrieval Immunohistochemistry
S. Shi (2011)
Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms
C. García-Alonso (2014)
PD-1 blockade induces responses by inhibiting adaptive immune resistance
P. Tumeh (2014)
Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis.
T. Tsujikawa (2017)
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Itay Tirosh (2016)
Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination.
M. G. Gustafsson (2008)
Cluster Size and Quinary Structure Determine the Rheological Effects of Antibody Self-Association at High Concentrations.
W. Wang (2018)
Bayesian Network Approach to Cell Signaling Pathway Modeling
K. Sachs (2002)
The Somatic Genomic Landscape of Glioblastoma
C. Brennan (2013)
Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
C. Giesen (2014)
Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis.
H. Phillips (2006)
Serum S100--a marker for disease monitoring in metastatic melanoma.
G. Henze (1997)
Immune Checkpoint Blockade in Cancer Therapy.
M. Postow (2015)
Antigen Retrieval in Immunohistochemistry
S.-R. Shi (2014)
Ras Stabilization Through Aberrant Activation of Wnt/β-Catenin Signaling Promotes Intestinal Tumorigenesis
Woo-Jeong Jeong (2012)
Tumor-stroma interactions in pancreatic ductal adenocarcinoma
D. Mahadevan (2007)
Abstract AP19: SINGLE–CELL RNA–SEQUENCING OF PATIENT–DERIVED OVARIAN CANCER CELLS AND PATIENT–DERIVED XENOGRAFT MODELS
Benjamin Izar (2017)
Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues.
Y. Wang (2017)
Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single‐cell Imaging
Jia-Ren Lin (2016)
Multiplexed ion beam imaging of human breast tumors
M. Angelo (2014)
Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues
J. H. Lee (2015)
Antibody-based protein multiplex platforms: technical and operational challenges.
Allison A. Ellington (2010)
viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia
El-ad David Amir (2013)
Lessons from the Cancer Genome
L. Garraway (2013)
Visualizing Data using t-SNE
L. V. D. Maaten (2008)
Preanalytical variables and phosphoepitope expression in FFPE tissue: quantitative epitope assessment after variable cold ischemic time
M. Vassilakopoulou (2015)
Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia.
B. Druker (2000)
This paper is referenced by
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis
Damien Arnol (2019)
Multi-omics profiling establishes the polypharmacology of FDA Approved CDK4/6 inhibitors and the potential for differential clinical activity
M. Hafner (2019)
Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis
Damien Arnol (2018)
Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity.
M. Hafner (2019)
Tumor Microenvironment Heterogeneity: Challenges and Opportunities
F. Runa (2017)
Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma
S. Coy (2018)
Mathematical and Computational Oncology: First International Symposium, ISMCO 2019, Lake Tahoe, NV, USA, October 14–16, 2019, Proceedings
George Bebis (2019)