Article thumbnail

Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations

By Anders Ståhlberg, Daniel Andersson, Johan Aurelius, Maryam Faiz, Marcela Pekna, Mikael Kubista and Milos Pekny

Abstract

Single-cell gene expression levels show substantial variations among cells in seemingly homogenous populations. Astrocytes perform many control and regulatory functions in the central nervous system. In contrast to neurons, we have limited knowledge about functional diversity of astrocytes and its molecular basis. To study astrocyte heterogeneity and stem/progenitor cell properties of astrocytes, we used single-cell gene expression profiling in primary mouse astrocytes and dissociated mouse neurosphere cells. The transcript number variability for astrocytes showed lognormal features and revealed that cells in primary cultures to a large extent co-express markers of astrocytes and neural stem/progenitor cells. We show how subpopulations of cells can be identified at single-cell level using unsupervised algorithms and that gene correlations can be used to identify differences in activity of important transcriptional pathways. We identified two subpopulations of astrocytes with distinct gene expression profiles. One had an expression profile very similar to that of neurosphere cells, whereas the other showed characteristics of activated astrocytes in vivo

Topics: Methods Online
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:3045576
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles

Citations

  1. (2001). A new mathematical model for relative quantification in real-time RT-PCR.
  2. (2008). A transcriptome database for astrocytes, neurons, and oligodendrocytes: a resource for understanding brain development and function.
  3. (2004). Absence of GFAP and vimentin prevents hypertrophy of astrocytic processes and improves post-traumatic regeneration.
  4. (2007). Actin-binding proteins coronin-1a and IBA-1 are effective microglial markers for immunohistochemistry.
  5. (2005). Adult human subventricular, subgranular, and subpial zones contain astrocytes with a specialized intermediate filament cytoskeleton.
  6. an endothelin ET(B) receptor antagonist, attenuates stab wound injury-induced reactive astrocytes in rat brain.
  7. (1999). Application of simplified potential curves to classification problems.
  8. (2005). Astrocyte activation and reactive gliosis.
  9. (2004). Astrocyte intermediate filaments in CNS pathologies and regeneration.
  10. (2002). Astroglia induce neurogenesis from adult neural stem cells.
  11. (2010). Bioinformatic identification and characterization of human endothelial cell-restricted genes.
  12. (2010). Biomarkers of glial cell proliferation and differentiation in culture.
  13. (2004). Comparison of reverse transcriptases in gene expression analysis.
  14. (2001). Control of synapse number by glia.
  15. (1989). Differential ultrastructural localization of myelin basic protein, myelin/oligodendroglial glycoprotein, and 20,30-cyclic nucleotide 30-phosphodiesterase in the CNS of adult rats.
  16. (2004). Discovery of meaningful associations in genomic data using partial correlation coefficients.
  17. (2008). Elevated a-synuclein mRNA levels in individual UV-laser-microdissected dopaminergic substantia nigra neurons in idiopathic Parkinson’s disease.
  18. (1994). Endothelin, endothelin receptors, and endothelian antagonists.
  19. (1997). Endothelins promote the activation of astrocytes in rat neostriatum through ET(B) receptors.
  20. (2005). Expression of neurodevelopmental markers by cultured porcine neural precursor cells.
  21. (1986). Expression of neurofilament subunits in neurons of the central and peripheral nervous system: an immunohistochemical study with monoclonal antibodies.
  22. (1998). Functional specialization and topographic segregation of hippocampal astrocytes.
  23. (2005). Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels.
  24. (1998). GFAP-deficient astrocytes are caple of stellation in vitro when cocultured with neurons and exhibit a reduced amount of intermediate filaments and an increased cell saturation density.
  25. (2006). GFAP-positive progenitor cells produce neurons and oligodendrocytes throughout the CNS.
  26. (2000). Glial fibrillary acidic protein: GFAP-thirty-one years (1969-2000).
  27. (2010). Glutamine synthetase deficiency in murine astrocytes results in neonatal death.
  28. (1990). Glutamine synthetase in the central nervous system is not confined to astrocytes.
  29. (2008). Human in vitro reporter model of neuronal development and early differentiation processes.
  30. (2008). Identification of positionally distinct astrocyte subtypes whose identities are specified by a homeodomain code.
  31. (2008). Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli.
  32. (1998). Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells.
  33. (2008). Nature, nurture, or chance: stochastic gene expression and its consequnences.
  34. (1995). Neuronal pentraxin, a secreted protein with homology to acute phase proteins of the immune system.
  35. (2008). Origin and progeny of reactive gliosis: a source of multipotent cells in the injured brain.
  36. (2006). Origins of extrinsic variability in eukaryotic gene expression.
  37. (1980). Preparation of separate astroglial and oligodendroglial cell cultures from rat cerebral tissue.
  38. (2004). Properties of the reverse transcription reaction in mRNA quantification.
  39. (2008). Protective role of reactive astrocytes in brain ischemia.
  40. (2008). Quantification of mRNA in single cells and modeling of RT-qPCR induced noise.
  41. (2006). Quantification of mRNA using real-time RT-PCR.
  42. (2009). Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells.
  43. (2009). Real-time PCR analysis for blood cell lineage specific markers.
  44. (2002). Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA.
  45. (2010). Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst.
  46. (2006). Single cell gene expression profiling in Alzheimer’s disease.
  47. (2004). Single-cell gene expression analysis: implications for neurodegenerative and neuropsychiatric disorders.
  48. (2010). Single-cell gene expression profiling using reverse transcription quantitative real-time PCR.
  49. (2008). Single-cell gene profiling defines differential progenitor subclasses in mammalian neurogenesis.
  50. (2003). Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity.
  51. (2003). Single-cell transcriptional analysis of neuronal progenitors.
  52. (2007). Sox-2 is expressed by glial and progenitor cells and Pax-6 is expressed by neuroblasts in the human subventricular zone.
  53. (2006). Stochastic mRNA synthesis in mammalian cells.
  54. (2007). Synemin is expressed in reactive astrocytes in neurotrauma and interacts differentially with vimentin and GFAP intermediate filament networks.
  55. (2009). Target identification for CNS diseases by transcriptional profiling.
  56. (2008). Terminal Continuation (TC) RNA amplification enables expression profiling using minute RNA input obtained from mouse brain.
  57. (2006). Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR.
  58. (2009). Transcriptome transfer produces a predictable cellular phenotype.
  59. (2003). Unusual topographical pattern of proximal astrogliosis around a cortical devascularizing lesion.
  60. (2005). Wnt signalling regulates adult hippocampal neurogenesis.