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

Chotima Böttcher
Chotima Böttcher, Charité – University Medicine Berlin


Microglia, the resident innate immune cells of the central nervous system (CNS), play an important role in brain development and homeostasis. Studies in animal models reveal 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 mass cytometry (CyTOF) to provide a comprehensive molecular view of human microglia in healthy and diseased brains. CyTOF is a powerful tool to study single-cell protein expression of human microglia (huMG), which 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 been demonstrated for analysing multiple cell types in human brain sections. IMC leverages mass spectrometry to acquire spatial data of cell-cell interactions on brain sections. Here, the use and limitations of CyTOF in studing huMG are discussed.


Chotima Böttcher is a group leader and principal investigator at the Charité – Universitätsmedizin Berlin, Germany. Dr. Böttcher obtained her PhD at Institute of Pharmacy, at Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany. Her research focuses on systems immunology in neuroscience, with particular emphasis on myeloid cells including monocytes and brain microglia/macrophages. The main goal is to identify cellular complexity and heterogeneity of the myeloid compartment of the human central nervous system and to further investigate how these signatures alter during neurodegeneration/neuroinflammation.


Böttcher C*, Schlickeiser S*, Sneeboer MAM*, Kunkel D, Knop A, Paza E, Fidzinski P, Kraus L, Snijders GJL, Kahn RS, Schulz AR, Mei HE, NBB-Psy, Hol EM, Siegmund B, Glauben R, Spruth EJ, de Witte LD, Priller J: Human microglia regional heterogeneity and phenotypes determined by multiplexed single-cell mass cytometry. Nat Neurosci 22, 78–90 (2019). (*equal contribution)

2.    Sankowski R*, Böttcher C*, Masuda T, Geirsdottir L, Sagar, Sindram E, Seredenina T, Muhs A, Scheiwe C, Shah MJ, Heiland DH, Schnell O, Gru¨n D*, Priller J*, Prinz M*: Mapping microglia diversity in the human brain through the integration of high-dimensional techniques. Nat Neurosci 22, 2098–2110 (2019). (*equal contribution)

3.    Böttcher C*, van der Poel M*, Fernández-Zapata C*, Schlickeiser S, Leman JKH, Hsiao CC, Mizee MR, Adelia, Vincenten MCJ, Kunkel D, Huitinga I*, Hamann J*, Priller J*. Single-cell mass cytometry reveals complex myeloid cell composition in active lesions of progressive multiple sclerosis. Acta Neuropathol Commun 8, 136 (2020). (*equal contribution)



Logo Charité