The use and limitations of single-cell mass cytometry for studying human microglia function

Camila Fernández-Zapata, Julia K.H. Leman, Josef Priller, Chotima Böttcher

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Microglia, the resident innate immune cells of the central nervous system (CNS), play an important role in brain development and homoeostasis, as well as in neuroinflammatory, neurodegenerative and psychiatric diseases. Studies in animal models have been used to determine the origin and development of microglia, and how these cells alter their transcriptional and phenotypic signatures during CNS pathology. However, little is known about their human counterparts. Recent studies in human brain samples have harnessed the power of multiplexed single-cell technologies such as single-cell RNA sequencing (scRNA-seq) and mass cytometry (cytometry by time-of-flight [CyTOF]) to provide a comprehensive molecular view of human microglia in healthy and diseased brains. CyTOF is a powerful tool to study high-dimensional protein expression of human microglia (huMG) at the single-cell level. This technology widens the possibilities of high-throughput quantification (of over 60 targeted molecules) at a single-cell resolution. CyTOF can be combined with scRNA-seq for comprehensive analysis, as it allows single-cell analysis of post-translational modifications of proteins, which provides insights into cell signalling dynamics in targeted cells. In addition, imaging mass cytometry (IMC) has recently become commercially available, and will be useful for analysing multiple cell types in human brain sections. IMC leverages mass spectrometry to acquire spatial data of cell–cell interactions on tissue sections, using (theoretically) over 40 markers at the same time. In this review, we summarise recent studies of huMG using CyTOF and IMC analyses. The uses and limitations as well as future directions of these technologies are discussed.

Original languageEnglish
Pages (from-to)1178-1191
Number of pages14
JournalBrain Pathology
Issue number6
StatePublished - Nov 2020
Externally publishedYes


  • depression
  • human microglia
  • imaging mass cytometry
  • mass cytometry
  • microglia function
  • multiple sclerosis


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