Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context

LipostarMSI: Comprehensive, Vendor-Neutral Software for Visualization, Data Analysis, and Automated Molecular Identification in Mass Spectrometry Imaging

(2020) Sara Tortorella et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Establishment and Maintenance of the Macrophage Niche

(2020) Martin Guilliams et al.   IMMUNITY

The Society for Immunotherapy in Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation

(2020) Janis M Taube et al.   Journal for ImmunoTherapy of Cancer

Morphometric cell classification for single‐cell MALDI‐MSI

(2020) Klára Ščupáková et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Meta-Analysis of Leukocyte Diversity in Atherosclerotic Mouse Aortas

(2020) Alma Zernecke et al.   CIRCULATION RESEARCH

Atheroma-Specific Lipids in ldlr–/– and apoe–/– Mice Using 2D and 3D Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

(2020) Jianhua Cao et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Limited proliferation capacity of aortic intima resident macrophages requires monocyte recruitment for atherosclerotic plaque progression

(2020) Jesse W. Williams et al.   NATURE IMMUNOLOGY

IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues

(2020) Andrea J. Radtke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Heterogeneity and plasticity in healthy and atherosclerotic vasculature explored by single cell sequencing

(2019) K Van Kuijk et al.   CARDIOVASCULAR RESEARCH

Data Processing Pipeline for Lipid Profiling of Carotid Atherosclerotic Plaque with Mass Spectrometry Imaging

(2019) Mirjam Visscher et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A Secreted Phospholipase A2 Induces Formation of Smooth Muscle Foam Cells Which Transdifferentiate to Macrophage-Like State

(2019) Karina Cristina Giannotti et al.   MOLECULES

Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity

(2019) Mashito Sakai et al.   IMMUNITY

Immune cell census in murine atherosclerosis: cytometry by time of flight illuminates vascular myeloid cell diversity

(2018) Jennifer E Cole et al.   CARDIOVASCULAR RESEARCH

A Milieu Molecule for TGF-β Required for Microglia Function in the Nervous System

(2018) Yan Qin et al.   CELL

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine AtherosclerosisNovelty and Significance

(2018) Clément Cochain et al.   CIRCULATION RESEARCH

Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass CytometryNovelty and Significance

(2018) Holger Winkels et al.   CIRCULATION RESEARCH

Automated, parallel mass spectrometry imaging and structural identification of lipids

(2018) Shane R. Ellis et al.   NATURE METHODS

Correlated metabolomic, genomic, and histologic phenotypes in histologically normal breast tissue

(2018) Xuezheng Sun et al.   PLoS One

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

(2018) Jia-Ren Lin et al.   eLife

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models

(2018) Kyeongdae Kim et al.   CIRCULATION RESEARCH

Hyaluronan Receptor LYVE-1-Expressing Macrophages Maintain Arterial Tone through Hyaluronan-Mediated Regulation of Smooth Muscle Cell Collagen

(2018) Hwee Ying Lim et al.   IMMUNITY

Improved Multiplex Immunohistochemistry for Immune Microenvironment Evaluation of Mouse Formalin-Fixed, Paraffin-Embedded Tissues

(2018) Noah Sorrelle et al.   JOURNAL OF IMMUNOLOGY

Super-multiplex vibrational imaging

(2017) Lu Wei et al.   NATURE

Proposal for a common nomenclature for fragment ions in mass spectra of lipids

(2017) Josch K. Pauling et al.   PLoS One

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Automated mapping of phenotype space with single-cell data

(2016) Nikolay Samusik et al.   NATURE METHODS

Self-renewing resident arterial macrophages arise from embryonic CX3CR1+ precursors and circulating monocytes immediately after birth

(2015) Sherine Ensan et al.   NATURE IMMUNOLOGY

KLF4-dependent phenotypic modulation of smooth muscle cells has a key role in atherosclerotic plaque pathogenesis

(2015) Laura S Shankman et al.   NATURE MEDICINE

Tissue-Specific Signals Control Reversible Program of Localization and Functional Polarization of Macrophages

(2014) Yasutaka Okabe et al.   CELL

Transdifferentiation of Vascular Smooth Muscle Cells to Macrophage-Like Cells During Atherogenesis

(2014) Susanne Feil et al.   CIRCULATION RESEARCH

Macrophage Activation and Polarization: Nomenclature and Experimental Guidelines

(2014) Peter J. Murray et al.   IMMUNITY

Embryonic and Adult-Derived Resident Cardiac Macrophages Are Maintained through Distinct Mechanisms at Steady State and during Inflammation

(2014) Slava Epelman et al.   IMMUNITY

Macrophage phenotypes in atherosclerosis

(2014) Sophie Colin et al.   IMMUNOLOGICAL REVIEWS

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

Alveolar macrophages develop from fetal monocytes that differentiate into long-lived cells in the first week of life via GM-CSF

(2013) Martin Guilliams et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Lysophosphatidic acid triggers mast cell-driven atherosclerotic plaque destabilization by increasing vascular inflammation

(2013) Martine Bot et al.   JOURNAL OF LIPID RESEARCH

A multispectral LED array for the reduction of background autofluorescence in brain tissue

(2013) Haison Duong et al.   JOURNAL OF NEUROSCIENCE METHODS

Tissue-resident macrophages

(2013) Luke C Davies et al.   NATURE IMMUNOLOGY

Local proliferation dominates lesional macrophage accumulation in atherosclerosis

(2013) Clinton S Robbins et al.   NATURE MEDICINE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Myeloid Type I Interferon Signaling Promotes Atherosclerosis by Stimulating Macrophage Recruitment to Lesions

(2010) Pieter Goossens et al.   Cell Metabolism

Combined Inhibition of CCL2, CX3CR1, and CCR5 Abrogates Ly6C hi and Ly6C lo Monocytosis and Almost Abolishes Atherosclerosis in Hypercholesterolemic Mice

(2008) Christophe Combadière et al.   CIRCULATION

A simple and fast algorithm for K-medoids clustering

(2008) Hae-Sang Park et al.   EXPERT SYSTEMS WITH APPLICATIONS