Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies

Memory CD4+ T cells are generated in the human fetal intestine

(2019) Na Li et al.   NATURE IMMUNOLOGY

The reconstructed natural history of type 1 diabetes mellitus

(2019) Paolo Pozzilli et al.   Nature Reviews Endocrinology

Multiplexed (18-Plex) Measurement of Signaling Targets and Cytotoxic T Cells in Trastuzumab-Treated Patients using Imaging Mass Cytometry

(2019) Daniel E. Carvajal-Hausdorf et al.   CLINICAL CANCER RESEARCH

A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry

(2019) Nicolas Damond et al.   Cell Metabolism

Multiplexed In Situ Imaging Mass Cytometry Analysis of the Human Endocrine Pancreas and Immune System in Type 1 Diabetes

(2019) Yue J. Wang et al.   Cell Metabolism

Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses

(2019) Mélanie Durand et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Multiplexed imaging of immune cells in staged multiple sclerosis lesions by mass cytometry

(2019) Valeria Ramaglia et al.   eLife

Multidimensional profiling of drug‐treated cells by Imaging Mass Cytometry

(2019) Alexandre Bouzekri et al.   FEBS Open Bio

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

(2019) Damien Arnol et al.   Cell Reports

The compartmentalized inflammatory response in the multiple sclerosis brain is composed of tissue-resident CD8+ T lymphocytes and B cells

(2018) Joana Machado-Santos et al.   BRAIN

Human dendritic cell subsets: an update

(2018) Matthew Collin et al.   IMMUNOLOGY

Ruthenium counterstaining for imaging mass cytometry

(2018) Raúl Catena et al.   JOURNAL OF PATHOLOGY

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

CD4+ T Helper Cells Play a Key Role in Maintaining Diabetogenic CD8+ T Cell Function in the Pancreas

(2018) Gabriel Espinosa-Carrasco et al.   Frontiers in Immunology

Tissue-Dependent Tumor Microenvironments and Their Impact on Immunotherapy Responses

(2018) Amanda J. Oliver et al.   Frontiers in Immunology

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry

(2018) Stéphane Chevrier et al.   Cell Systems

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

(2018) Daniel Schulz et al.   Cell Systems

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Conventional and Neo-Antigenic Peptides Presented by β Cells Are Targeted by Circulating Naïve CD8+ T Cells in Type 1 Diabetic and Healthy Donors

(2018) Sergio Gonzalez-Duque et al.   Cell Metabolism

LAG3+ Regulatory T Cells Restrain Interleukin-23-Producing CX3CR1+ Gut-Resident Macrophages during Group 3 Innate Lymphoid Cell-Driven Colitis

(2018) David Bauché et al.   IMMUNITY

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

Spatiotemporal segregation of human marginal zone and memory B cell populations in lymphoid tissue

(2018) Yuan Zhao et al.   Nature Communications

Developmental and Functional Heterogeneity of Monocytes

(2018) Martin Guilliams et al.   IMMUNITY

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Dendritic Cells Display Subset and Tissue-Specific Maturation Dynamics over Human Life

(2017) Tomer Granot et al.   IMMUNITY

Dissecting human ILC heterogeneity: more than just three subsets

(2017) Yannick Simoni et al.   IMMUNOLOGY

Dermatologist-level classification of skin cancer with deep neural networks

(2017) Andre Esteva et al.   NATURE

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Opportunities and challenges in phenotypic drug discovery: an industry perspective

(2017) John G. Moffat et al.   NATURE REVIEWS DRUG DISCOVERY

Cisplatin is retained in the cochlea indefinitely following chemotherapy

(2017) Andrew M. Breglio et al.   Nature Communications

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

(2017) Takahiro Tsujikawa et al.   Cell Reports

Tissue specific microenvironments: a key tool for tissue engineering and regenerative medicine

(2017) Patrick C. Sachs et al.   Journal of Biological Engineering

Differential intratumoral distributions of CD8 and CD163 immune cells as prognostic biomarkers in breast cancer

(2017) Sotirios P. Fortis et al.   Journal for ImmunoTherapy of Cancer

An updated histological classification system for multiple sclerosis lesions

(2016) Tanja Kuhlmann et al.   ACTA NEUROPATHOLOGICA

Quantitative mass spectrometry imaging of small-molecule neurotransmitters in rat brain tissue sections using nanospray desorption electrospray ionization

(2016) Hilde-Marléne Bergman et al.   ANALYST

An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments

(2016) Janina Oetjen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

CXCL9 and CXCL10 predict survival and are regulated by cyclooxygenase inhibition in advanced serous ovarian cancer

(2016) Holger Bronger et al.   BRITISH JOURNAL OF CANCER

Computational methods for trajectory inference from single-cell transcriptomics

(2016) Robrecht Cannoodt et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

TNF-α expression, risk factors, and inflammatory exposures in ovarian cancer: evidence for an inflammatory pathway of ovarian carcinogenesis?

(2016) Mamta Gupta et al.   HUMAN PATHOLOGY

Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species

(2016) Martin Guilliams et al.   IMMUNITY

A High-Dimensional Atlas of Human T Cell Diversity Reveals Tissue-Specific Trafficking and Cytokine Signatures

(2016) Michael Thomas Wong et al.   IMMUNITY

Inflammatory triggers associated with exacerbations of COPD orchestrate plasticity of group 2 innate lymphoid cells in the lungs

(2016) Jonathan S Silver et al.   NATURE IMMUNOLOGY

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

(2016) David A. Van Valen et al.   PLoS Computational Biology

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

Association of AR-V7 on Circulating Tumor Cells as a Treatment-Specific Biomarker With Outcomes and Survival in Castration-Resistant Prostate Cancer

(2016) Howard I. Scher et al.   JAMA Oncology

Biodistribution of cisplatin revealed by imaging mass cytometry identifies extensive collagen binding in tumor and normal tissues

(2016) Qing Chang et al.   Scientific Reports

Netrin 1 regulates blood–brain barrier function and neuroinflammation

(2015) Cornelia Podjaski et al.   BRAIN

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Microscopy-Based High-Content Screening

(2015) Michael Boutros et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

The Next Immune-Checkpoint Inhibitors: PD-1/PD-L1 Blockade in Melanoma

(2015) Kathleen M. Mahoney et al.   CLINICAL THERAPEUTICS

Automatic single cell segmentation on highly multiplexed tissue images

(2015) Peter J. Schüffler et al.   CYTOMETRY PART A

Statistical analysis of molecule colocalization in bioimaging

(2015) Thibault Lagache et al.   CYTOMETRY PART A

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

Disease-modifying treatments for multiple sclerosis - a review of approved medications

(2015) Ø. Torkildsen et al.   EUROPEAN JOURNAL OF NEUROLOGY

Immunohistochemistry and mass spectrometry for highly multiplexed cellular molecular imaging

(2015) Richard M Levenson et al.   LABORATORY INVESTIGATION

Early-life compartmentalization of human T cell differentiation and regulatory function in mucosal and lymphoid tissues

(2015) Joseph J C Thome et al.   NATURE MEDICINE

Expression and distribution of neuropeptides in the nervous system of the crabCarcinus maenasand their roles in environmental stress

(2015) Yuzhuo Zhang et al.   PROTEOMICS

A versatile cost-effective method for the analysis of fresh frozen tissue sections via matrix-assisted laser desorption/ionisation imaging mass spectrometry

(2015) Matthew B. O'Rourke et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

Maraviroc: a review of its use in HIV infection and beyond

(2015) Georgette Kanmogne et al.   Drug Design Development and Therapy

A Paracrine Role for IL6 in Prostate Cancer Patients: Lack of Production by Primary or Metastatic Tumor Cells

(2015) S.-H. Yu et al.   Cancer Immunology Research

On tests of spatial pattern based on simulation envelopes

(2014) Adrian Baddeley et al.   ECOLOGICAL MONOGRAPHS

Autofluorescence spectroscopy and imaging: a tool for biomedical research and diagnosis

(2014) A.C. Croce et al.   EUROPEAN JOURNAL OF HISTOCHEMISTRY

Proteomics in translational cancer research: biomarker discovery for clinical applications

(2014) William CS Cho   Expert Review of Proteomics

In Situ Characterization of Proteins Using Laserspray Ionization on a High-Performance MALDI-LTQ-Orbitrap Mass Spectrometer

(2014) Bingming Chen et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

(2014) M. J. Wawer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of the tissue microenvironment as a therapeutic target in hepatocellular carcinoma

(2014) Bhavna Rani   WORLD JOURNAL OF GASTROENTEROLOGY

Plasticity of Human CD4 T Cell Subsets

(2014) Jens Geginat et al.   Frontiers in Immunology

The tumor microenvironment at a glance

(2013) F. R. Balkwill et al.   JOURNAL OF CELL SCIENCE

Type 1 diabetes

(2013) Mark A Atkinson et al.   LANCET

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantum dot imaging platform for single-cell molecular profiling

(2013) Pavel Zrazhevskiy et al.   Nature Communications

Tumoral Lymphocytic Infiltration and Expression of the Chemokine CXCL10 in Breast Cancers from the Ontario Familial Breast Cancer Registry

(2012) A. M. Mulligan et al.   CLINICAL CANCER RESEARCH

Network for Pancreatic Organ Donors with Diabetes (nPOD): developing a tissue biobank for type 1 diabetes

(2012) Martha Campbell-Thompson et al.   DIABETES-METABOLISM RESEARCH AND REVIEWS

Histo-Cytometry: A Method for Highly Multiplex Quantitative Tissue Imaging Analysis Applied to Dendritic Cell Subset Microanatomy in Lymph Nodes

(2012) Michael Y. Gerner et al.   IMMUNITY

Distribution and Compartmentalization of Human Circulating and Tissue-Resident Memory T Cell Subsets

(2012) Taheri Sathaliyawala et al.   IMMUNITY

Immature Renal Dendritic Cells Recruit Regulatory CXCR6+ Invariant Natural Killer T Cells to Attenuate Crescentic GN

(2012) J.-H. Riedel et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fluid biopsy in patients with metastatic prostate, pancreatic and breast cancers

(2012) Dena Marrinucci et al.   PHYSICAL BIOLOGY

A deep profiler's guide to cytometry

(2012) Sean C. Bendall et al.   TRENDS IN IMMUNOLOGY

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Origins of regulated cell-to-cell variability

(2011) Berend Snijder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The role of the tissue microenvironment in the regulation of cancer cell motility and invasion

(2010) Jan Brábek et al.   Cell Communication and Signaling

Quantitative, Architectural Analysis of Immune Cell Subsets in Tumor-Draining Lymph Nodes from Breast Cancer Patients and Healthy Lymph Nodes

(2010) A. Francesca Setiadi et al.   PLoS One

Development of Monocytes, Macrophages, and Dendritic Cells

(2010) F. Geissmann et al.   SCIENCE

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

Mass Spectrometry, Review of the Basics: Electrospray, MALDI, and Commonly Used Mass Analyzers

(2009) Anas El-Aneed et al.   APPLIED SPECTROSCOPY REVIEWS

The relation between inflammation and neurodegeneration in multiple sclerosis brains

(2009) Josa M. Frischer et al.   BRAIN

Molecular footprints of a germinal center derivation of human IgM+(IgD+)CD27+B cells and the dynamics of memory B cell generation

(2009) Marc Seifert et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry

(2008) Olga I. Ornatsky et al.   JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY

Renal Dendritic Cells Stimulate IL-10 Production and Attenuate Nephrotoxic Nephritis

(2008) J. Scholz et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

The application of inductively coupled plasma mass spectrometry in clinical pharmacological oncology research

(2008) Elke E.M. Brouwers et al.   MASS SPECTROMETRY REVIEWS