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Towards a transcriptome definition of microglial cells

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Abstract.

This study provides an expression signature of interferon-gamma (IFN-γ)-activated microglia. Microglia are macrophage precursor cells residing in the brain and spinal cord. The microglial phenotype is highly plastic and changes in response to numerous pathological stimuli. IFN-γ has been established as a strong immunological activator of microglial cells both in vitro and in vivo. Affymetrix RG_U34A microarrays were used to determine the effect of IFN-γ stimulation on migroglia cells isolated from newborn Lewis rat brains. More than 8,000 gene sequences were examined, i.e., 7,000 known genes and 1,000 expressed sequence tag (EST) clusters. Under baseline conditions, microglia expressed 326 of 8,000 genes examined (approximately 4% of all genes, 182 known and 144 ESTs). Transcription of only 34 of 7,000 known genes and 8 of 1,000 ESTs was induced by IFN-γ stimulation. The majority of the newly expressed genes encode pro-inflammatory cytokines and components of the MHC-mediated antigen presentation pathway. The expression of 60 of 182 identified genes and of 9 of 144 ESTs was increased by IFN-γ, whereas 29 of 182 known genes and 7 of 144 ESTs were down-regulated or undetectable in IFN-γ-stimulated cultures. Overall, the activating effect of IFN-γ on the microglial transcriptome showed restriction to pathways involved in antigen presentation, protein degradation, actin binding, cell adhesion, apoptosis, and cell signaling. In comparison, down-regulatory effects of IFN-γ stimulation appeared to be confined to pathways of growth regulation, remodeling of the extracellular matrix, lipid metabolism, and lysosomal processing. In addition, transcriptomic profiling revealed previously unknown microglial genes that were de novo expressed, such as calponin 3, or indicated differential regulatory responses, such as down-regulation of cathepsins that are up-regulated in response to other microglia stimulators.

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Acknowledgements.

We are indebted to Helma Tyrlas, Max Planck Institute of Neurobiology, for the cell culture work. We express our gratitude to Dr. Stuart Peirson, Division of Neuroscience, Imperial College London for his help and guidance in qRT-PCR methods and data analysis. This project was in part supported by a bioinformatics grant from the Hammersmith Hospitals Trust.

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Authors and Affiliations

  1. University Department of Neuropathology, Neurosciences Division, Faculty of Medicine, Imperial College London, London, UK

    L. B. Moran, D. C. Duke, F. E. Turkheimer & M. B. Graeber

  2. School of Medical Radiation Sciences, Faculty of Health Sciences, University of Sydney, Sydney, Australia

    R. B. Banati

  3. University Department of Neuropathology, Neurosciences Division, Faculty of Medicine, Imperial College London, Charing Cross Campus, Fulham Palace Road, W6 8RF, London, UK

    M. B. Graeber

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  1. L. B. Moran
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  2. D. C. Duke
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  3. F. E. Turkheimer
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  5. M. B. Graeber
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Correspondence to M. B. Graeber.

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Moran, L.B., Duke, D.C., Turkheimer, F.E. et al. Towards a transcriptome definition of microglial cells. Neurogenetics 5, 95–108 (2004). https://doi.org/10.1007/s10048-004-0172-5

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