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

Timothy R. Hammond, Connor Dufort, Lasse Dissing-Olesen, Stefanie Giera, Adam Young, Alec Wysoker, Alec J. Walker, Frederick Gergits, Michael Segel, James Nemesh, Samuel E. Marsh, Arpiar Saunders, Evan Macosko, Florent Ginhoux, Jinmiao Chen, Robin J.M. Franklin, Xianhua Piao, Steven A. McCarroll, Beth Stevens

Research output: Contribution to journalArticlepeer-review

328 Scopus citations

Abstract

Microglia, the resident immune cells of the brain, rapidly change states in response to their environment, but we lack molecular and functional signatures of different microglial populations. Here, we analyzed the RNA expression patterns of more than 76,000 individual microglia in mice during development, in old age, and after brain injury. Our analysis uncovered at least nine transcriptionally distinct microglial states, which expressed unique sets of genes and were localized in the brain using specific markers. The greatest microglial heterogeneity was found at young ages; however, several states—including chemokine-enriched inflammatory microglia—persisted throughout the lifespan or increased in the aged brain. Multiple reactive microglial subtypes were also found following demyelinating injury in mice, at least one of which was also found in human multiple sclerosis lesions. These distinct microglia signatures can be used to better understand microglia function and to identify and manipulate specific subpopulations in health and disease.

Original languageEnglish (US)
Pages (from-to)253-271.e6
JournalImmunity
Volume50
Issue number1
DOIs
StatePublished - Jan 15 2019
Externally publishedYes

Keywords

  • activation
  • brain
  • demyelination
  • development
  • diversity
  • glia
  • heterogeneity
  • injury
  • microglia
  • single-cell RNA seq

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology
  • Infectious Diseases

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