Current tools to interrogate microglial biology

Stem-cell-derived human microglia transplanted into mouse brain to study human disease

(2021) Nicola Fattorelli et al.   Nature Protocols

Microglia and Central Nervous System–Associated Macrophages—From Origin to Disease Modulation

(2021) Marco Prinz et al.   Annual Review of Immunology

Proteogenomic and metabolomic characterization of human glioblastoma

(2021) Liang-Bo Wang et al.   CANCER CELL

Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8+ T cells during the primary immune response

(2021) Lauren S. Levine et al.   IMMUNITY

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

(2021) Kristen R. Maynard et al.   NATURE NEUROSCIENCE

Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease

(2021) Sudha R. Guttikonda et al.   NATURE NEUROSCIENCE

White matter aging drives microglial diversity

(2021) Shima Safaiyan et al.   NEURON

Single-cell RNA sequencing reveals functional heterogeneity of glioma-associated brain macrophages

(2021) Natalia Ochocka et al.   Nature Communications

Single-cell RNA-seq analysis reveals compartment-specific heterogeneity and plasticity of microglia

(2021) Junying Zheng et al.   iScience

Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

(2021) Ana Rita Pombo Antunes et al.   NATURE NEUROSCIENCE

Barcoded viral tracing of single-cell interactions in central nervous system inflammation

(2021) Iain C. Clark et al.   SCIENCE

Efficient conversion of human induced pluripotent stem cells into microglia by defined transcription factors

(2021) Shih-Wei Chen et al.   Stem Cell Reports

Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions

(2021) Marius Schwabenland et al.   IMMUNITY

Unpicking the proteome in single cells

(2020) Nikolai Slavov   SCIENCE

Microglia Heterogeneity in the Single-Cell Era

(2020) Takahiro Masuda et al.   Cell Reports

Single-cell analysis targeting the proteome

(2020) Mahmoud Labib et al.   Nature Reviews Chemistry

Single-Cell Mapping of Human Brain Cancer Reveals Tumor-Specific Instruction of Tissue-Invading Leukocytes

(2020) Ekaterina Friebel et al.   CELL

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development

(2020) Sebastian G. Utz et al.   CELL

Deciphering human macrophage development at single-cell resolution

(2020) Zhilei Bian et al.   NATURE

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury

(2020) Elke Ydens et al.   NATURE NEUROSCIENCE

Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric mouse brain

(2020) Ranjie Xu et al.   Nature Communications

A CX3CR1 Reporter hESC Line Facilitates Integrative Analysis of In-Vitro-Derived Microglia and Improved Microglia Identity upon Neuron-Glia Co-culture

(2020) Alexandra Grubman et al.   Stem Cell Reports

Single-Cell Atlas Reveals Complexity of the Immunosuppressive Microenvironment of Initial and Recurrent Glioblastoma

(2020) Weilun Fu et al.   Frontiers in Immunology

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

(2020) Wei-Ting Chen et al.   CELL

Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

(2020) Yonatan Katzenelenbogen et al.   CELL

Microglia promote glioblastoma via mTOR‐mediated immunosuppression of the tumour microenvironment

(2020) Anaelle A Dumas et al.   EMBO JOURNAL

Novel Hexb-based tools for studying microglia in the CNS

(2020) Takahiro Masuda et al.   NATURE IMMUNOLOGY

To Kill a Microglia: A Case for CSF1R Inhibitors

(2020) Kim N. Green et al.   TRENDS IN IMMUNOLOGY

Immune phenotyping of diverse syngeneic murine brain tumors identifies immunologically distinct types

(2020) Jasneet Kaur Khalsa et al.   Nature Communications

A new genetic strategy for targeting microglia in development and disease

(2020) Gabriel L McKinsey et al.   eLife

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

The use and limitations of single‐cell mass cytometry for studying human microglia function

(2020) Camila Fernández‐Zapata et al.   BRAIN PATHOLOGY

Single-cell metabolic profiling of human cytotoxic T cells

(2020) Felix J. Hartmann et al.   NATURE BIOTECHNOLOGY

Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

(2020) Nicola Thrupp et al.   Cell Reports

Single-cell mass cytometry reveals complex myeloid cell composition in active lesions of progressive multiple sclerosis

(2020) Chotima Böttcher et al.   Acta Neuropathologica Communications

CNS macrophages differentially rely on an intronic Csf1r enhancer for their development

(2020) David A. D. Munro et al.   DEVELOPMENT

A Binary Cre Transgenic Approach Dissects Microglia and CNS Border-Associated Macrophages

(2020) Jung-Seok Kim et al.   IMMUNITY

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

Generation of pure monocultures of human microglia-like cells from induced pluripotent stem cells

(2020) Poulomi Banerjee et al.   Stem Cell Research

Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease

(2020) Marta Olah et al.   Nature Communications

Multi-modal Single-Cell Analysis Reveals Brain Immune Landscape Plasticity during Aging and Gut Microbiota Dysbiosis

(2020) Samantha M. Golomb et al.   Cell Reports

Incorporating Tumor-Associated Macrophages into Engineered Models of Glioma

(2020) Erin A. Akins et al.   iScience

Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

(2020) Ana J. Chucair-Elliott et al.   Communications Biology

Cell-type-specific metabolic labeling, detection and identification of nascent proteomes in vivo

(2019) Beatriz Alvarez-Castelao et al.   Nature Protocols

Concise Review: Modeling Neurodegenerative Diseases with Human Pluripotent Stem Cell-Derived Microglia

(2019) Walther Haenseler et al.   STEM CELLS

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation

(2019) Marta Joana Costa Jordão et al.   SCIENCE

Cerebral organoids at the air–liquid interface generate diverse nerve tracts with functional output

(2019) Stefano L. Giandomenico et al.   NATURE NEUROSCIENCE

Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution

(2019) Takahiro Masuda et al.   NATURE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

(2019) Hannah Van Hove et al.   NATURE NEUROSCIENCE

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

Neuronal vulnerability and multilineage diversity in multiple sclerosis

(2019) Lucas Schirmer et al.   NATURE

Macrophages at CNS interfaces: ontogeny and function in health and disease

(2019) Katrin Kierdorf et al.   NATURE REVIEWS NEUROSCIENCE

Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo

(2019) Jonathan Hasselmann et al.   NEURON

Targeting microglia in brain disorders

(2019) Josef Priller et al.   SCIENCE

Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations

(2019) Rocío Rojo et al.   Nature Communications

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

(2019) Valeria Ramaglia et al.   eLife

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain

(2019) Jorge L. Del-Aguila et al.   Alzheimers Research & Therapy

The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions

(2019) Calvin Park et al.   Acta Neuropathologica Communications

Microglia Biology: One Century of Evolving Concepts

(2019) Marco Prinz et al.   CELL

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Engineering of human brain organoids with a functional vascular-like system

(2019) Bilal Cakir et al.   NATURE METHODS

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

(2019) Alexandra Grubman et al.   NATURE NEUROSCIENCE

Mapping microglia states in the human brain through the integration of high-dimensional techniques

(2019) Roman Sankowski et al.   NATURE NEUROSCIENCE

PSEN1ΔE9, APPswe, and APOE4 Confer Disparate Phenotypes in Human iPSC-Derived Microglia

(2019) Henna Konttinen et al.   Stem Cell Reports

Blood vessel formation in cerebral organoids formed from human embryonic stem cells

(2019) Onju Ham et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A novel Tmem119-tdTomato reporter mouse model for studying microglia in the central nervous system

(2019) Chunsheng Ruan et al.   BRAIN BEHAVIOR AND IMMUNITY

Comparative analysis of CreER transgenic mice for the study of brain macrophages: A case study

(2019) Louise Chappell‐Maor et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Identifying the variables that drive tamoxifen‐independent CreERT2 recombination: Implications for microglial fate mapping and gene deletions

(2019) Hannah Van Hove et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Transcriptional profiling of microglia; current state of the art and future perspectives

(2019) Emma Gerrits et al.   GLIA

Heterozygous CX3CR1 Deficiency in Microglia Restores Neuronal β-Amyloid Clearance Pathways and Slows Progression of Alzheimer's Like-Disease in PS1-APP Mice

(2019) Suzanne E. Hickman et al.   Frontiers in Immunology

Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration

(2018) Aleksandra Deczkowska et al.   CELL

High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease

(2018) Dunja Mrdjen et al.   IMMUNITY

Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia

(2018) James C. Cronk et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

An in vivo model of functional and vascularized human brain organoids

(2018) Abed AlFatah Mansour et al.   NATURE BIOTECHNOLOGY

Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies

(2018) Zhana Haimon et al.   NATURE IMMUNOLOGY

Repopulated microglia are solely derived from the proliferation of residual microglia after acute depletion

(2018) Yubin Huang et al.   NATURE NEUROSCIENCE

Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models

(2018) Bahareh Ajami et al.   NATURE NEUROSCIENCE

Modelling microglial function with induced pluripotent stem cells: an update

(2018) Jennifer M. Pocock et al.   NATURE REVIEWS NEUROSCIENCE

A Combination of Ontogeny and CNS Environment Establishes Microglial Identity

(2018) F. Chris Bennett et al.   NEURON

Generation of human vascularized brain organoids

(2018) Missy T. Pham et al.   NEUROREPORT

Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer’s Disease Not Evident in Mouse Models

(2018) Brad A. Friedman et al.   Cell Reports

Functional Studies of Missense TREM2 Mutations in Human Stem Cell-Derived Microglia

(2018) Philip W. Brownjohn et al.   Stem Cell Reports

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

(2018) Leeat Keren et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

An Overview of in vitro Methods to Study Microglia

(2018) Raissa Timmerman et al.   Frontiers in Cellular Neuroscience

Human Induced Pluripotent Stem Cell-Derived Microglia-Like Cells Harboring TREM2 Missense Mutations Show Specific Deficits in Phagocytosis

(2018) Pablo Garcia-Reitboeck et al.   Cell Reports

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

Development and validation of a simplified method to generate human microglia from pluripotent stem cells

(2018) Amanda McQuade et al.   Molecular Neurodegeneration

Human microglia regional heterogeneity and phenotypes determined by multiplexed single-cell mass cytometry

(2018) Chotima Böttcher et al.   NATURE NEUROSCIENCE

Microglia metabolism in health and disease

(2018) Katharina Borst et al.   NEUROCHEMISTRY INTERNATIONAL

Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing

(2018) Qingyun Li et al.   NEURON

Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge

(2018) Anat Shemer et al.   Nature Communications

Microglia innately develop within cerebral organoids

(2018) Paul R. Ormel et al.   Nature Communications

Myeloid Cells in the Central Nervous System

(2017) Jasmin Herz et al.   IMMUNITY

Induced-Pluripotent-Stem-Cell-Derived Primitive Macrophages Provide a Platform for Modeling Tissue-Resident Macrophage Differentiation and Function

(2017) Kazuyuki Takata et al.   IMMUNITY

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases

(2017) Susanne Krasemann et al.   IMMUNITY

Transcriptional control of microglia phenotypes in health and disease

(2017) Inge R. Holtman et al.   JOURNAL OF CLINICAL INVESTIGATION

Cell-specific deletion of C1qa identifies microglia as the dominant source of C1q in mouse brain

(2017) Maria I. Fonseca et al.   Journal of Neuroinflammation

Guided self-organization and cortical plate formation in human brain organoids

(2017) Madeline A Lancaster et al.   NATURE BIOTECHNOLOGY

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Differentiation of human and murine induced pluripotent stem cells to microglia-like cells

(2017) Hetal Pandya et al.   NATURE NEUROSCIENCE

A new fate mapping system reveals context-dependent random or clonal expansion of microglia

(2017) Tuan Leng Tay et al.   NATURE NEUROSCIENCE

iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases

(2017) Edsel M. Abud et al.   NEURON

Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo

(2017) Hyun Cheol Roh et al.   Cell Reports

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

Coupled Proliferation and Apoptosis Maintain the Rapid Turnover of Microglia in the Adult Brain

(2017) Katharine Askew et al.   Cell Reports

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

(2017) Hansruedi Mathys et al.   Cell Reports

Directed Differentiation of Human Pluripotent Stem Cells to Microglia

(2017) Panagiotis Douvaras et al.   Stem Cell Reports

A Highly Efficient Human Pluripotent Stem Cell Microglia Model Displays a Neuronal-Co-culture-Specific Expression Profile and Inflammatory Response

(2017) Walther Haenseler et al.   Stem Cell Reports

Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector

(2017) Ziqing Liu et al.   Scientific Reports

Transcriptome‐based profiling of yolk sac‐derived macrophages reveals a role for Irf8 in macrophage maturation

(2016) Nora Hagemeyer et al.   EMBO JOURNAL

Microglial Physiology and Pathophysiology: Insights from Genome-wide Transcriptional Profiling

(2016) Andrea Crotti et al.   IMMUNITY

Sall1 is a transcriptional regulator defining microglia identity and function

(2016) Anne Buttgereit et al.   NATURE IMMUNOLOGY

Origin, fate and dynamics of macrophages at central nervous system interfaces

(2016) Tobias Goldmann et al.   NATURE IMMUNOLOGY

Efficient derivation of microglia-like cells from human pluripotent stem cells

(2016) Julien Muffat et al.   NATURE MEDICINE

New tools for studying microglia in the mouse and human CNS

(2016) Mariko L. Bennett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Microglia development follows a stepwise program to regulate brain homeostasis

(2016) O. Matcovitch-Natan et al.   SCIENCE

Genetic Cell Ablation Reveals Clusters of Local Self-Renewing Microglia in the Mammalian Central Nervous System

(2015) Julia Bruttger et al.   IMMUNITY

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Homeostasis and Effector Function of Lymphopenia-Induced "Memory-Like" T Cells in Constitutively T Cell-Depleted Mice

(2014) D. Voehringer et al.   JOURNAL OF IMMUNOLOGY

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

Tissue-resident macrophages originate from yolk-sac-derived erythro-myeloid progenitors

(2014) Elisa Gomez Perdiguero et al.   NATURE

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

(2014) Charlotte Giesen et al.   NATURE METHODS

Tissue-Resident Macrophages Self-Maintain Locally throughout Adult Life with Minimal Contribution from Circulating Monocytes

(2013) Daigo Hashimoto et al.   IMMUNITY

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Inducible control of gene expression with destabilized Cre

(2013) Richard Sando et al.   NATURE METHODS

A new type of microglia gene targeting shows TAK1 to be pivotal in CNS autoimmune inflammation

(2013) Tobias Goldmann et al.   NATURE NEUROSCIENCE

Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways

(2013) Katrin Kierdorf et al.   NATURE NEUROSCIENCE

Identification of a unique TGF-β–dependent molecular and functional signature in microglia

(2013) Oleg Butovsky et al.   NATURE NEUROSCIENCE

Interaction of Tmem119 and the bone morphogenetic protein pathway in the commitment of myoblastic into osteoblastic cells

(2012) Ken-ichiro Tanaka et al.   BONE

Fate Mapping Reveals Origins and Dynamics of Monocytes and Tissue Macrophages under Homeostasis

(2012) Simon Yona et al.   IMMUNITY

IL-34 is a tissue-restricted ligand of CSF1R required for the development of Langerhans cells and microglia

(2012) Yaming Wang et al.   NATURE IMMUNOLOGY

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

(2012) Emmanuel L Gautier et al.   NATURE IMMUNOLOGY

A Lineage of Myeloid Cells Independent of Myb and Hematopoietic Stem Cells

(2012) C. Schulz et al.   SCIENCE

Distinct and Non-Redundant Roles of Microglia and Myeloid Subsets in Mouse Models of Alzheimer's Disease

(2011) A. Mildner et al.   JOURNAL OF NEUROSCIENCE

CX3CR1 Deficiency Leads to Impairment of Hippocampal Cognitive Function and Synaptic Plasticity

(2011) J. T. Rogers et al.   JOURNAL OF NEUROSCIENCE

Infiltrating monocytes trigger EAE progression, but do not contribute to the resident microglia pool

(2011) Bahareh Ajami et al.   NATURE NEUROSCIENCE

CX3CR1 Deficiency Alters Microglial Activation and Reduces Beta-Amyloid Deposition in Two Alzheimer's Disease Mouse Models

(2010) Sungho Lee et al.   AMERICAN JOURNAL OF PATHOLOGY

Fate Mapping Analysis Reveals That Adult Microglia Derive from Primitive Macrophages

(2010) F. Ginhoux et al.   SCIENCE

Split-Cre Complementation Indicates Coincident Activity of Different Genes In Vivo

(2009) Johannes Hirrlinger et al.   PLoS One

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA