Resources
Tools and links for microglial research
Journal resources
An Overview of in vitro Methods to Study Microglia
Timmerman, R., Burm, S.M. and Bajramovic, J.J., 2018. An overview of in vitro methods to study microglia. Frontiers in cellular neuroscience, 12, p.242.
Abstract
Neuroinflammation is a common feature in neurodegenerative diseases and strategies to modulate neuroinflammatory processes are increasingly considered as therapeutic options. In such strategies, glia cells rather than neurons represent the cellular targets. Microglia, the resident macrophages of the central nervous system, are principal players in neuroinflammation and detailed cellular biological knowledge of this particular cell type is therefore of pivotal importance. The last decade has shed new light on the origin, characteristics and functions of microglia, underlining the need for specific in vitro methodology to study these cells in detail. In this review we provide a comprehensive overview of existing methodology such as cell lines, stem cell-derived microglia and primary dissociated cell cultures, as well as discuss recent developments. As there is no in vitro method available yet that recapitulates all hallmarks of adult homeostatic microglia, we also discuss the advantages and limitations of existing models across different species.
Advanced in vitro models: Microglia in action
Cakir, B., Kiral, F.R. and Park, I.H., 2022. Advanced in vitro models: Microglia in action. Neuron, 110(21), pp.3444-3457.
Abstract
In the central nervous system (CNS), microglia carry out multiple tasks related to brain development, maintenance of brain homeostasis, and function of the CNS. Recent advanced in vitro model systems allow us to perform more detailed and specific analyses of microglial functions in the CNS. The development of human pluripotent stem cells (hPSCs)-based 2D and 3D cell culture methods, particularly advancements in brain organoid models, offers a better platform to dissect microglial function in various contexts. Despite the improvement of these methods, there are still definite restrictions. Understanding their drawbacks and benefits ensures their proper use. In this primer, we review current developments regarding in vitro microglial production and characterization and their use to address fundamental questions about microglial function in healthy and diseased states, and we discuss potential future improvements with a particular emphasis on brain organoid models.
Novel Hexb-based tools for studying microglia in the CNS
Masuda, T., Amann, L., Sankowski, R., Staszewski, O., Lenz, M., Snaidero, N., Costa Jordão, M.J., Böttcher, C., Kierdorf, K., Jung, S. and Priller, J., 2020. Novel Hexb-based tools for studying microglia in the CNS. Nature immunology, 21(7), pp.802-815.
Abstract
Microglia and central nervous system (CNS)-associated macrophages (CAMs), such as perivascular and meningeal macrophages, are implicated in virtually all diseases of the CNS. However, little is known about their cell-type-specific roles in the absence of suitable tools that would allow for functional discrimination between the ontogenetically closely related microglia and CAMs. To develop a new microglia gene targeting model, we first applied massively parallel single-cell analyses to compare microglia and CAM signatures during homeostasis and disease and identified hexosaminidase subunit beta (Hexb) as a stably expressed microglia core gene, whereas other microglia core genes were substantially downregulated during pathologies. Next, we generated HexbtdTomato mice to stably monitor microglia behavior in vivo. Finally, the Hexb locus was employed for tamoxifen-inducible Cre-mediated gene manipulation in microglia and for fate mapping of microglia but not CAMs. In sum, we provide valuable new genetic tools to specifically study microglia functions in the CNS.
Directed evolution of adeno-associated virus for efficient gene delivery to microglia
Lin, R., Zhou, Y., Yan, T., Wang, R., Li, H., Wu, Z., Zhang, X., Zhou, X., Zhao, F., Zhang, L. and Li, Y., 2022. Directed evolution of adeno-associated virus for efficient gene delivery to microglia. Nature Methods, 19(8), pp.976-985.
Abstract
As the resident immune cells in the central nervous system (CNS), microglia orchestrate immune responses and dynamically sculpt neural circuits in the CNS. Microglial dysfunction and mutations of microglia-specific genes have been implicated in many diseases of the CNS. Developing effective and safe vehicles for transgene delivery into microglia will facilitate the studies of microglia biology and microglia-associated disease mechanisms. Here, we report the discovery of adeno-associated virus (AAV) variants that mediate efficient in vitro and in vivo microglial transduction via directed evolution of the AAV capsid protein. These AAV-cMG and AAV-MG variants are capable of delivering various genetic payloads into microglia with high efficiency, and enable sufficient transgene expression to support fluorescent labeling, Ca2+ and neurotransmitter imaging and genome editing in microglia in vivo. Furthermore, single-cell RNA sequencing shows that the AAV-MG variants mediate in vivo transgene delivery without inducing microglia immune activation. These AAV variants should facilitate the use of various genetically encoded sensors and effectors in the study of microglia-related biology.
New tools for studying microglia in the mouse and human CNS
Bennett, M.L., Bennett, F.C., Liddelow, S.A., Ajami, B., Zamanian, J.L., Fernhoff, N.B., Mulinyawe, S.B., Bohlen, C.J., Adil, A., Tucker, A. and Weissman, I.L., 2016. New tools for studying microglia in the mouse and human CNS. Proceedings of the National Academy of Sciences, 113(12), pp.E1738-E1746.
Abstract
The specific function of microglia, the tissue resident macrophages of the brain and spinal cord, has been difficult to ascertain because of a lack of tools to distinguish microglia from other immune cells, thereby limiting specific immunostaining, purification, and manipulation. Because of their unique developmental origins and predicted functions, the distinction of microglia from other myeloid cells is critically important for understanding brain development and disease; better tools would greatly facilitate studies of microglia function in the developing, adult, and injured CNS. Here, we identify transmembrane protein 119 (Tmem119), a cell-surface protein of unknown function, as a highly expressed microglia-specific marker in both mouse and human. We developed monoclonal antibodies to its intracellular and extracellular domains that enable the immunostaining of microglia in histological sections in healthy and diseased brains, as well as isolation of pure nonactivated microglia by FACS. Using our antibodies, we provide, to our knowledge, the first RNAseq profiles of highly pure mouse microglia during development and after an immune challenge. We used these to demonstrate that mouse microglia mature by the second postnatal week and to predict novel microglial functions. Together, we anticipate these resources will be valuable for the future study and understanding of microglia in health and disease.
Overview of General and Discriminating Markers of Differential Microglia Phenotypes
Jurga, A.M., Paleczna, M. and Kuter, K.Z., 2020. Overview of general and discriminating markers of differential microglia phenotypes. Frontiers in Cellular Neuroscience, 14.
Abstract
Inflammatory processes and microglia activation accompany most of the pathophysiological diseases in the central nervous system. It is proven that glial pathology precedes and even drives the development of multiple neurodegenerative conditions. A growing number of studies point out the importance of microglia in brain development as well as in physiological functioning. These resident brain immune cells are divergent from the peripherally infiltrated macrophages, but their precise in situ discrimination is surprisingly difficult. Microglial heterogeneity in the brain is especially visible in their morphology and cell density in particular brain structures but also in the expression of cellular markers. This often determines their role in physiology or pathology of brain functioning. The species differences between rodent and human markers add complexity to the whole picture. Furthermore, due to activation, microglia show a broad spectrum of phenotypes ranging from the pro-inflammatory, potentially cytotoxic M1 to the anti-inflammatory, scavenging, and regenerative M2. A precise distinction of specific phenotypes is nowadays essential to study microglial functions and tissue state in such a quickly changing environment. Due to the overwhelming amount of data on multiple sets of markers that is available for such studies, the choice of appropriate markers is a scientific challenge. This review gathers, classifies, and describes known and recently discovered protein markers expressed by microglial cells in their different phenotypes. The presented microglia markers include qualitative and semi-quantitative, general and specific, surface and intracellular proteins, as well as secreted molecules. The information provided here creates a comprehensive and practical guide through the current knowledge and will facilitate the choosing of proper, more specific markers for detailed studies on microglia and neuroinflammatory mechanisms in various physiological as well as pathological conditions. Both basic research and clinical medicine need clearly described and validated molecular markers of microglia phenotype, which are essential in diagnostics, treatment, and prevention of diseases engaging glia activation.
Microglial Markers
Kozloski, G.A., 2019. Microglial Markers. MATER METHODS, 9:2844.
Abstract
Brain microglia, derived entirely from yolk sac macrophages, are important for phagocytosis of apoptotic neurons and synaptic pruning. This review discusses microglia markers cited in the recent literature.
MGEnrichment: a web application for microglia gene list enrichment analysis
Jao, J., Ciernia, A.V.. MGEnrichment: a web application for microglia gene list enrichment analysis. BioRXi, June 2021.
Abstract
Gene expression analysis is becoming increasingly utilized in neuro-immunology research, and there is a growing need for non-programming scientists to be able to analyze their own genomic data. MGEnrichment is a web application developed both to disseminate to the community our curated database of microglia-relevant gene lists, and to allow non-programming scientists to easily conduct statistical enrichment analysis on their gene expression data. Users can upload their own gene IDs to assess the relevance of their expression data against gene lists from other studies. We include example datasets of differentially expressed genes (DEGs) from human postmortem brain samples from Autism Spectrum Disorder (ASD) and matched controls. We demonstrate how MGEnrichment can be used to expand the interpretations of these DEG lists in terms of regulation of microglial gene expression and provide novel insights into how ASD DEGs may be implicated specifically in microglial development, microbiome responses and relationships to other neuropsychiatric disorders. This tool will be particularly useful for those working in microglia, autism spectrum disorders, and neuro-immune activation research. MGEnrichment is available at https://ciernialab.shinyapps.io/MGEnrichmentApp/ and further online documentation and datasets can be found at https://github.com/ciernialab/MGEnrichmentApp. The app is released under the GNU GPLv3 open source license.
Online resources
Microglia Genomic Atlas
Genetic and transcriptomic database comprised of 255 primary human microglia samples isolated ex vivo from four different brain regions of 100 human subjects with neurodegenerative, neurological, or neuropsychiatric disorders, as well as unaffected controls.
Microglia Gene List Enrichment Calculator
Database of microglial gene expression profiles across a number of conditions for users to compare against enriched genes from a personal dataset.
The Myeloid Landscape 2
Gene expression data from a number of studies characterising both mouse and human microglia from hosts associated with different conditions. Conditions include: Alzheimer’s disease, Multiple Sclerosis, and ageing.
Microglia Single Cell Atlas of Health and Disease
Gene expression data from mouse microglia characterising changes across a number of ages and a focal demyelination injury by lysolecithin injection.
DropViz
A mouse brain atlas generated using Drop-Seq by the McCarroll lab from the Broad Institute. Visualizes expression of genes amongst brain cell type clusters.
Brain RNA-Seq
RNA-Seq data from human and mouse brain samples collected by the Barres lab.
100 Years of Microglia
Summarised articles regarding the 100 year history of microglial research by the Federation of European Neuroscience.
neuronline.sfn.org/scientific-research/100-years-of-microglia
Latest Microglial Research
Latest microglial research published by Nature.
Video resources
Meet the Microglia
An introduction to microglia by Richard Ransohoff
Microglia in Health and Disease
An introduction to microglial synaptic pruning by Beth Stevens
The Role of Microglia in Health and Disease
How Microglia Sculpt Brain Circuitry in Health and Disease
Murderous Microglia
Differences in microglia across male and female brains by Margaret McCarthy
Isolating Pure Microglia
Video protocol showing how to isolate microglial cells from an adult mouse brain by Miltenyi Biotec
Cognate neuron-microglia interaction
Negative feedback control of neuronal activity by microglia by Anne Schaefer
APOE, TREM2, and microglia
APOE TREM and Microglia in the Pathogenesis of Tau-mediated Neurodegeneration by David Holtzman
Microglial motility
Timelapse imaging of microglia moving in culture created by the Barres lab