Skip to main content

Advertisement

Springer Nature Link
Log in

Towards a transcriptome definition of microglial cells

  • Original Article
  • Published:
Neurogenetics Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Canada)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3A–E
Fig. 4A–C

Similar content being viewed by others

References

  1. Kreutzberg GW (1996) Microglia: a sensor for pathological events in the CNS. Trends Neurosci 19:312–318

    CAS  PubMed  Google Scholar 

  2. Lawson LJ, Perry VH, Dri P, Gordon S (1990) Heterogeneity in the distribution and morphology of microglia in the normal adult mouse brain. Neuroscience 39:151–170

    CAS  PubMed  Google Scholar 

  3. Kreutzberg GW (1995) Microglia, the first line of defence in brain pathologies. Arzneimittelforschung 45:357–360

    CAS  PubMed  Google Scholar 

  4. Streit WJ, Graeber MB, Kreutzberg GW (1988) Functional plasticity of microglia: a review. Glia 1:301–307

    CAS  PubMed  Google Scholar 

  5. Streit WJ, Walter SA, Pennell NA (1999) Reactive microgliosis. Prog Neurobiol 57:563–581

    CAS  PubMed  Google Scholar 

  6. Kato H, Walz W (2000) The initiation of the microglial response. Brain Pathol 10:137–143

    CAS  PubMed  Google Scholar 

  7. Faff L, Nolte C (2000) Extracellular acidification decreases the basal motility of cultured mouse microglia via the rearrangement of the actin cytoskeleton. Brain Res 853:22–31

    Article  CAS  PubMed  Google Scholar 

  8. Slepko N, Levi G (1996) Progressive activation of adult microglial cells in vitro. Glia 16:241–246

    Article  CAS  PubMed  Google Scholar 

  9. Kato H, Kogure K, Araki T, Itoyama Y (1995) Graded expression of immunomolecules on activated microglia in the hippocampus following ischemia in a rat model of ischemic tolerance. Brain Res 694:85–93

    Article  CAS  PubMed  Google Scholar 

  10. Nakajima K, Kohsaka S (1993) Functional roles of microglia in the brain. Neurosci Res 17:187–203

    Article  CAS  PubMed  Google Scholar 

  11. Liu B, Hong JS (2003) Role of microglia in inflammation-mediated neurodegenerative diseases: mechanisms and strategies for therapeutic intervention. J Pharmacol Exp Ther 304:1-7

    Article  CAS  PubMed  Google Scholar 

  12. Graeber MB (2003) Microglia. In: Aminoff MJ, Daroff RB (eds) Encyclopedia of the neurological sciences. Academic Press, San Diego

  13. Banati RB, Gehrmann J, Schubert P, Kreutzberg GW (1993) Cytotoxicity of microglia. Glia 7:111–118

    PubMed  Google Scholar 

  14. Streit WJ, Graeber MB, Kreutzberg GW (1989) Peripheral nerve lesion produces increased levels of major histocompatibility complex antigens in the central nervous system. J Neuroimmunol 21:117–123

    CAS  PubMed  Google Scholar 

  15. Graeber MB, Streit WJ, Kreutzberg GW (1988) Axotomy of the rat facial nerve leads to increased CR3 complement receptor expression by activated microglial cells. J Neurosci Res 21:18–24

    CAS  PubMed  Google Scholar 

  16. Colton CA, Gilbert DL (1987) Production of superoxide anions by a CNS macrophage, the microglia. FEBS Lett 223:284–288

    Article  CAS  PubMed  Google Scholar 

  17. Kiefer R, Lindholm D, Kreutzberg GW (1993) Interleukin-6 and transforming growth factor-beta 1 mRNAs are induced in rat facial nucleus following motoneuron axotomy. Eur J Neurosci 5:775–781

    CAS  PubMed  Google Scholar 

  18. Lindholm D, Castren E, Kiefer R, Zafra F, Thoenen H (1992) Transforming growth factor-beta 1 in the rat brain: increase after injury and inhibition of astrocyte proliferation. J Cell Biol 117:395–400

    CAS  PubMed  Google Scholar 

  19. Graeber MB, Banati RB, Streit WJ, Kreutzberg GW (1989) Immunophenotypic characterization of rat brain macrophages in culture. Neurosci Lett 103:241–246

    Article  CAS  PubMed  Google Scholar 

  20. Elkabes S, DiCicco-Bloom EM, Black IB (1996) Brain microglia/macrophages express neurotrophins that selectively regulate microglial proliferation and function. J Neurosci 16:2508–2521

    CAS  PubMed  Google Scholar 

  21. Hamanoue M, Takemoto N, Matsumoto K, Nakamura T, Nakajima K, Kohsaka S (1996) Neurotrophic effect of hepatocyte growth factor on central nervous system neurons in vitro. J Neurosci Res 43:554–564

    Google Scholar 

  22. Streit WJ, Kreutzberg GW (1988) Response of endogenous glial cells to motor neuron degeneration induced by toxic ricin. J Comp Neurol 268:248–263

    CAS  PubMed  Google Scholar 

  23. Giulian D, Ingeman JE (1988) Colony-stimulating factors as promoters of ameboid microglia. J Neurosci 8:4707–4717

    CAS  PubMed  Google Scholar 

  24. Raivich G, Gehrmann J, Kreutzberg GW (1991) Increase of macrophage colony-stimulating factor and granulocyte-macrophage colony-stimulating factor receptors in the regenerating rat facial nucleus. J Neurosci Res 30:682–686

    CAS  PubMed  Google Scholar 

  25. Suzumura A, Sawada M, Yamamoto H, Marunouchi T (1990) Effects of colony stimulating factors on isolated microglia in vitro. J Neuroimmunol 30:111–120

    Article  CAS  PubMed  Google Scholar 

  26. Gazzinelli RT, Hakim FT, Hieny S, Shearer GM, Sher A (1991) Synergistic role of CD4+ and CD8+ T lymphocytes in IFN-gamma production and protective immunity induced by an attenuated Toxoplasma gondii vaccine. J Immunol 146:286–292

    CAS  PubMed  Google Scholar 

  27. Stoll G, Jander S, Schroeter M (2000) Cytokines in CNS disorders: neurotoxicity versus neuroprotection. J Neural Transm 59 [Suppl]:81–89

    Google Scholar 

  28. Boehm U, Klamp T, Groot M, Howard JC (1997) Cellular responses to interferon-gamma. Annu Rev Immunol 15:749–795

    CAS  PubMed  Google Scholar 

  29. Paglinawan R, Malipiero U, Schlapbach R, Frei K, Reith W, Fontana A (2003) TGFbeta directs gene expression of activated microglia to an anti-inflammatory phenotype strongly focusing on chemokine genes and cell migratory genes. Glia 44:219–231

    Article  PubMed  Google Scholar 

  30. Frei K, Siepl C, Groscurth P, Bodmer S, Schwerdel C, Fontana A (1987) Antigen presentation and tumor cytotoxicity by interferon-gamma-treated microglial cells. Eur J Immunol 17:1271–1278

    CAS  PubMed  Google Scholar 

  31. Giulian D, Baker TJ (1986) Characterization of ameboid microglia isolated from developing mammalian brain. J Neurosci 6:2163–2178

    CAS  PubMed  Google Scholar 

  32. Moran LB, Thykjaer T, Orntoft TF, Graeber MB (2002) Towards a molecular definition of microglia (abstract). Neuropathol Appl Neurobiol 28:153

    Article  Google Scholar 

  33. Duke DC, Moran LB, Banati RB, Turkheimer FE, Graeber MB (2003) The transcriptome signature of microglia following stimulation with interferon gamma. Abstracts of the British Neuroscience Association 17th National Meeting, Harrogate, 10.04

  34. Sasik R, Calvo E, Corbeil J (2002) Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Bioinformatics 18:1633–1640

    Google Scholar 

  35. Cox DR, Snell EJ (1989) Analysis of binary data. Chapman Hall, London, pp 49–52

  36. Peirson SN, Butler JN, Foster RG (2003) Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res 31:e73

    Article  PubMed  Google Scholar 

  37. Steiniger B, Meide PH van der (1988) Rat ependyma and microglia cells express class II MHC antigens after intravenous infusion of recombinant gamma interferon. J Neuroimmunol 19:111–118

    Article  CAS  PubMed  Google Scholar 

  38. Vass K, Lassmann H (1990) Intrathecal application of interferon gamma. Progressive appearance of MHC antigens within the rat nervous system. Am J Pathol 137:789–800

    CAS  PubMed  Google Scholar 

  39. Suzumura A, Mezitis SG, Gonatas NK, Silberberg DH (1987) MHC antigen expression on bulk isolated macrophage-microglia from newborn mouse brain: induction of Ia antigen expression by gamma-interferon. J Neuroimmunol 15:263–278

    Article  CAS  PubMed  Google Scholar 

  40. Haga S, Aizawa T, Ishii T, Ikeda K (1996) Complement gene expression in mouse microglia and astrocytes in culture: comparisons with mouse peritoneal macrophages. Neurosci Lett 216:191–194

    Article  CAS  PubMed  Google Scholar 

  41. Shrikant P, Weber E, Jilling T, Benveniste EN (1995) Intercellular adhesion molecule-1 gene expression by glial cells. Differential mechanisms of inhibition by IL-10 and IL-6. J Immunol 155:1489–1501

    CAS  PubMed  Google Scholar 

  42. Suzuki M, Hisamatsu T, Podolsky DK (2003) Gamma interferon augments the intracellular pathway for lipopolysaccharide (LPS) recognition in human intestinal epithelial cells through coordinated up-regulation of LPS uptake and expression of the intracellular Toll-like receptor 4-MD-2 complex. Infect Immun 71:3503–3511

    Article  CAS  PubMed  Google Scholar 

  43. Held TK, Weihua X, Yuan L, Kalvakolanu DV, Cross AS (1999) Gamma interferon augments macrophage activation by lipopolysaccharide by two distinct mechanisms, at the signal transduction level and via an autocrine mechanism involving tumor necrosis factor alpha and interleukin-1. Infect Immun 67:206–212

    CAS  PubMed  Google Scholar 

  44. Aebi M, Fah J, Hurt N, Samuel CE, Thomis D, Bazzigher L, Pavlovic J, Haller O, Staeheli P (1989) cDNA structures and regulation of two interferon-induced human Mx proteins. Mol Cell Biol 9:5062–5072

    CAS  PubMed  Google Scholar 

  45. Cheng YS, Patterson CE, Sraeheli P (1991) Interferon-induced guanylate-binding proteins lack an N(T)KXD consensus motif and binding GMP in addition to GDP and GTP. Mol Cel Biol 11:4717–4725

    Article  CAS  PubMed  Google Scholar 

  46. Hurley SD, Walter SA, Semple-Rowland SL, Streit WJ (1999) Cytokine transcripts expressed by microglia in vitro are not expressed by ameboid microglia of the developing rat central nervous system. Glia 25:304–309

    Article  CAS  PubMed  Google Scholar 

  47. Nakajima K, Honda S, Tohyama Y, Imai Y, Kohsaka S, Kurihara T (2001) Neurotrophin secretion from cultured microglia. J Neurosci Res 65:322–331

    Article  CAS  PubMed  Google Scholar 

  48. Re F, Belyanskaya SL, Riese RJ, Cipriani B, Fischer FR, Granucci F, Ricciardi-Castagnoli P, Brosnan C, Stern LJ, Strominger JL, Santambrogio L (2002) Granulocyte-macrophage colony-stimulating factor induces an expression program in neonatal microglia that primes them for antigen presentation. J Immunol 169:2264–2273

    CAS  PubMed  Google Scholar 

  49. Walker DG, Lue LF, Beach TG (2001) Gene expression profiling of amyloid beta peptide-stimulated human post-mortem brain microglia. Neurobiol Aging 22:957–966

    Article  CAS  PubMed  Google Scholar 

  50. Woodroofe MN, Hayes GM, Cuzner ML (1989) Fc receptor density, MHC antigen expression and superoxide production are increased in interferon-gamma-treated microglia isolated from adult rat brain. Immunology 68:421–426

    CAS  PubMed  Google Scholar 

  51. Stohwasser R, Giesebrecht J, Kraft R, Muller EC, Hausler KG, Kettenmann H, Hanisch UK, Kloetzel PM (2000) Biochemical analysis of proteasomes from mouse microglia: induction of immunoproteasomes by interferon-gamma and lipopolysaccharide. Glia 29:355–365

    Article  CAS  PubMed  Google Scholar 

  52. Gresser O, Weber E, Hellwig A, Riese S, Regnier-Vigouroux A (2001) Immunocompetent astrocytes and microglia display major differences in the processing of the invariant chain and in the expression of active cathepsin L and cathepsin S. Eur J Immunol 31:1813–1824

    Article  CAS  PubMed  Google Scholar 

  53. Dick TP, Ruppert T, Groettrup M, Kloetzel PM, Kuehn L, Koszinowski UH, Stevanovic S, Schild H, Rammensee HG (1996) Coordinated dual cleavages induced by the proteasome regulator PA28 lead to dominant MHC ligands. Cell 86:253–262

    CAS  PubMed  Google Scholar 

  54. Groettrup M, Kraft R, Kostka S, Standera S, Stohwasser R, Kloetzel PM (1996) A third interferon-gamma-induced subunit exchange in the 20S proteasome. Eur J Immunol 26:863–869

    CAS  PubMed  Google Scholar 

  55. Korotzer AR, Watt J, Cribbs D, Tenner AJ, Burdick D, Glabe C, Cotman CW (1995) Cultured rat microglia express C1q and receptor for C1q: implications for amyloid effects on microglia. Exp Neurol 134:214–221

    Article  CAS  PubMed  Google Scholar 

  56. Oehmichen M, Wietholter H, Gencic M (1980) Cytochemical markers for mononuclear phagocytes as demonstrated in reactive microglia and globoid cells. Acta Histochem 66:243–252

    CAS  PubMed  Google Scholar 

  57. Krady JK, Basu A, Levison SW, Milner RJ (2002) Differential expression of protein tyrosine kinase genes during microglial activation. Glia 40:11–24

    Article  PubMed  Google Scholar 

  58. Lafortune L, Nalbantoglu J, Antel JP (1996) Expression of tumor necrosis factor alpha (TNF alpha) and interleukin 6 (IL-6) mRNA in adult human astrocytes: comparison with adult microglia and fetal astrocytes. J Neuropathol Exp Neurol 55:515–521

    CAS  PubMed  Google Scholar 

  59. Ziegler SF, Wilson CB, Perlmutter RM (1988) Augmented expression of a myeloid-specific protein tyrosine kinase gene (hck) after macrophage activation. J Exp Med 168:1801–1810

    CAS  PubMed  Google Scholar 

  60. Banati RB, Newcombe J, Gunn RN, Cagnin A, Turkheimer F, Heppner F, Price G, Wegner F, Giovannoni G, Miller DH, Perkin GD, Smith T, Hewson AK, Bydder G, Kreutzberg GW, Jones T, Cuzner ML, Myers R (2000) The peripheral benzodiazepine binding site in the brain in multiple sclerosis: quantitative in vivo imaging of microglia as a measure of disease activity. Brain 123:2321–2337

    Article  PubMed  Google Scholar 

  61. Banati RB (2002) Visualising microglial activation in vivo. Glia 40:206–217

    Article  PubMed  Google Scholar 

  62. Jonasson L, Hansson GK, Bondjers G, Noe L, Etienne J (1990) Interferon-gamma inhibits lipoprotein lipase in human monocyte-derived macrophages. Biochim Biophys Acta 1053:43–48

    Article  CAS  PubMed  Google Scholar 

  63. Renier G, Lambert A (1995) Lipoprotein lipase synergizes with interferon gamma to induce macrophage nitric oxide synthetase mRNA expression and nitric oxide production. Arterioscler Thromb Vasc Biol 15:392–399

    Google Scholar 

  64. Banati RB, Rothe G, Valet G, Kreutzberg GW (1993) Detection of lysosomal cysteine proteinases in microglia: flow cytometric measurement and histochemical localization of cathepsin B and L. Glia 7:183–191

    CAS  PubMed  Google Scholar 

  65. Cataldo AM, Barnett JL, Pieroni C, Nixon RA (1997) Increased neuronal endocytosis and protease delivery to early endosomes in sporadic Alzheimer’s disease: neuropathologic evidence for a mechanism of increased beta-amyloidogenesis. J Neurosci 17:6142–6151

    CAS  PubMed  Google Scholar 

  66. Huang RP, Ozawa M, Kadomatsu K, Muramatsu T (1993) Embigin, a member of the immunoglobulin superfamily expressed in embryonic cells, enhances cell-substratum adhesion. Dev Biol 155:307–314

    Article  CAS  PubMed  Google Scholar 

  67. Brigelius-Flohe R (1999) Tissue-specific functions of individual glutathione peroxidases. Free Radic Biol Med 27:951–965

    Article  PubMed  Google Scholar 

  68. Dreher I, Schutze N, Baur A, Hesse K, Schneider D, Kohrle J, Jakob F (1998) Selenoproteins are expressed in fetal human osteoblast-like cells. Biochem Biophys Res Commun 245:101–107

    Article  CAS  PubMed  Google Scholar 

  69. Applegate D, Feng W, Green RS, Taubman MB (1994) Cloning and expression of a novel acidic calponin isoform from rat aortic vascular smooth muscle. J Biol Chem 269:10683–10690

    CAS  PubMed  Google Scholar 

  70. Plantier M, Fattoum A, Menn B, Ben Ari Y, Der TE, Represa A (1999) Acidic calponin immunoreactivity in postnatal rat brain and cultures: subcellular localization in growth cones, under the plasma membrane and along actin and glial filaments. Eur J Neurosci 11:2801–2812

    CAS  PubMed  Google Scholar 

  71. Ferhat L, Charton G, Represa A, Ben Ari Y, Der TE, Khrestchatisky M (1996) Acidic calponin cloned from neural cells is differentially expressed during rat brain development. Eur J Neurosci 8:1501–1509

    CAS  PubMed  Google Scholar 

  72. Represa A, Trabelsi-Terzidis H, Plantier M, Fattoum A, Jorquera I, Agassandian C, Ben Ari Y, Der TE (1995) Distribution of caldesmon and of the acidic isoform of calponin in cultured cerebellar neurons and in different regions of the rat brain: an immunofluorescence and confocal microscopy study. Exp Cell Res 221:333–343

    Article  CAS  PubMed  Google Scholar 

  73. Trabelsi-Terzidis H, Fattoum A, Represa A, Dessi F, Ben Ari Y, Der TE (1995) Expression of an acidic isoform of calponin in rat brain: western blots on one- or two-dimensional gels and immunolocalization in cultured cells. Biochem J 306:211–215

    CAS  PubMed  Google Scholar 

  74. Fukui Y, Engler S, Inoue S, Hostos EL de (1999) Architectural dynamics and gene replacement of coronin suggest its role in cytokinesis. Cell Motil Cytoskeleton 42:204–217

    Article  CAS  PubMed  Google Scholar 

  75. Zheng PY, Jones NL (2003) Helicobacter pylori strains expressing the vacuolating cytotoxin interrupt phagosome maturation in macrophages by recruiting and retaining TACO (coronin 1) protein. Cell Microbiol 5:25–40

    Article  CAS  PubMed  Google Scholar 

  76. Kaul SC, Mitsui Y, Komatsu Y, Reddel RR, Wadhwa R (1996) A highly expressed 81 kDa protein in immortalized mouse fibroblast: its proliferative function and identity with ezrin. Oncogene 13:1231–1237

    CAS  PubMed  Google Scholar 

  77. Bretscher A (1989) Rapid phosphorylation and reorganization of ezrin and spectrin accompany morphological changes induced in A-431 cells by epidermal growth factor. J Cell Biol 108:921–930

    CAS  PubMed  Google Scholar 

  78. Kaul SC, Kawai R, Nomura H, Mitsui Y, Reddel RR, Wadhwa R (1999) Identification of a 55-kDa ezrin-related protein that induces cytoskeletal changes and localizes to the nucleolus. Exp Cell Res 250:51–61

    Article  CAS  PubMed  Google Scholar 

Download references

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.

Author information

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

Authors
  1. L. B. Moran
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. C. Duke
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. F. E. Turkheimer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. R. B. Banati
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. M. B. Graeber
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. B. Graeber.

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10048-004-0172-5

Keywords

Search

Navigation